MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Biophysical Journal' source. Mon, 06 Feb 2012 20:24:45 +0100 http://www.medworm.com/index.php?rid=5577345&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225792%26dopt%3DAbstract Authors: Gambini C, Abou B, Ponton A, Cornelissen AJ Abstract Mechanical properties of the extracellular matrix (ECM) play a key role in tissue organization and morphogenesis. Rheological properties of jellyfish ECM (mesoglea) were measured in vivo at the cellular scale by passive microrheology techniques: microbeads were injected in jellyfish ECM and their Brownian motion was recorded to determine the mechanical properties of the surrounding medium. Microrheology results were compared with macrorheological measurements performed with a shear rheometer on slices of jellyfish mesoglea. We found that the ECM behaved as a viscoelastic gel at the macroscopic scale and as a much softer and heterogeneous viscoelastic structure at the microscopic scale. The fibrous architecture of the me... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577345 Wed, 04 Jan 2012 05:00:00 +0100 5577345 http://www.medworm.com/index.php?rid=5577344&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225793%26dopt%3DAbstract Authors: Fogelson AL, Hussain YH, Leiderman K Abstract A previously validated mathematical model of intravascular platelet deposition and tissue factor (TF)-initiated coagulation under flow is extended and used to assess the influence on thrombin production of the activation of factor XI (fXI) by thrombin and of the activation of factor IX (fIX) by fXIa. It is found that the importance of the thrombin-fXIa-fIXa feedback loop to robust thrombin production depends on the concentration of platelets in the blood near the injury. At a near-wall platelet concentration of ∼250,000/μL, typical in vessels in which the shear rate is <200 s(-1), thrombin activation of fXI makes a significant difference only at low densities of exposed TF. If the near-wall platelet concentration is signi... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577344 Wed, 04 Jan 2012 05:00:00 +0100 5577344 http://www.medworm.com/index.php?rid=5577343&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225794%26dopt%3DAbstract Authors: Strasser M, Theis FJ, Marr C Abstract A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. Commonly, this switch has been modeled in a deterministic framework where transcription and translation are lumped together. In this description, bistability occurs for transcription factor cooperativity, whereas autoactivation leads to a tristable system with an additional undecided state. In this contribution, we study the stability and dynamics of a two-stage gene expression switch within a probabilistic framework inspired by the properties of the Pu/Gata toggle switch in myeloid progenitor cells. We focus ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577343 Wed, 04 Jan 2012 05:00:00 +0100 5577343 http://www.medworm.com/index.php?rid=5577342&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225795%26dopt%3DAbstract Authors: Walton RD, Smith RM, Mitrea BG, White E, Bernus O, Pertsov AM Abstract Optical mapping has become an indispensible tool for studying cardiac electrical activity. However, due to the three-dimensional nature of the optical signal, the optical upstroke is significantly longer than the electrical upstroke. This raises the issue of how to accurately determine the activation time on the epicardial surface. The purpose of this study was to establish a link between the optical upstroke and exact surface activation time using computer simulations, with subsequent validation by a combination of microelectrode recordings and optical mapping experiments. To simulate wave propagation and associated optical signals, we used a hybrid electro-optical model. We found that the time of the ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577342 Wed, 04 Jan 2012 05:00:00 +0100 5577342 http://www.medworm.com/index.php?rid=5577341&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225796%26dopt%3DAbstract Authors: Mahendran KR, Romero-Ruiz M, Schlösinger A, Winterhalter M, Nussberger S Abstract Mitochondrial proteins are almost exclusively imported into mitochondria from the cytosol in an unfolded or partially folded conformation. Regardless of whether they are destined for the outer or inner membrane, the intermembrane space, or the matrix, proteins begin the importation process by crossing the mitochondrial outer membrane via a specialized protein import machinery whose main component is the Tom40 channel. High-resolution ion conductance measurements through the Tom40 channel in the presence of the mitochondrial presequence peptide pF(1)β revealed the kinetics of peptide binding. Here we show that the rates for association k(on) and dissociation k(off) strongly depend on the app... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577341 Wed, 04 Jan 2012 05:00:00 +0100 5577341 http://www.medworm.com/index.php?rid=5577340&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225797%26dopt%3DAbstract Authors: Qian S, Huang HW Abstract The force model of protein-mediated membrane fusion hypothesizes that fusion is driven by mechanical forces exerted on the membranes, but many details are unknown. Here, we investigated by x-ray diffraction the consequence of applying compressive force on a stack of membranes against the hydration barrier. We found that as the osmotic pressure increased, the lamellar phase transformed first to a new phase of tetragonal lattice (T-phase) over a narrow range of relative humidity, and then to a phase of rhombohedral lattice. The unit cell structure changed from parallel bilayers to a bent configuration with a point contact between adjacent bilayers and then to the stalk hemifusion configuration. The T-phase is discussed as a possible transition stat... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577340 Wed, 04 Jan 2012 05:00:00 +0100 5577340 http://www.medworm.com/index.php?rid=5577339&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225798%26dopt%3DAbstract Authors: Dhar P, Eck E, Israelachvili JN, Lee DW, Min Y, Ramachandran A, Waring AJ, Zasadzinski JA Abstract The size distribution of domains in phase-separated lung surfactant monolayers influences monolayer viscoelasticity and compressibility which, in turn, influence monolayer collapse and set the compression at which the minimum surface tension is reached. The surfactant-specific protein SP-B decreases the mean domain size and polydispersity as shown by fluorescence microscopy. From the images, the line tension and dipole density difference are determined by comparing the measured size distributions with a theory derived by minimizing the free energy associated with the domain energy and mixing entropy. We find that SP-B increases the line tension, dipole density difference, and... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577339 Wed, 04 Jan 2012 05:00:00 +0100 5577339 http://www.medworm.com/index.php?rid=5577338&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225799%26dopt%3DAbstract Authors: Redondo-Morata L, Oncins G, Sanz F Abstract How do metal cations affect the stability and structure of phospholipid bilayers? What role does ion binding play in the insertion of proteins and the overall mechanical stability of biological membranes? Investigators have used different theoretical and microscopic approaches to study the mechanical properties of lipid bilayers. Although they are crucial for such studies, molecular-dynamics simulations cannot yet span the complexity of biological membranes. In addition, there are still some experimental difficulties when it comes to testing the ion binding to lipid bilayers in an accurate way. Hence, there is a need to establish a new approach from the perspective of the nanometric scale, where most of the specific molecular ph... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577338 Wed, 04 Jan 2012 05:00:00 +0100 5577338 http://www.medworm.com/index.php?rid=5577337&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225800%26dopt%3DAbstract We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocyte cytoskeleton. In this model, three types of coarse-grained particles are introduced to represent clusters of lipid molecules, actin junctions, and band-3 complexes, respectively. The proposed model facilitates simulations that span large length scales (approximately micrometers) and timescales (approximately milliseconds). By tuning the interaction potential parameters, we were able to control the diffusivity and bending rigidity of the membrane model. We studied the membra... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577337 Wed, 04 Jan 2012 05:00:00 +0100 5577337 http://www.medworm.com/index.php?rid=5577336&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225801%26dopt%3DAbstract Authors: Schink S, Renner S, Alim K, Arnaut V, Simmel FC, Gerland U Abstract Nanopore translocation experiments are increasingly applied to probe the secondary structures of RNA and DNA molecules. Here, we report two vital steps toward establishing nanopore translocation as a tool for the systematic and quantitative analysis of polynucleotide folding: 1), Using α-hemolysin pores and a diverse set of different DNA hairpins, we demonstrate that backward nanopore force spectroscopy is particularly well suited for quantitative analysis. In contrast to forward translocation from the vestibule side of the pore, backward translocation times do not appear to be significantly affected by pore-DNA interactions. 2), We develop and verify experimentally a versatile mesoscopic theoretical fram... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577336 Wed, 04 Jan 2012 05:00:00 +0100 5577336 http://www.medworm.com/index.php?rid=5577335&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225802%26dopt%3DAbstract Authors: Lin J, Persson F, Fritzsche J, Tegenfeldt JO, Saleh OA Abstract During a variety of biological and technological processes, biopolymers are simultaneously subject to both confinement and external forces. Although significant efforts have gone into understanding the physics of polymers that are only confined, or only under tension, little work has been done to explore the effects of the interplay of force and confinement. Here, we study the combined effects of stretching and confinement on a polymer's configurational freedom. We measure the elastic response of long double-stranded DNA molecules that are partially confined to thin, nanofabricated slits. We account for the data through a model in which the DNA's short-wavelength transverse elastic modes are cut off by applied... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577335 Wed, 04 Jan 2012 05:00:00 +0100 5577335 http://www.medworm.com/index.php?rid=5577334&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225803%26dopt%3DAbstract We present a statistical mechanical model that explicitly includes all misfolded microstates with nonnative Watson-Crick (WC) and non-WC contacts. Rates of interconversion between different microstates are described in terms of two adjustable parameters: the strength of the non-WC interactions (ΔG(nWC)) and the rate at which a basepair is formed adjacent to an existing basepair (k(bp)(+)). The model accurately reproduces the temperature and loop-length dependence of the measured relaxation rates in temperature-jump studies of a 7-bp stem, single-stranded DNA hairpin with 4-20-nt-long poly(dT) loops, with ΔG(nWC) ≈ -2.4 kcal/mol and k(bp)(+) ≥ (1 ns)(-1), in 100 mM NaCl. Thus, our model provides a microscopic interpretation of the slow hairpin folding times as well as an estimate ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577334 Wed, 04 Jan 2012 05:00:00 +0100 5577334 http://www.medworm.com/index.php?rid=5577333&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225804%26dopt%3DAbstract Authors: Kang Y, Lü S, Ren P, Huo B, Long M Abstract By mediating the tethering and rolling of leukocytes on vascular surfaces, the interactions between P-selectin and the P-selectin glycoprotein ligand 1 (PSGL-1) play crucial roles during inflammation cascade. Tensile stretch produced by rolling leukocytes and shear stress exerted by blood flow constitute the two types of mechanical forces that act on the P-selectin/PSGL-1 bond. These forces modulate not only dissociation kinetics of this bond, but also the leukocyte adhesion dynamics. However, the respective contribution of the two forces to bond dissociation and to the corresponding microstructural bases remains unclear. To mimic the mechanical microenvironment, we developed two molecular dynamics approaches; namely, an approac... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577333 Wed, 04 Jan 2012 05:00:00 +0100 5577333 http://www.medworm.com/index.php?rid=5577332&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225805%26dopt%3DAbstract Authors: Shah BR, Maeno A, Matsuo H, Tachibana H, Akasaka K Abstract The dynamics of amyloid fibrils, including their formation and dissociation, could be of vital importance in life. We studied the kinetics of dissociation of the amyloid fibrils from wild-type hen lysozyme at 25°C in vitro as a function of pressure using Trp fluorescence as a probe. Upon 100-fold dilution of 8 mg ml(-1) fibril solution in 80 mM NaCl, pH 2.2, no immediate change occurred in Trp fluorescence, but at pressures of 50-450 MPa the fluorescence intensity decreased rapidly with time (k(obs) = 0.00193 min(-1) at 0.1 MPa, 0.0348 min(-1) at 400 MPa). This phenomenon is attributable to the pressure-accelerated dissociation of amyloid fibrils into monomeric hen lysozyme. From the pressure dependence of... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577332 Wed, 04 Jan 2012 05:00:00 +0100 5577332 http://www.medworm.com/index.php?rid=5577331&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225806%26dopt%3DAbstract In this study, we tested this prevailing view by examining the effect of mutating these basic lysines to alanines, and assessing the impact of altering the pH environment. Unexpectedly, mutating these basic lysine residues or changing the pH to 4 or 10, which could alter the charge of lysines, did not measurably impair DNA translocation or affect the one-way traffic property of the channel. The results support our recent findings regarding the dsDNA packaging mechanism known as the "push through a one-way valve". PMID: 22225806 [PubMed - in process] (Source: Biophysical Journal) Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577331 Wed, 04 Jan 2012 05:00:00 +0100 5577331 http://www.medworm.com/index.php?rid=5577330&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225807%26dopt%3DAbstract Authors: Istrate AN, Tsvetkov PO, Mantsyzov AB, Kulikova AA, Kozin SA, Makarov AA, Polshakov VI Abstract In an attempt to reveal the mechanism of rats' resistance to Alzheimer's disease, we determined the structure of the metal-binding domain 1-16 of rat β-amyloid (rat Aβ(1-16)) in solution in the absence and presence of zinc ions. A zinc-induced dimerization of the domain was detected. The zinc coordination site was found to involve residues His-6 and His-14 of both peptide chains. We used experimental restraints obtained from analyses of NMR and isothermal titration calorimetry data to perform structure calculations. The calculations employed an explicit water environment and a simulated annealing molecular-dynamics protocol followed by quantum-mechanical/molecular-mechanical o... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577330 Wed, 04 Jan 2012 05:00:00 +0100 5577330 http://www.medworm.com/index.php?rid=5577329&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225808%26dopt%3DAbstract Authors: Proctor EA, Yin S, Tropsha A, Dokholyan NV Abstract Virtual screening is one of the major tools used in computer-aided drug discovery. In structure-based virtual screening, the scoring function is critical to identifying the correct docking pose and accurately predicting the binding affinities of compounds. However, the performance of existing scoring functions has been shown to be uneven for different targets, and some important drug targets have proven especially challenging. In these targets, scoring functions cannot accurately identify the native or near-native binding pose of the ligand from among decoy poses, which affects both the accuracy of the binding affinity prediction and the ability of virtual screening to identify true binders in chemical libraries. Here, we... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577329 Wed, 04 Jan 2012 05:00:00 +0100 5577329 http://www.medworm.com/index.php?rid=5577328&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225809%26dopt%3DAbstract Authors: Martín-García F, Mendieta-Moreno JI, López-Viñas E, Gómez-Puertas P, Mendieta J Abstract Activation of the water molecule involved in GTP hydrolysis within the HRas⋅RasGAP system is analyzed using a tailored approach based on hybrid quantum mechanics/molecular mechanics (QM/MM) simulation. A new path emerges: transfer of a proton from the attacking water molecule to a second water molecule, then a different proton is transferred from this second water molecule to the GTP. Gln(61) will stabilize the transient OH(-) and H(3)O(+) molecules thus generated. This newly proposed mechanism was generated by using, for the first time to our knowledge, the entire HRas-RasGAP protein complex in a QM/MM simulation context. It also offers a rational explanation for previous exper... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577328 Wed, 04 Jan 2012 05:00:00 +0100 5577328 http://www.medworm.com/index.php?rid=5577327&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225810%26dopt%3DAbstract Authors: Camilloni C, Schaal D, Schweimer K, Schwarzinger S, De Simone A Abstract The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides. In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a group of neurodegenerative disorders known as transmissible spongiform encephalo... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577327 Wed, 04 Jan 2012 05:00:00 +0100 5577327 http://www.medworm.com/index.php?rid=5577326&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225811%26dopt%3DAbstract Authors: Helms CC, Ariëns RA, Uitte de Willige S, Standeven KF, Guthold M Abstract Fibrin fibers, which are ∼100 nm in diameter, are the major structural component of a blood clot. The mechanical properties of single fibrin fibers determine the behavior of a blood clot and, thus, have a critical influence on heart attacks, strokes, and embolisms. Cross-linking is thought to fortify blood clots; though, the role of α-α cross-links in fibrin fiber assembly and their effect on the mechanical properties of single fibrin fibers are poorly understood. To address this knowledge gap, we used a combined fluorescence and atomic force microscope technique to determine the stiffness (modulus), extensibility, and elasticity of individual, uncross-linked, exclusively α-α cross-linked (γ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577326 Wed, 04 Jan 2012 05:00:00 +0100 5577326 http://www.medworm.com/index.php?rid=5577325&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225812%26dopt%3DAbstract In this study, we determined the abundance and distribution of two sialic acids to assess differences in their availability to an exogenous probe in isolated mucins and mucous gels. We used atomic force microscopy to obtain force maps of human preocular mucous and purified ocular mucins by probing and locating the interactions between tip-tethered lectins Maackia amurensis and Sambucus nigra and their respective receptors, α-2,3 and α-2,6 N-acetylneuraminic (sialic) acids. The rupture force distributions were not affected by neighboring sugar-bearing molecules. Energy contours for both lectin-sugar bonds were fitted to a two-barrier model, suggesting a conformational change before dissociation. In contrast to data from purified mucin molecules, the preocular gels presented numerous large... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577325 Wed, 04 Jan 2012 05:00:00 +0100 5577325 http://www.medworm.com/index.php?rid=5577324&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225813%26dopt%3DAbstract Authors: Picas L, Rico F, Scheuring S Abstract Biological membranes define not only the cell boundaries but any compartment within the cell. To some extent, the functionality of membranes is related to the elastic properties of the lipid bilayer and the mechanical and hydrophobic matching with functional membrane proteins. Supported lipid bilayers (SLBs) are valid biomimetic systems for the study of membrane biophysical properties. Here, we acquired high-resolution topographic and quantitative mechanics data of phase-separated SLBs using a recent atomic force microscopy (AFM) imaging mode based on force measurements. This technique allows us to quantitatively map at high resolution the mechanical differences of lipid phases at different loading forces. We have applied this approach... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5577324 Wed, 04 Jan 2012 05:00:00 +0100 5577324 http://www.medworm.com/index.php?rid=5558897&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208184%26dopt%3DAbstract Authors: Elson EL Abstract In recent years fluorescence correlation spectroscopy (FCS) has become a routine method for determining diffusion coefficients, chemical rate constants, molecular concentrations, fluorescence brightness, triplet state lifetimes, and other molecular parameters. FCS measures the spatial and temporal correlation of individual molecules with themselves and so provides a bridge between classical ensemble and contemporary single-molecule measurements. It also provides information on concentration and molecular number fluctuations for nonlinear reaction systems that complement single-molecule measurements. Typically implemented on a fluorescence microscope, FCS samples femtoliter volumes and so is especially useful for characterizing small dynamic systems such a... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558897 Wed, 21 Dec 2011 05:00:00 +0100 5558897 http://www.medworm.com/index.php?rid=5558896&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208185%26dopt%3DAbstract Authors: Bishop MJ, Vigmond E, Plank G Abstract Cardiac tissue is always surrounded by conducting fluid, both in vivo (blood) and in experimental preparations (Tyrode's solution), which acts to increase conduction velocity (CV) close to the tissue-fluid interface, inducing transmural wavefront curvature. Despite its potential importance, computer modeling studies focused on arrhythmia mechanisms have previously not accounted for these bath-loading effects. Here, we investigate the increase in CV and concomitant change in transmural wavefront profiles upon both propagation and arrhythmia dynamics within models of differing anatomical complexity. In simplified slab models, in absence of transmural fiber rotation, bath-loading induced transmural wavefront curvature dominates, signifi... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558896 Wed, 21 Dec 2011 05:00:00 +0100 5558896 http://www.medworm.com/index.php?rid=5558895&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208186%26dopt%3DAbstract Authors: Morelli MJ, Allen RJ, Rein Ten Wolde P Abstract The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558895 Wed, 21 Dec 2011 05:00:00 +0100 5558895 http://www.medworm.com/index.php?rid=5558894&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208187%26dopt%3DAbstract In this study, a combination of experimental and computational multiscale studies is used to investigate the role of intrinsic and extrinsic noise in I(Ks) in modulating temporal and spatial variability in ventricular repolarization in human and guinea pig. Results show that under physiological conditions: i), stochastic fluctuations in I(Ks) gating properties (i.e., intrinsic noise) cause significant beat-to-beat variability in action potential duration (APD) in isolated cells, whereas cell-to-cell differences in channel numbers (i.e., extrinsic noise) also contribute to cell-to-cell APD differences; ii), in tissue, electrotonic interactions mask the effect of I(Ks) noise, resulting in a significant decrease in APD temporal and spatial variability compared to isolated cells. Pathological ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558894 Wed, 21 Dec 2011 05:00:00 +0100 5558894 http://www.medworm.com/index.php?rid=5558893&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208188%26dopt%3DAbstract This study was designed to investigate the regulation of cell-adhesion strength by the size and position of focal adhesions (FA). The cell-adhesive interface was engineered to direct FA assembly to the periphery of the cell-spreading area to delineate the cell-adhesive area from the cell-spreading area. It was observed that redistributing the same adhesive area over a larger cell-spreading area significantly enhanced cell-adhesion strength, but only up to a threshold area. Moreover, the size of the peripheral FAs, which was interpreted as an adhesive patch, did not directly govern the adhesion strength. Interestingly, this is in contrast to the previously reported functional role of FAs in regulating cellular traction where sizes of the peripheral FAs play a critical role. These findings d... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558893 Wed, 21 Dec 2011 05:00:00 +0100 5558893 http://www.medworm.com/index.php?rid=5558892&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208189%26dopt%3DAbstract Authors: Alqazzaz M, Thompson AJ, Price KL, Breitinger HG, Lummis SC Abstract The Gloeobacter ligand-gated ion channel (GLIC) is a bacterial homolog of vertebrate Cys-loop ligand-gated ion channels. Its pore-lining region in particular has a high sequence homology to these related proteins. Here we use electrophysiology to examine a range of compounds that block the channels of Cys-loop receptors to probe their pharmacological similarity with GLIC. The data reveal that a number of these compounds also block GLIC, although the pharmacological profile is distinct from these other proteins. The most potent compound was lindane, a GABA(A) receptor antagonist, with an IC(50) of 0.2 μM. Docking studies indicated two potential binding sites for this ligand in the pore, at the 9' or betwe... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558892 Wed, 21 Dec 2011 05:00:00 +0100 5558892 http://www.medworm.com/index.php?rid=5558891&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208190%26dopt%3DAbstract Authors: Walcott S, Kim DH, Wirtz D, Sun SX Abstract A cell plated on a two-dimensional substrate forms adhesions with that surface. These adhesions, which consist of aggregates of various proteins, are thought to be important in mechanosensation, the process by which the cell senses and responds to the mechanical properties of the substrate (e.g., stiffness). On the basis of experimental measurements, we model these proteins as idealized molecules that can bind to the substrate in a strain-dependent manner and can undergo a force-dependent state transition. The model forms molecular aggregates that are similar to adhesions. Substrate stiffness affects whether a simulated adhesion is initially formed and how long it grows, but not how that adhesion grows or shrinks. Our own experim... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558891 Wed, 21 Dec 2011 05:00:00 +0100 5558891 http://www.medworm.com/index.php?rid=5558890&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208191%26dopt%3DAbstract Authors: Ryham R, Berezovik I, Cohen FS Abstract A new theory, to our knowledge, is developed that describes the dynamics of a lipidic pore in a liposome. The equations of the theory capture the experimentally observed three-stage functional form of pore radius over time-stage 1, rapid pore enlargement; stage 2, slow pore shrinkage; and stage 3, rapid pore closure. They also show that lipid flow is kinetically limited by the values of both membrane and aqueous viscosity; therefore, pore evolution is affected by both viscosities. The theory predicts that for a giant liposome, tens of microns in radius, water viscosity dominates over the effects of membrane viscosity. The edge tension of a lipidic pore is calculated by using the theory to quantitatively account for pore kinetics in s... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558890 Wed, 21 Dec 2011 05:00:00 +0100 5558890 http://www.medworm.com/index.php?rid=5558889&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208192%26dopt%3DAbstract We present a combined analysis of (2)H-alanine quadrupolar splittings together with (15)N/(1)H dipolar couplings and (15)N chemical shifts, using two models to treat the dynamics, for the systematic evaluation of transmembrane peptides based on the GWALP23 sequence (acetyl-GGALW(LA)(6)LWLAGA-amide). The results indicate that derivatives of GWALP23 incorporating diverse guest residues adopt a range of apparent tilt angles that span 5°-35° in lipid bilayer membranes. By comparing individual and combined analyses of specifically (2)H- or (15)N-labeled peptides incorporated in magnetically or mechanically aligned lipid bilayers, we examine the influence of data-set size/identity, and of explicitly modeled dynamics, on the deduced average orientations of the peptides. We conclude that peptide... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558889 Wed, 21 Dec 2011 05:00:00 +0100 5558889 http://www.medworm.com/index.php?rid=5558888&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208193%26dopt%3DAbstract Authors: Maula T, Kurita M, Yamaguchi S, Yamamoto T, Katsumura S, Slotte JP Abstract To study the role of the interfacial properties of ceramides in their interlipid interactions, we synthesized palmitoylceramide (PCer) analogs in which a methyl group was introduced to the amide-nitrogen or the C3-oxygen of the sphingosine backbone. A differential scanning calorimetry analysis of equimolar mixtures of palmitoylsphingomyelin (PSM) and PCer showed that these sphingolipids formed a complex gel phase that melted between 67°C and 74°C. The PCer analogs also formed gel phases with PSM, but they melted at lower temperatures compared with the system with PCer. In complex bilayers composed of an unsaturated glycerophospholipid, PSM, and cholesterol, the 3O-methylated ceramide formed a cho... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558888 Wed, 21 Dec 2011 05:00:00 +0100 5558888 http://www.medworm.com/index.php?rid=5558887&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208194%26dopt%3DAbstract Authors: Holten-Andersen N, Michael Henderson J, Walther FJ, Waring AJ, Ruchala P, Notter RH, Lee KY Abstract We investigated the effects of KL(4), a 21-residue amphipathic peptide approximating the overall ratio of positively charged to hydrophobic amino acids in surfactant protein B (SP-B), on the structure and collapse of dipalmitoylphosphatidylcholine and palmitoyl-oleoyl-phosphatidylglycerol monolayers. As reported in prior work on model lung surfactant phospholipid films containing SP-B and SP-B peptides, our experiments show that KL(4) improves surfactant film reversibility during repetitive interfacial cycling in association with the formation of reversible collapse structures on multiple length scales. Emphasis is on exploring a general mechanistic connection between pepti... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558887 Wed, 21 Dec 2011 05:00:00 +0100 5558887 http://www.medworm.com/index.php?rid=5558886&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208195%26dopt%3DAbstract We present what to our knowledge is a new method of optimized torsion-angle normal-mode analysis, in which the normal modes move along curved paths in Cartesian space. We show that optimized torsion-angle normal modes reproduce protein conformational changes more accurately than Cartesian normal modes. We also show that orthogonalizing the displacement vectors from torsion-angle normal-mode analysis and projecting them as straight lines in Cartesian space does not lead to better performance than Cartesian normal modes. Clearly, protein motion is more naturally described by curved paths in Cartesian space. PMID: 22208195 [PubMed - in process] (Source: Biophysical Journal) Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558886 Wed, 21 Dec 2011 05:00:00 +0100 5558886 http://www.medworm.com/index.php?rid=5558885&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208196%26dopt%3DAbstract Authors: Matesanz R, Rodríguez-Salarichs J, Pera B, Canales A, Andreu JM, Jiménez-Barbero J, Bras W, Nogales A, Fang WS, Díaz JF Abstract Microtubules assembled with paclitaxel and docetaxel differ in their numbers of protofilaments, reflecting modification of the lateral association between αβ-tubulin molecules in the microtubule wall. These modifications of microtubule structure, through a not-yet-characterized mechanism, are most likely related to the changes in tubulin-tubulin interactions responsible for microtubule stabilization by these antitumor compounds. We have used a set of modified taxanes to study the structural mechanism of microtubule stabilization by these ligands. Using small-angle x-ray scattering, we have determined how modifications in the shape and size o... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558885 Wed, 21 Dec 2011 05:00:00 +0100 5558885 http://www.medworm.com/index.php?rid=5558884&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208197%26dopt%3DAbstract Authors: Zheng W, Tekpinar M Abstract Small-angle x-ray scattering (SAXS) is a powerful technique widely used to explore conformational states and transitions of biomolecular assemblies in solution. For accurate model reconstruction from SAXS data, one promising approach is to flexibly fit a known high-resolution protein structure to low-resolution SAXS data by computer simulations. This is a highly challenging task due to low information content in SAXS data. To meet this challenge, we have developed what we believe to be a novel method based on a coarse-grained (one-bead-per-residue) protein representation and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method optimizes a p... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558884 Wed, 21 Dec 2011 05:00:00 +0100 5558884 http://www.medworm.com/index.php?rid=5558883&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208198%26dopt%3DAbstract Authors: Suzuki Y, Gilmore JL, Yoshimura SH, Henderson RM, Lyubchenko YL, Takeyasu K Abstract Many DNA regulatory factors require communication between distantly separated DNA sites for their activity. The type IIF restriction enzyme SfiI is often used as a model system of site communication. Here, we used fast-scanning atomic force microscopy to monitor the DNA cleavage process with SfiI and the changes in the single SfiI-DNA complex in the presence of either Mg(2+) or Ca(2+) at a scan rate of 1-2 fps. The increased time resolution allowed us to visualize the concerted cleavage of the protein at two cognate sites. The four termini generated by the cleavage were released in a multistep manner. The high temporal resolution enabled us to visualize the translocation of a DNA strand o... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558883 Wed, 21 Dec 2011 05:00:00 +0100 5558883 http://www.medworm.com/index.php?rid=5558882&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22208199%26dopt%3DAbstract Authors: Krueger S, Shin JH, Raghunandan S, Curtis JE, Kelman Z Abstract The minichromosome maintenance (MCM) proteins are thought to function as the replicative helicases in archaea and eukarya. In this work we determined the solution structure of the N-terminal portion of the MCM complex from the archaeon Methanothermobacter thermautotrophicus (N-mtMCM) in the presence and absence of DNA using small-angle neutron scattering (SANS). N-mtMCM is a multimeric protein complex that consists of 12 monomers, each of which contains three distinct domains and two unstructured regions. Using an all-atom approach incorporating modern force field and Monte Carlo methods to allow the unstructured regions of each monomer to be varied independently, we generated an ensemble of biologically relev... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5558882 Wed, 21 Dec 2011 05:00:00 +0100 5558882 http://www.medworm.com/index.php?rid=5491711&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098729%26dopt%3DAbstract Authors: Vilar JM, Saiz L Abstract Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized chemical reactions. There are many important situations, however, in which the properties of the compartments change continuously in a way that cannot naturally be described by chemical reactions. Here, we develop an approach based on transport along a trafficking coordinate to precisely describe these processes and we apply it explicitly to the TGF-β signal transduction network, which plays a fundamental role in many diseases and cellular processes. The results of this newly introduced approach accurately capture th... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491711 Wed, 16 Nov 2011 05:00:00 +0100 5491711 http://www.medworm.com/index.php?rid=5491710&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098730%26dopt%3DAbstract Authors: Morishita Y, Iwasa Y Abstract Robust positioning of cells in a tissue against unavoidable noises is important for achieving normal and reproducible morphogenesis. The position in a tissue is represented by morphogen concentrations, and cells read them to recognize their spatial coordinates. From the engineering viewpoint, these positioning processes can be regarded as an information coding. Organisms are conjectured to adopt good coding designs with high reliability for a given number of available morphogen species and their chemical properties. To answer, quantitatively, the questions of how good coding is adopted, and subsequently when, where, and to what extent each morphogen contributes to positioning, we need a way to evaluate the goodness of coding. In this article, ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491710 Wed, 16 Nov 2011 05:00:00 +0100 5491710 http://www.medworm.com/index.php?rid=5491709&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098731%26dopt%3DAbstract We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491709 Wed, 16 Nov 2011 05:00:00 +0100 5491709 http://www.medworm.com/index.php?rid=5491708&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098732%26dopt%3DAbstract Authors: Nans A, Mohandas N, Stokes DL Abstract Erythrocytes possess a spectrin-based cytoskeleton that provides elasticity and mechanical stability necessary to survive the shear forces within the microvasculature. The architecture of this membrane skeleton and the nature of its intermolecular contacts determine the mechanical properties of the skeleton and confer the characteristic biconcave shape of red cells. We have used cryo-electron tomography to evaluate the three-dimensional topology in intact, unexpanded membrane skeletons from mouse erythrocytes frozen in physiological buffer. The tomograms reveal a complex network of spectrin filaments converging at actin-based nodes and a gradual decrease in both the density and the thickness of the network from the center to the edge ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491708 Wed, 16 Nov 2011 05:00:00 +0100 5491708 http://www.medworm.com/index.php?rid=5491707&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098733%26dopt%3DAbstract This study reports how quantal size, or the quantity of chemical messengers within a storage granule, is regulated in platelet dense-body granules via dynamic adaption of granule size according to changing levels of granule contents. Mechanistic studies using carbon-fiber microelectrode fast-scan cyclic voltammetry and amperometry methods correlated with transmission electron microscopy analysis reveal the impact of granule structural changes on granular content secretion kinetics and highlight the dynamic interplay between soluble granule contents and membrane components in exocytosis. Despite the distinct chemical profile of platelet dense-body granules, these secretory granules act according to general biochemical/biophysical phenomena using charge-charge interactions to sequester chemi... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491707 Wed, 16 Nov 2011 05:00:00 +0100 5491707 http://www.medworm.com/index.php?rid=5491706&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098734%26dopt%3DAbstract Authors: Weidemann T, Worch R, Kurgonaite K, Hintersteiner M, Bökel C, Schwille P Abstract Interleukin-4 (IL-4) is an important class I cytokine involved in adaptive immunity. IL-4 binds with high affinity to the single-pass transmembrane receptor IL-4Rα. Subsequently, IL-4Rα/IL-4 is believed to engage a second receptor chain, either IL-2Rγ or IL-13Rα1, to form type I or II receptor complexes, respectively. This ternary complex formation then triggers downstream signaling via intracellular Janus kinases bound to the cytoplasmic receptor tails. Here, we study the successive steps of complex formation at the single cell level with confocal fluorescence imaging and correlation spectroscopy. We characterize binding and signaling of fluorescently labeled IL-4 by flow cytometry of I... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491706 Wed, 16 Nov 2011 05:00:00 +0100 5491706 http://www.medworm.com/index.php?rid=5491705&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098735%26dopt%3DAbstract Authors: Sato D, Bers DM Abstract Spontaneous calcium (Ca) sparks are initiated by single ryanodine receptor (RyR) opening. Once one RyR channel opens, it elevates local [Ca] in the cleft space ([Ca](Cleft)), which opens other RyR channels in the same Ca release unit (CaRU) via Ca-induced Ca-release. Experiments by Zima et al. (J. Physiol. 588:4743-4757, 2010) demonstrate that spontaneous Ca sparks occur only when intrasarcoplasmic-reticulum (SR) [Ca] ([Ca](SR)) is above a threshold level, but that RyR-mediated SR Ca leak exists without Ca sparks well below this threshold [Ca](SR). We examine here how single RyR opening at lower [Ca](SR) can fail to recruit Ca sparks at a CaRU, while still contributing to SR Ca leak. We assess this using a physiologically detailed mathematical mo... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491705 Wed, 16 Nov 2011 05:00:00 +0100 5491705 http://www.medworm.com/index.php?rid=5491704&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098736%26dopt%3DAbstract Authors: Heinzelmann G, Baştuğ T, Kuyucak S Abstract Glutamate/Aspartate transporters cotransport three Na(+) and one H(+) ions with the substrate and countertransport one K(+) ion. The binding sites for the substrate and two Na(+) ions have been observed in the crystal structure of the archeal homolog Glt(Ph), while the binding site for the third Na(+) ion has been proposed from computational studies and confirmed by experiments. Here we perform detailed free energy simulations of Glt(Ph), giving a comprehensive characterization of the substrate and ion binding sites, and calculating their binding free energies in various configurations. Our results show unequivocally that the substrate binds after the binding of two Na(+) ions. They also shed light into Asp/Glu selectivity of G... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491704 Wed, 16 Nov 2011 05:00:00 +0100 5491704 http://www.medworm.com/index.php?rid=5491703&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098737%26dopt%3DAbstract Authors: Talukder I, Kazi R, Wollmuth LP Abstract NMDA receptors are glutamate-activated ion channel complexes central to the functioning of the mammalian nervous system. Opening of the NMDA receptor ion channel pore is initiated by agonist-induced conformational changes in the extracellular ligand-binding domain (LBD) but the dynamic mechanism of this process remains unresolved. We studied how a disulfide bond in the obligatory GluN1 subunit-the sole site of redox modulation in NMDA receptors-controls this activation gating mechanism. This disulfide bond is located in the hinge region of the LBD, and presumably constrains agonist-induced cleft closure of the clamshell-like LBD. Elimination of this bond, by either DTT-mediated reduction or mutagenesis, enhances gating efficiency s... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491703 Wed, 16 Nov 2011 05:00:00 +0100 5491703 http://www.medworm.com/index.php?rid=5491702&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098738%26dopt%3DAbstract Authors: Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, Grabe M Abstract Sodium coupled cotransporters of the five-helix inverted repeat (5HIR) superfamily use an alternating access mechanism to transport a myriad of small molecules across the cell membrane. One of the primary steps in this mechanism is the conformational transition from a state poised to bind extracellular substrates to a state that is competent to deliver substrate to the cytoplasm. Here, we construct a coarse-grained model of the 5HIR benzylhydantoin transporter Mhp1 that incorporates experimental structures of the outward- and inward-open states to investigate the mechanism of this conformational change. Using the weighted ensemble path-sampling method, we rigorously sample the outward- to inwa... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491702 Wed, 16 Nov 2011 05:00:00 +0100 5491702 http://www.medworm.com/index.php?rid=5491701&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098739%26dopt%3DAbstract Authors: Depriest A, Phelan P, Martha Skerrett I Abstract The channel proteins of gap junctions are encoded by two distinct gene families, connexins, which are exclusive to chordates, and innexins/pannexins, which are found throughout the animal kingdom. Although the relationship between the primary structure and function of the vertebrate connexins has been relatively well studied, there are, to our knowledge, no structure-function analyses of invertebrate innexins. In the first such study, we have used tryptophan scanning to probe the first transmembrane domain (M1) of the Drosophila innexin Shaking-B(Lethal), which is a component of rectifying electrical synapses in the Giant Fiber escape neural circuit. Tryptophan was substituted sequentially for 16 amino acids within M1 of Sh... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491701 Wed, 16 Nov 2011 05:00:00 +0100 5491701 http://www.medworm.com/index.php?rid=5491700&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098740%26dopt%3DAbstract Authors: Pathak P, London E Abstract Mixtures of unsaturated lipids, sphingolipids, and cholesterol form coexisting liquid-disordered and sphingolipid and cholesterol-rich liquid-ordered (Lo) phases in water. The detergent Triton X-100 does not readily solubilize Lo domains, but does solubilize liquid-disordered domains, and is commonly used to prepare detergent-resistant membranes from cells and model membranes. However, it has been proposed that in membranes with mixtures of sphingomyelin (SM), 1-palmitoyl 2-oleoyl phosphatidylcholine (POPC), and cholesterol Triton X-100 may induce Lo domain formation, and therefore detergent-resistant membranes may not reflect the presence of preexisting domains. To examine this hypothesis, the effect of Triton on Lo domain formation was measure... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491700 Wed, 16 Nov 2011 05:00:00 +0100 5491700 http://www.medworm.com/index.php?rid=5491699&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098741%26dopt%3DAbstract Authors: Apellániz B, Ivankin A, Nir S, Gidalevitz D, Nieva JL Abstract Electron microscopy structural determinations suggest that the membrane-proximal external region (MPER) of glycoprotein 41 (gp41) may associate with the HIV-1 membrane interface. It is further proposed that MPER-induced disruption and/or deformation of the lipid bilayer ensue during viral fusion. However, it is predicted that the cholesterol content of this membrane (∼45 mol %) will act against MPER binding and restructuring activity, in agreement with alternative structural models proposing that the MPER constitutes a gp41 ectodomain component that does not insert into the viral membrane. Here, using MPER-based peptides, we test the hypothesis that cholesterol impedes the membrane association and destabili... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491699 Wed, 16 Nov 2011 05:00:00 +0100 5491699 http://www.medworm.com/index.php?rid=5491698&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098742%26dopt%3DAbstract Authors: Ovchinnikov V, Cecchini M, Vanden-Eijnden E, Karplus M Abstract Myosin VI (MVI) is a dimeric molecular motor that translocates backwards on actin filaments with a surprisingly large and variable step size, given its short lever arm. A recent x-ray structure of MVI indicates that the large step size can be explained in part by a novel conformation of the converter subdomain in the prepowerstroke state, in which a 53-residue insert, unique to MVI, reorients the lever arm nearly parallel to the actin filament. To determine whether the existence of the novel converter conformation could contribute to the step-size variability, we used a path-based free-energy simulation tool, the string method, to show that there is a small free-energy difference between the novel converter co... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491698 Wed, 16 Nov 2011 05:00:00 +0100 5491698 http://www.medworm.com/index.php?rid=5491697&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098743%26dopt%3DAbstract Authors: Bickham DC, West TG, Webb MR, Woledge RC, Curtin NA, Ferenczi MA Abstract Muscle fiber contraction involves the cyclical interaction of myosin cross-bridges with actin filaments, linked to hydrolysis of ATP that provides the required energy. We show here the relationship between cross-bridge states, force generation, and Pi release during ramp stretches of active mammalian skeletal muscle fibers at 20°C. The results show that force and Pi release respond quickly to the application of stretch: force rises rapidly, whereas the rate of Pi release decreases abruptly and remains low for the duration of the stretch. These measurements show that biochemical change on the millisecond timescale accompanies the mechanical and structural responses in active muscle fibers. A cross-b... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491697 Wed, 16 Nov 2011 05:00:00 +0100 5491697 http://www.medworm.com/index.php?rid=5491696&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098744%26dopt%3DAbstract Authors: Rodriguez AG, Han SJ, Regnier M, Sniadecki NJ Abstract During neonatal development, there is an increase in myocardial stiffness that coincides with an increase in the contractility of the heart. In vitro assays have shown that substrate stiffness plays a role in regulating the twitch forces produced by immature cardiomyocytes. However, its effect on twitch power is unclear due to difficulties in measuring the twitch velocity of cardiomyocytes. Here, we introduce what we consider a novel approach to quantify twitch power by combining the temporal resolution of optical line scanning with the subcellular force resolution of micropost arrays. Using this approach, twitch power was found to be greater for cells cultured on stiffer posts, despite having lower twitch velocities.... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491696 Wed, 16 Nov 2011 05:00:00 +0100 5491696 http://www.medworm.com/index.php?rid=5491695&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098745%26dopt%3DAbstract Authors: Afek A, Sela I, Musa-Lempel N, Lukatsky DB Abstract Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model organism. We perform a genome-wide computational analysis of the nonspecific transcription factor (TF)-DNA binding free-energy landscape and compare this landscape with experimentally determined nucleosome-binding preferences. We show that DNA regions with enhanced nonspecific TF-DNA binding are statistically significantly depleted of nucleosomes. We suggest therefore that the competition between TFs with histones for nonspecific binding to genomic sequences might be an important mechanism infl... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491695 Wed, 16 Nov 2011 05:00:00 +0100 5491695 http://www.medworm.com/index.php?rid=5491694&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098746%26dopt%3DAbstract Authors: Meng D, Hjelm RP, Hu J, Wu J Abstract The genomic material of hepatitis B virus (HBV) is confined within a fenestrated nucleocapsid consisting of 240 identical copies of the capsid protein, which has a rigid core and a positively charged and highly flexible C-terminal domain (CTD). Although previous mutagenesis studies have demonstrated the importance of the CTD in viral RNA packaging and reverse transcription, the microscopic structure of the CTD and its interaction with encapsidated nucleic acids at various stages of viral maturation remain poorly understood. Here, we present a theoretical analysis of the radial distributions of the CTD chains and nucleic acids in the hepatitis B virus nucleocapsid at the beginning and final stages of viral reverse transcription based on... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491694 Wed, 16 Nov 2011 05:00:00 +0100 5491694 http://www.medworm.com/index.php?rid=5491693&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098747%26dopt%3DAbstract Authors: Bateman DA, Tycko R, Wickner RB Abstract Transthyretin (TTR) is a largely β-sheet serum protein responsible for transporting thyroxine and vitamin A. TTR is found in amyloid deposits of patients with senile systemic amyloidosis. TTR mutants lead to familial amyloidotic polyneuropathy and familial amyloid cardiomyopathy, with an earlier age of onset. Studies of amyloid fibrils of familial amyloidotic polyneuropathy mutant TTR suggest a structure similar to the native state with only a simple opening of a β-strand-loop-strand region exposing the two main β-sheets of the protein for fibril elongation. However, we find that the wild-type TTR sequence forms amyloid fibrils that are considerably different from the previously suggested amyloid structure. Using protease digesti... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491693 Wed, 16 Nov 2011 05:00:00 +0100 5491693 http://www.medworm.com/index.php?rid=5491692&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098748%26dopt%3DAbstract Authors: Cheon M, Chang I, Hall CK Abstract Protein aggregation is associated with fatal neurodegenerative diseases, including Alzheimer's and Parkinson's. Mapping out kinetics along the aggregation pathway could provide valuable insights into the mechanisms that drive oligomerization and fibrillization, but that is beyond the current scope of computational research. Here we trace out the full kinetics of the spontaneous formation of fibrils by 48 Aβ(16-22) peptides, following the trajectories in molecular detail from an initial random configuration to a final configuration of twisted protofilaments with cross-β-structure. We accomplish this by performing large-scale molecular-dynamics simulations based on an implicit-solvent, intermediate-resolution protein model, PRIME20. Stru... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491692 Wed, 16 Nov 2011 05:00:00 +0100 5491692 http://www.medworm.com/index.php?rid=5491691&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098749%26dopt%3DAbstract Authors: Li W, Liu Y, Perez T, Gunton JD, Sorensen CM, Chakrabarti A Abstract We show that the kinetics of nanochain formation of amelogenin molecules is well described by a combination of translational and rotational diffusion of a simplified anisotropic bipolar model consisting of hydrophobic spherical colloid particles and a point charge located on each particle surface. The colloid particles interact via a standard depletion attraction whereas the point charges interact through a screened Coulomb repulsion. We study the kinetics via a Brownian dynamics simulation of both translational and rotational motions and show that the anisotropy brought in by the charge dramatically affects the kinetic pathway of cluster formation and our simple model captures the main features of the ex... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491691 Wed, 16 Nov 2011 05:00:00 +0100 5491691 http://www.medworm.com/index.php?rid=5491688&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098750%26dopt%3DAbstract Authors: Pandit A, Shirzad-Wasei N, Wlodarczyk LM, van Roon H, Boekema EJ, Dekker JP, de Grip WJ Abstract Self-aggregation of isolated plant light-harvesting complexes (LHCs) upon detergent extraction is associated with fluorescence quenching and is used as an in vitro model to study the photophysical processes of nonphotochemical quenching (NPQ). In the NPQ state, in vivo induced under excess solar light conditions, harmful excitation energy is safely dissipated as heat. To prevent self-aggregation and probe the conformations of LHCs in a lipid environment devoid from detergent interactions, we assembled LHCII trimer complexes into lipid nanodiscs consisting of a bilayer lipid matrix surrounded by a membrane scaffold protein (MSP). The LHCII nanodiscs were characterized by fluo... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491688 Wed, 16 Nov 2011 05:00:00 +0100 5491688 http://www.medworm.com/index.php?rid=5491671&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098751%26dopt%3DAbstract Authors: Ahlstrom LS, Miyashita O Abstract The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are fo... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491671 Wed, 16 Nov 2011 05:00:00 +0100 5491671 http://www.medworm.com/index.php?rid=5491668&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098752%26dopt%3DAbstract Authors: Xu D, Zhang Y Abstract Most protein structural prediction algorithms assemble structures as reduced models that represent amino acids by a reduced number of atoms to speed up the conformational search. Building accurate full-atom models from these reduced models is a necessary step toward a detailed function analysis. However, it is difficult to ensure that the atomic models retain the desired global topology while maintaining a sound local atomic geometry because the reduced models often have unphysical local distortions. To address this issue, we developed a new program, called ModRefiner, to construct and refine protein structures from Cα traces based on a two-step, atomic-level energy minimization. The main-chain structures are first constructed from initial Cα trace... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491668 Wed, 16 Nov 2011 05:00:00 +0100 5491668 http://www.medworm.com/index.php?rid=5491667&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098753%26dopt%3DAbstract Authors: Bakshi S, Bratton BP, Weisshaar JC Abstract Photoactivation localization microscopy (PALM) is used to study the spatial distribution and diffusion of single copies of the protein Kaede in the cytoplasm of live Escherichia coli under moderate growth conditions (67 min doubling time). The spatial distribution of Kaede is uniform within the cytoplasm. The cytoplasmic radius of 380 ± 30 nm varies little from cell to cell. Single-particle tracking using 4 ms exposure times reveals negatively curved plots of mean-square displacement versus time. A detailed comparison with Monte Carlo simulations in a spherocylindrical volume shows that the curvature can be quantitatively understood in terms of free diffusion within a confining volume. The mean diffusion coefficient across ce... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491667 Wed, 16 Nov 2011 05:00:00 +0100 5491667 http://www.medworm.com/index.php?rid=5491666&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098754%26dopt%3DAbstract Authors: Tønnesen J, Nadrigny F, Willig KI, Wedlich-Söldner R, Nägerl UV Abstract The advent of superresolution microscopy has opened up new research opportunities into dynamic processes at the nanoscale inside living biological specimens. This is particularly true for synapses, which are very small, highly dynamic, and embedded in brain tissue. Stimulated emission depletion (STED) microscopy, a recently developed laser-scanning technique, has been shown to be well suited for imaging living synapses in brain slices using yellow fluorescent protein as a single label. However, it would be highly desirable to be able to image presynaptic boutons and postsynaptic spines, which together form synapses, using two different fluorophores. As STED microscopy uses separate laser beams for ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491666 Wed, 16 Nov 2011 05:00:00 +0100 5491666 http://www.medworm.com/index.php?rid=5491665&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098755%26dopt%3DAbstract Authors: Rodnin MV, Kyrychenko A, Kienker P, Sharma O, Vargas-Uribe M, Collier RJ, Finkelstein A, Ladokhin AS Abstract The translocation (T) domain plays a key role in the action of diphtheria toxin and is responsible for transferring the N-terminus-attached catalytic domain across the endosomal membrane into the cytosol in response to acidification. The T-domain undergoes a series of pH-triggered conformational changes that take place in solution and on the membrane interface, and ultimately result in transbilayer insertion and N-terminus translocation. Structure-function studies along this pathway have been hindered because the protein population occupies multiple conformations at the same time. Here we report that replacement of the three C-terminal histidine residues, H322, H3... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491665 Wed, 16 Nov 2011 05:00:00 +0100 5491665 http://www.medworm.com/index.php?rid=5491664&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098756%26dopt%3DAbstract Authors: Re S, Miyashita N, Yamaguchi Y, Sugita Y Abstract Structural diversity of N-glycans is essential for specific binding to their receptor proteins. To gain insights into structural and dynamic aspects in atomic detail not normally accessible by experiment, we here perform extensive molecular-dynamics simulations of N-glycans in solution using the replica-exchange method. The simulations show that five distinct conformers exist in solution for the N-glycans with and without bisecting GlcNAc. Importantly, the population sizes of three of the conformers are drastically reduced upon the introduction of bisecting GlcNAc. This is caused by a local hydrogen-bond rearrangement proximal to the bisecting GlcNAc. These simulations show that an N-glycan modification like the bisecting ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491664 Wed, 16 Nov 2011 05:00:00 +0100 5491664 http://www.medworm.com/index.php?rid=5491663&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098757%26dopt%3DAbstract Authors: Zhang Y, Voth GA Abstract Using a reactive molecular dynamics simulation methodology, the free energy barrier for water-mediated proton transport between the two proton gating residues Glu(203) and Glu(148) in the ClC-ec1 antiporter, including the Grotthuss mechanism of proton hopping, was calculated. Three different chloride-binding states, with 1), both the central and internal Cl(-), 2), the central Cl(-) only, and 3), the internal Cl(-) only, were considered and the coupling to the H(+) transport studied. The results show that both the central and internal Cl(-) are essential for the proton transport from Glu(203) to Glu(148) to have a favorite free energy driving force. The rotation of the Glu(148) side chain was also found to be independent of the internal chloride b... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491663 Wed, 16 Nov 2011 05:00:00 +0100 5491663 http://www.medworm.com/index.php?rid=5491662&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098758%26dopt%3DAbstract Authors: Tomonaga Y, Hidaka T, Kawamura I, Nishio T, Ohsawa K, Okitsu T, Wada A, Sudo Y, Kamo N, Ramamoorthy A, Naito A Abstract A novel, to our knowledge, in situ photoirradiation system for solid-state NMR measurements is improved and demonstrated to successfully identify the M-photointermediate of pharaonis phoborhodopsin (ppR or sensory rhodopsin II), that of the complex with transducer (ppR/pHtrII), and T204A mutant embedded in a model membrane. The (13)C NMR signals from [20-(13)C]retinal-ppR and ppR/pHtrII revealed that multiple M-intermediates with 13-cis, 15-anti retinal configuration coexisted under the continuously photoirradiated condition. NMR signals observed from the photoactivated retinal provide insights into the process of photocycle in the ppR/pHtrII complex. ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491662 Wed, 16 Nov 2011 05:00:00 +0100 5491662 http://www.medworm.com/index.php?rid=5491661&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22098759%26dopt%3DAbstract Authors: Krzyszczyk P, Wolgemuth CW Abstract When plated onto a substrate, cells spread. Many cell types, including smooth muscle cells and fibroblasts, spread more effectively on stiffer substrates, and a simple empirical relationship has been determined that relates a cell's spread area to the substrate stiffness. In addition, some crawling cells when plated onto a stiff substrate will not migrate onto soft substrate, a process called "durotaxis". Here we show that the resistive force predicted previously for dynamic adhesion molecules can account for both of these mechanosensory effects. PMID: 22098759 [PubMed - in process] (Source: Biophysical Journal) Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5491661 Wed, 16 Nov 2011 05:00:00 +0100 5491661 http://www.medworm.com/index.php?rid=5417420&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067144%26dopt%3DAbstract Authors: Pradhan RK, Qi F, Beard DA, Dash RK Abstract Ca(2+) is an important regulatory ion and alteration of mitochondrial Ca(2+) homeostasis can lead to cellular dysfunction and apoptosis. Ca(2+) is transported into respiring mitochondria via the Ca(2+) uniporter, which is known to be inhibited by Mg(2+). This uniporter-mediated mitochondrial Ca(2+) transport is also shown to be influenced by inorganic phosphate (Pi). Despite a large number of experimental studies, the kinetic mechanisms associated with the Mg(2+) inhibition and Pi regulation of the uniporter function are not well established. To gain a quantitative understanding of the effects of Mg(2+) and Pi on the uniporter function, we developed here a mathematical model based on known kinetic properties of the uniporter and... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417420 Wed, 02 Nov 2011 04:00:00 +0100 5417420 http://www.medworm.com/index.php?rid=5417419&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067145%26dopt%3DAbstract Authors: Aguda BD, Kim Y, Kim HS, Friedman A, Fine HA Abstract A kinetic model of a molecular control system for the cellular decision to proliferate or differentiate is formulated and analyzed for the purpose of understanding how the system can break down in cancer cells. The proposed core of this control system is composed of the transcription factors Myc and p53. The network of interactions between these factors involves negative and positive feedback loops that are linked to pathways involved in differentiation, cell cycle, and apoptosis. Understanding the dynamics of the Myc-p53 control system is aided by the postulate that there exists a cancer zone defined as a range of oncogenic Myc activities where the probability of initiating cancer is high. We propose that an essential ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417419 Wed, 02 Nov 2011 04:00:00 +0100 5417419 http://www.medworm.com/index.php?rid=5417418&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067146%26dopt%3DAbstract We present a novel (to our knowledge) multiscale computational approach for quantifying the hydrophobic mismatch-driven remodeling of membrane bilayers by multihelical membrane proteins. The method accounts for both the membrane remodeling energy and the energy contribution from any partial (incomplete) alleviation of the hydrophobic mismatch by membrane remodeling. Overcoming previous limitations, it allows for radially asymmetric bilayer deformations produced by multihelical proteins, and takes into account the irregular membrane-protein boundaries. The approach is illustrated by application to two G-protein coupled receptors: rhodopsin in bilayers of different thickness, and the serotonin 5-HT(2A) receptor bound to pharmacologically different ligands. Analysis of the results identifies ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417418 Wed, 02 Nov 2011 04:00:00 +0100 5417418 http://www.medworm.com/index.php?rid=5417417&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067147%26dopt%3DAbstract In this study, we developed a Markov model of the inner membrane anion channel in which reactive-oxidative-species (ROS)-induced opening of the inner membrane anion channel causes transient mitochondrial depolarizations in a single mitochondrion that occur in a nonperiodic manner, simulating flickering. We then coupled the individual mitochondria into a network, in which flickers occur randomly and sparsely when a small number of mitochondria are in the state of high superoxide production. As the number of mitochondria in the high-superoxide-production state increases, short-lived or abortive waves due to ROS-induced ROS release coexist with flickers. When the number of mitochondria in the high-superoxide-production state reaches a critical number, recurring propagating waves are observed.... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417417 Wed, 02 Nov 2011 04:00:00 +0100 5417417 http://www.medworm.com/index.php?rid=5417416&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067148%26dopt%3DAbstract Authors: Jepihhina N, Beraud N, Sepp M, Birkedal R, Vendelin M Abstract Intracellular diffusion restrictions for ADP and other molecules have been predicted earlier based on experiments on permeabilized fibers or cardiomyocytes. However, it is possible that the effective diffusion distance is larger than the cell dimensions due to clumping of cells and incomplete separation of cells in fiber preparations. The aim of this work was to check whether diffusion restrictions exist inside rat cardiomyocytes or are caused by large effective diffusion distance. For that, we determined the response of oxidative phosphorylation (OxPhos) to exogenous ADP and ATP stimulation in permeabilized rat cardiomyocytes using fluorescence microscopy. The state of OxPhos was monitored via NADH and flavopr... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417416 Wed, 02 Nov 2011 04:00:00 +0100 5417416 http://www.medworm.com/index.php?rid=5417415&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067149%26dopt%3DAbstract Authors: Zeng Y, Lai T, Koh CG, Leduc PR, Chiam KH Abstract Circular dorsal ruffles (CDRs) are transient actin-rich ringlike structures that form on the dorsal surface of growth-factor stimulated cells. However, the dynamics and mechanism of formation of CDRs are still unknown. It has been observed that CDR formation leads to stress fibers disappearing near the CDRs. Because stress fiber formation can be modified by substrate stiffness, we examined the effect of substrate stiffness on CDR formation by seeding NIH 3T3 fibroblasts on glass and polydimethylsiloxane substrates of varying stiffnesses from 20 kPa to 1800 kPa. We found that increasing substrate stiffness increased the lifetime of the CDRs. We developed a mathematical model of the signaling pathways involved in CDR forma... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417415 Wed, 02 Nov 2011 04:00:00 +0100 5417415 http://www.medworm.com/index.php?rid=5417414&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067150%26dopt%3DAbstract Authors: Fabry B, Klemm AH, Kienle S, Schäffer TE, Goldmann WH Abstract Focal adhesion kinase (FAK) is a central focal adhesion protein that promotes focal adhesion turnover, but the role of FAK for cell mechanical stability is unknown. We measured the mechanical properties of wild-type (FAKwt), FAK-deficient (FAK-/-), FAK-silenced (siFAK), and siControl mouse embryonic fibroblasts by magnetic tweezer, atomic force microscopy, traction microscopy, and nanoscale particle tracking microrheology. FAK-deficient cells showed lower cell stiffness, reduced adhesion strength, and increased cytoskeletal dynamics compared to wild-type cells. These observations imply a reduced stability of the cytoskeleton in FAK-deficient cells. We attribute the reduced cytoskeletal stability to rho-kinase ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417414 Wed, 02 Nov 2011 04:00:00 +0100 5417414 http://www.medworm.com/index.php?rid=5417413&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067151%26dopt%3DAbstract Authors: McKee CT, Raghunathan VK, Nealey PF, Russell P, Murphy CJ Abstract The influence of nucleus shape and orientation on the elastic modulus of epithelial cells was investigated with atomic force microscopy. The shape and orientation were controlled by presenting the epithelial cells with anisotropic parallel ridges and grooves of varying pitch at the cell substratum. As the cells oriented to the underlying topography, the volume of the nucleus increased as the pitch of the topography increased from 400 nm to 2000 nm. The increase in nucleus volume was reflected by an increase in the measured elastic modulus of the topographically aligned cells. Significant alterations in the shape of the nucleus, by intimate contact with the topographic ridge and grooves of the underlying c... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417413 Wed, 02 Nov 2011 04:00:00 +0100 5417413 http://www.medworm.com/index.php?rid=5417412&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067152%26dopt%3DAbstract Authors: Jones DK, Peters CH, Tolhurst SA, Claydon TW, Ruben PC Abstract Low pH depolarizes the voltage dependence of voltage-gated sodium (Na(V)) channel activation and fast inactivation. A complete description of Na(V) channel proton modulation, however, has not been reported. The majority of Na(V) channel proton modulation studies have been completed in intact tissue. Additionally, several Na(V) channel isoforms are expressed in cardiac tissue. Characterizing the proton modulation of the cardiac Na(V) channel, Na(V)1.5, will thus help define its contribution to ischemic arrhythmogenesis, where extracellular pH drops from pH 7.4 to as low as pH 6.0 within ∼10 min of its onset. We expressed the human variant of Na(V)1.5 with and without the modulating β(1) subunit in Xenopus o... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417412 Wed, 02 Nov 2011 04:00:00 +0100 5417412 http://www.medworm.com/index.php?rid=5417411&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067153%26dopt%3DAbstract Authors: Hirano M, Onishi Y, Yanagida T, Ide T Abstract The KcsA channel is a representative potassium channel that is activated by changes in pH. Previous studies suggested that the region that senses pH is entirely within its transmembrane segments. However, we recently revealed that the cytoplasmic domain also has an important role, because its conformation was observed to change dramatically in response to pH changes. Here, to investigate the effects of the cytoplasmic domain on pH-dependent gating, we made a chimera mutant channel consisting of the cytoplasmic domain of the KcsA channel and the transmembrane region of the MthK channel. The chimera showed a pH dependency similar to that of KcsA, indicating that the cytoplasmic domain can act as a pH sensor. To identify how this... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417411 Wed, 02 Nov 2011 04:00:00 +0100 5417411 http://www.medworm.com/index.php?rid=5417410&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067154%26dopt%3DAbstract Authors: Lin SH, Perera MN, Nguyen T, Datskovskiy D, Miles M, Colombini M Abstract When activated, the proapoptotic protein Bax permeabilizes the mitochondrial outer membrane, allowing the release of proteins into the cytosol and thus initiating the execution phase of apoptosis. When activated Bax was reconstituted into phospholipid membranes, we discovered a new, to our knowledge, property of Bax channels: voltage gating. We also found that the same Bax sample under the same experimental conditions could give rise to two radically different channels: Type A, which is small, well behaved, homogeneous, and voltage-gated, and Type B, which is large, noisy, and voltage-independent. One Type B channel can be converted irreversibly into a population of Type A channels by the addition of... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417410 Wed, 02 Nov 2011 04:00:00 +0100 5417410 http://www.medworm.com/index.php?rid=5417409&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067155%26dopt%3DAbstract Authors: Guo T, Fruen BR, Nitu FR, Nguyen TD, Yang Y, Cornea RL, Bers DM Abstract Calmodulin (CaM) binding to the type 2 ryanodine receptor (RyR2) regulates Ca release from the cardiac sarcoplasmic reticulum (SR). However, the structural basis of CaM regulation of the RyR2 is poorly defined, and the presence of other potential CaM binding partners in cardiac myocytes complicates resolution of CaM's regulatory interactions with RyR2. Here, we show that a fluorescence-resonance-energy-transfer (FRET)-based approach can effectively resolve RyR2 CaM binding, both in isolated SR membrane vesicles and in permeabilized ventricular myocytes. A small FRET donor was targeted to the RyR2 cytoplasmic assembly via fluorescent labeling of the FKBP12.6 subunit. Acceptor fluorophore was attached a... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417409 Wed, 02 Nov 2011 04:00:00 +0100 5417409 http://www.medworm.com/index.php?rid=5417408&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067156%26dopt%3DAbstract Authors: Ellenbroek WG, Wang YH, Christian DA, Discher DE, Janmey PA, Liu AJ Abstract Polyphosphoinositides are among the most highly charged molecules in the cell membrane, and the most common polyphosphoinositide, phosphatidylinositol-4,5-bisphosphate (PIP(2)), is involved in many mechanical and biochemical processes in the cell membrane. Divalent cations such as calcium can cause clustering of the polyanionic PIP(2), but the origin and strength of the effective attractions leading to clustering has been unclear. In addition, the question of whether the ion-mediated attractions could be strong enough to alter the mechanical properties of the membrane, to our knowledge, has not been addressed. We study phase separation in mixed monolayers of neutral and highly negatively charged l... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417408 Wed, 02 Nov 2011 04:00:00 +0100 5417408 http://www.medworm.com/index.php?rid=5417407&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067157%26dopt%3DAbstract Authors: Senthil Kumar VS, O'Neall-Hennessey E, Reshetnikova L, Brown JH, Robinson H, Szent-Györgyi AG, Cohen C Abstract We have determined the crystal structure of a phosphorylated smooth-muscle myosin light chain domain (LCD). This reconstituted LCD is of a sea scallop catch muscle myosin with its phosphorylatable regulatory light chain (RLC SmoA). In the crystal structure, Arg(16), an arginine residue that is present in this isoform but not in vertebrate smooth-muscle RLC, stabilizes the phosphorylation site. This arginine interacts with the carbonyl group of the phosphorylation-site serine in the unphosphorylated LCD (determined previously), and with the phosphate group when the serine is phosphorylated. However, the overall conformation of the LCD is essentially unchanged upo... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417407 Wed, 02 Nov 2011 04:00:00 +0100 5417407 http://www.medworm.com/index.php?rid=5417406&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067158%26dopt%3DAbstract Authors: Reese L, Melbinger A, Frey E Abstract The assembly and disassembly dynamics of microtubules (MTs) is tightly controlled by MT-associated proteins. Here, we investigate how plus-end-directed depolymerases of the kinesin-8 family regulate MT depolymerization dynamics. Using an individual-based model, we reproduce experimental findings. Moreover, crowding is identified as the key regulatory mechanism of depolymerization dynamics. Our analysis reveals two qualitatively distinct regimes. For motor densities above a particular threshold, a macroscopic traffic jam emerges at the plus-end and the MT dynamics become independent of the motor concentration. Below this threshold, microscopic traffic jams at the tip arise that cancel out the effect of the depolymerization kinetics such... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417406 Wed, 02 Nov 2011 04:00:00 +0100 5417406 http://www.medworm.com/index.php?rid=5417405&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067159%26dopt%3DAbstract Authors: Sugawa M, Okada KA, Masaike T, Nishizaka T Abstract F(1)-ATPase is a water-soluble portion of F(o)F(1)-ATP synthase and rotary molecular motor that exhibits reversibility in chemical reactions. The rotational motion of the shaft subunit γ has been carefully scrutinized in previous studies, but a tilting motion of the shaft has never been explicitly postulated. Here we found a change in the radius of rotation of the probe attached to the shaft subunit γ between two different intermediate states in ATP hydrolysis: one waiting for ATP binding, and the other waiting for ATP hydrolysis and/or subsequent product release. Analysis of this radial difference indicates a ∼4° outward tilting of the γ-subunit induced by ATP binding. The tilt angle is a new parameter, to our know... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417405 Wed, 02 Nov 2011 04:00:00 +0100 5417405 http://www.medworm.com/index.php?rid=5417404&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067160%26dopt%3DAbstract Authors: Wang Q, Zhao C, Sw. DM Abstract Many animals regulate power generation for locomotion by varying the number of muscle fibers used for movement. However, insects with asynchronous flight muscles may regulate the power required for flight by varying the calcium concentration ([Ca(2+)]). In vivo myoplasmic calcium levels in Drosophila flight muscle have been found to vary twofold during flight and to correlate with aerodynamic power generation and wing beat frequency. This mechanism can only be possible if [Ca(2+)] also modulates the flight muscle power output and muscle kinetics to match the aerodynamic requirements. We found that the in vitro power produced by skinned Drosophila asynchronous flight muscle fibers increased with increasing [Ca(2+)]. Positive muscle power ge... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417404 Wed, 02 Nov 2011 04:00:00 +0100 5417404 http://www.medworm.com/index.php?rid=5417403&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067161%26dopt%3DAbstract Authors: Luan B, Martyna G, Stolovitzky G Abstract Sequencing DNA in a synthetic solid-state nanopore is potentially a low-cost and high-throughput method. Essential to the nanopore-based DNA sequencing method is the ability to control the motion of a single-stranded DNA (ssDNA) molecule at single-base resolution. Experimental studies showed that the average translocation speed of DNA driven by a biasing electric field can be affected by ionic concentration, solvent viscosity, or temperature. Even though it is possible to slow down the average translocation speed, instantaneous motion of DNA is too diffusive to allow each DNA base to stay in front of a sensor site for its measurement. Using extensive all-atom molecular dynamics simulations, we study the diffusion constant, friction... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417403 Wed, 02 Nov 2011 04:00:00 +0100 5417403 http://www.medworm.com/index.php?rid=5417402&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067162%26dopt%3DAbstract Authors: Law SM, Feig M Abstract DNA mismatch recognition and repair is vital for preserving the fidelity of the genome. Conserved across prokaryotes and eukaryotes, MutS is the primary protein that is responsible for recognizing a variety of DNA mismatches. From molecular dynamics simulations of the Escherichia coli MutS-DNA complex, we describe significant conformational dynamics in the DNA surrounding a G·T mismatch that involves weakening of the basepair hydrogen bonding in the basepair adjacent to the mismatch and, in one simulation, complete base opening via the major groove. The energetics of base flipping was further examined with Hamiltonian replica exchange free energy calculations revealing a stable flipped-out state with an initial barrier of ∼2 kcal/mol. Furthermor... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417402 Wed, 02 Nov 2011 04:00:00 +0100 5417402 http://www.medworm.com/index.php?rid=5417401&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067163%26dopt%3DAbstract Authors: Cabriolu R, Kashchiev D, Auer S Abstract We consider the size distribution of amyloid nanofibrils (protofilaments) in nucleating protein solutions when the nucleation process occurs by the mechanism of direct polymerization of β-strands (extended peptides or protein segments) into β-sheets. Employing the atomistic nucleation theory, we derive a general expression for the stationary size distribution of amyloid nanofibrils constituted of successively layered β-sheets. The application of this expression to amyloid β(1-40) (Aβ(40)) fibrils allows us to determine the nanofibril size distribution as a function of the protein concentration and temperature. The distribution is most remarkable with its exhibiting a series of peaks positioned at "magic" nanofibril sizes (or le... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417401 Wed, 02 Nov 2011 04:00:00 +0100 5417401 http://www.medworm.com/index.php?rid=5417400&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067164%26dopt%3DAbstract Authors: Hu KN, McGlinchey RP, Wickner RB, Tycko R Abstract Although amyloid fibrils are generally considered to be causative or contributing agents in amyloid diseases, several amyloid fibrils are also believed to have biological functions. Among these are fibrils formed by Pmel17 within melanosomes, which act as a template for melanin deposition. We use solid-state NMR to show that the molecular structures of fibrils formed by the 130-residue pseudo-repeat domain Pmel17:RPT are polymorphic even within the biologically relevant pH range. Thus, biological function in amyloid fibrils does not necessarily imply a unique molecular structure. Solid-state NMR spectra of three Pmel17:RPT polymorphs show that in all cases, only a subset (∼30%) of the full amino acid sequence contributes... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417400 Wed, 02 Nov 2011 04:00:00 +0100 5417400 http://www.medworm.com/index.php?rid=5417399&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067165%26dopt%3DAbstract Authors: Pritchard-Bell A, Shell MS Abstract Decades of work has investigated the energy landscapes of simple protein models, but what do the landscapes of real, large, atomically detailed proteins look like? We explore an approach to this problem that systematically extracts simple funnel models of actual proteins using ensembles of structure predictions and physics-based atomic force fields and sampling. Central to our effort are calculations of a quantity called the relative entropy, which quantifies the extent to which a given set of structure decoys and a putative native structure can be projected onto a theoretical funnel description. We examine 86 structure prediction targets and one coupled folding-binding system, and find that in a majority of cases the relative entropy ro... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417399 Wed, 02 Nov 2011 04:00:00 +0100 5417399 http://www.medworm.com/index.php?rid=5417398&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067166%26dopt%3DAbstract Authors: Hazy E, Bokor M, Kalmar L, Gelencser A, Kamasa P, Han KH, Tompa K, Tompa P Abstract The propensity of α-synuclein to form amyloid plays an important role in Parkinson's disease. Three familial mutations, A30P, E46K, and A53T, correlate with Parkinson's disease. Therefore, unraveling the structural effects of these mutations has basic implications in understanding the molecular basis of the disease. Here, we address this issue through comparing details of the hydration of wild-type α-synuclein and its A53T mutant by a combination of wide-line NMR, differential scanning calorimetry, and molecular dynamics simulations. All three approaches suggest a hydrate shell compatible with a largely disordered state of both proteins. Its fine details, however, are different, with the ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417398 Wed, 02 Nov 2011 04:00:00 +0100 5417398 http://www.medworm.com/index.php?rid=5417397&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067167%26dopt%3DAbstract In this study, we investigate the conformations of Aβ(16-22) octamers in the absence and presence of a single-walled carbon nanotube (SWCNT) by performing extensive all-atom replica exchange molecular-dynamics simulations in explicit solvent. Our simulations starting from eight random chains demonstrate that the addition of SWCNT into Aβ(16-22) solution prevents β-sheet formation. Simulation starting from a prefibrillar β-sheet octamer shows that SWCNT destabilizes the β-sheet structure. A detailed analysis of the Aβ(16-22)/SWCNT/water interactions reveals that both the inhibition of β-sheet formation and the destabilization of prefibrillar β-sheets by SWCNT result from the same physical forces: hydrophobic and π-stacking interactions (with the latter playing a more important role... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417397 Wed, 02 Nov 2011 04:00:00 +0100 5417397 http://www.medworm.com/index.php?rid=5417396&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067168%26dopt%3DAbstract Authors: Ibata K, Takimoto S, Morisaku T, Miyawaki A, Yasui M Abstract Water can pass through biological membranes via two pathways: simple diffusion through the lipid bilayer, or water-selective facilitated diffusion through aquaporins (AQPs). Although AQPs play an important role in osmotic water permeability (P(f)), the role of AQPs in diffusional water permeability remains unclear because of the difficulty of measuring diffusional water permeability (P(d)). Here, we report an accurate and instantaneous method for measuring the P(d) of a single HeLa S3 cell using coherent anti-Stokes Raman scattering (CARS) microscopy with a quick perfusion device for H(2)O/D(2)O exchange. Ultra-high-speed line-scan CARS images were obtained every 0.488 ms. The average decay time constant of CA... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417396 Wed, 02 Nov 2011 04:00:00 +0100 5417396 http://www.medworm.com/index.php?rid=5417395&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067169%26dopt%3DAbstract We present a theoretical technique for quantifying the cellular copy-number of fluorophores that relies on the random nature of the photobleaching process. Our approach does not require single-molecule sensitivity, and therefore can be used with commonly used epifluorescence microscopes. Fluctuations arising from photobleaching can be used to estimate the proportionality between fluorescence intensity and copy-number, which can then be used with subsequent intensity measurements to estimate copy-number. We calculate the statistical errors of our approach and verify them with stochastic simulations. By using fluctuations over the entire photobleaching process, we obtain significantly smaller errors than previous approaches that have used fluctuations arising from cytoplasmic proteins partit... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417395 Wed, 02 Nov 2011 04:00:00 +0100 5417395 http://www.medworm.com/index.php?rid=5417394&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067170%26dopt%3DAbstract Authors: Daddysman MK, Fecko CJ Abstract Investigations into the spatiotemporal dynamics of DNA repair using live-cell imaging are aided by the ability to generate well defined regions of ultravioletlike photolesions in an optical microscope. We demonstrate that multiphoton excitation of DNA in live cells with visible femtosecond pulses produces thymine cyclopyrimidine dimers (CPDs), the primary ultraviolet DNA photoproduct. The CPDs are produced with a cubic to supercubic power dependence using pulses in the wavelength range from at least 400 to 525 nm. We show that the CPDs are confined in all three spatial dimensions, making multiphoton excitation of DNA with visible light an ideal technique for generating localized DNA photolesions in a wide variety of samples, from cultured c... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417394 Wed, 02 Nov 2011 04:00:00 +0100 5417394 http://www.medworm.com/index.php?rid=5417391&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067171%26dopt%3DAbstract Authors: Nia HT, Han L, Li Y, Ortiz C, Grodzinsky A Abstract Atomic-force-microscopy-based oscillatory loading was used in conjunction with finite element modeling to quantify and predict the frequency-dependent mechanical properties of the superficial zone of young bovine articular cartilage at deformation amplitudes, δ, of ∼15 nm; i.e., at macromolecular length scales. Using a spherical probe tip (R ∼ 12.5 μm), the magnitude of the dynamic complex indentation modulus, |E(∗)|, and phase angle, φ, between the force and tip displacement sinusoids, were measured in the frequency range f ∼ 0.2-130 Hz at an offset indentation depth of δ(0) ∼ 3 μm. The experimentally measured |E(∗)| and φ corresponded well with that predicted by a fibril-reinforced poroelastic model ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5417391 Wed, 02 Nov 2011 04:00:00 +0100 5417391 http://www.medworm.com/index.php?rid=5378169&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004732%26dopt%3DAbstract Authors: Wolf DE PMID: 22004732 [PubMed - in process] (Source: Biophysical Journal) Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378169 Wed, 19 Oct 2011 04:00:00 +0100 5378169 http://www.medworm.com/index.php?rid=5378168&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004733%26dopt%3DAbstract Authors: Drocco JA, Grimm O, Tank DW, Wieschaus E Abstract Protein lifetime is of critical importance for most biological processes and plays a central role in cell signaling and embryonic development, where it impacts the absolute concentration of signaling molecules and, potentially, the shape of morphogen gradients. Early conceptual and mathematical models of gradient formation proposed that steady-state gradients are established by an equilibration between the lifetime of a morphogen and its rates of synthesis and diffusion, though whether gradients in fact reach steady state before being read out is a matter of controversy. In any case, this class of models predicts that protein lifetime is a key determinant of both the time to steady state and the spatial extent of a gradient... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378168 Wed, 19 Oct 2011 04:00:00 +0100 5378168 http://www.medworm.com/index.php?rid=5378167&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004734%26dopt%3DAbstract Authors: Balandina AN, Shibeko AM, Kireev DA, Novikova AA, Shmirev II, Panteleev MA, Ataullakhanov FI Abstract Blood coagulation is triggered not only by surface tissue factor (TF) density but also by surface TF distribution. We investigated recognition of surface TF distribution patterns during blood coagulation and identified the underlying molecular mechanisms. For these investigations, we employed 1), an in vitro reaction-diffusion experimental model of coagulation; and 2), numerical simulations using a mathematical model of coagulation in a three-dimensional space. When TF was uniformly immobilized over the activating surface, the clotting initiation time in normal plasma increased from 4 min to >120 min, with a decrease in TF density from 100 to 0.7 pmol/m(2). In cont... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378167 Wed, 19 Oct 2011 04:00:00 +0100 5378167 http://www.medworm.com/index.php?rid=5378166&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004735%26dopt%3DAbstract Authors: Venkatraman L, Li H, Dewey CF, White JK, Bhowmick SS, Yu H, Tucker-Kellogg L Abstract Plasmin (PLS) and urokinase-type plasminogen activator (UPA) are ubiquitous proteases that regulate the extracellular environment. Although they are secreted in inactive forms, they can activate each other through proteolytic cleavage. This mutual interplay creates the potential for complex dynamics, which we investigated using mathematical modeling and in vitro experiments. We constructed ordinary differential equations to model the conversion of precursor plasminogen into active PLS, and precursor urokinase (scUPA) into active urokinase (tcUPA). Although neither PLS nor UPA exhibits allosteric cooperativity, modeling showed that cooperativity occurred at the system level because of sub... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378166 Wed, 19 Oct 2011 04:00:00 +0100 5378166 http://www.medworm.com/index.php?rid=5378165&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004736%26dopt%3DAbstract Authors: Tokarev AA, Butylin AA, Ermakova EA, Shnol EE, Panasenko GP, Ataullakhanov FI Abstract Blood flows through vessels as a segregated suspension. Erythrocytes distribute closer to the vessel axis, whereas platelets accumulate near vessel walls. Directed platelet migration to the vessel walls promotes their hemostatic function. The mechanisms underlying this migration remain poorly understood, although various hypotheses have been proposed to explain this phenomenon (e.g., the available volume model and the drift-flux model). To study this issue, we constructed a mathematical model that predicts the platelet distribution profile across the flow in the presence of erythrocytes. This model considers platelet and erythrocyte dimensions and assumes an even platelet distribution be... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378165 Wed, 19 Oct 2011 04:00:00 +0100 5378165 http://www.medworm.com/index.php?rid=5378164&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004737%26dopt%3DAbstract In this report, we formulate a simple mechanism in pollen tubes by which deposition causes turnover of cell wall cross-links, thereby facilitating mechanical deformation. Accordingly, deposition and mechanics are coupled and are both integral aspects of the morphogenetic process. Among the key experimental qualifications of this model are: its ability to precisely reproduce the morphologies of pollen tubes; its prediction of the growth oscillations exhibited by rapidly growing pollen tubes; and its prediction of the observed phase relationships between variables such as wall thickness, cell morphology, and growth rate within oscillatory cells. In short, the model captures the rich phenomenology of pollen tube morphogenesis and has implications for other plant cell types. PMID: 22004737... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378164 Wed, 19 Oct 2011 04:00:00 +0100 5378164 http://www.medworm.com/index.php?rid=5378163&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004738%26dopt%3DAbstract Authors: Liu W, Montana V, Parpura V, Mohideen U Abstract Interactions between synaptobrevin 2 (Sb2) and syntaxin 1A (Sx1A) can be readily isolated and studied with the use of force spectroscopy single-molecule measurements. We studied interactions between Sx1A and Sb2 in two different orientations (parallel and antiparallel) using four different terminus configurations of these proteins. Force-loading experiments indicated that protein pairs in any configuration/orientation are zippered. We measured the extension and force for disassembly of these interactions, calculated the spontaneous dissociation lifetimes, and determined their free energies, enthalpies, and entropies. Although the free energies were very similar for all four configurations (∼28 k(B)T (Eyring model) and ∼2... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378163 Wed, 19 Oct 2011 04:00:00 +0100 5378163 http://www.medworm.com/index.php?rid=5378162&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004739%26dopt%3DAbstract We report a new (to our knowledge) mechanism of receptor force control in cell adhesion originating from friction between cell adhesion ligands and the supporting substrate. Adherent human endothelial cells have been studied experimentally on polymer substrates noncovalently coated with fluorescent-labeled fibronectin (FN). The cellular traction force correlated with the mobility of FN during cell-driven FN fibrillogenesis. The experimental findings have been explained within a mechanistic two-dimensional model of the load transfer at focal adhesion sites. Myosin motor activity in conjunction with sliding of FN ligands noncovalently coupled to the surface of the polymer substrates is shown to result in a controlled traction force of adherent cells. We conclude that the friction of adhesion... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378162 Wed, 19 Oct 2011 04:00:00 +0100 5378162 http://www.medworm.com/index.php?rid=5378155&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004740%26dopt%3DAbstract Authors: Tigerholm J, Fransén E Abstract In diseases of the brain, the distribution and properties of ion channels display deviations from healthy control subjects. We studied three cases of ion channel alteration related to epileptogenesis. The first case of ion channel alteration represents an enhanced sodium current, the second case addresses the downregulation of the transient potassium current K(A), and the third case relates to kinetic properties of K(A) in a patient with temporal lobe epilepsy. Using computational modeling and optimization, we aimed at reversing the pathological characteristics and restoring normal neural function by altering ion channel properties. We identified two key aspects of neural dysfunction in epileptogenesis: an enhanced response to synaptic inpu... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378155 Wed, 19 Oct 2011 04:00:00 +0100 5378155 http://www.medworm.com/index.php?rid=5378148&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004741%26dopt%3DAbstract Authors: Celedon A, Hale CM, Wirtz D Abstract The organization of chromatin in the cell nucleus is crucial for gene expression regulation. However, physically probing the nuclear interior is challenging because high forces have to be applied using minimally invasive techniques. Here, magnetic nanorods embedded in the nucleus of living cells are subjected to controlled rotational forces, producing micron-sized displacements in the nuclear interior. The resulting time-dependent rotation of the nanorods is analyzed in terms of viscoelastic parameters of the nucleus, in wild-type and Lamin A/C deficient cells. This method and analysis reveal that Lamin A/C knockout, together perhaps with other changes that result from the knockout, induce significant decreases in the nuclear viscosity ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378148 Wed, 19 Oct 2011 04:00:00 +0100 5378148 http://www.medworm.com/index.php?rid=5378145&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004742%26dopt%3DAbstract Authors: Sasseville LJ, Cuervo JE, Lapointe JY, Noskov SY Abstract Although water permeation across cell membranes occurs through several types of membrane proteins, the only permeation mechanism resolved at atomic scale is that through aquaporins. Crystallization of the Vibrio parahaemolyticus sodium-galactose transporter (vSGLT) allows investigation of putative water permeation pathways through both vSGLT and the homologous human Na-glucose cotransporter (hSGLT1) using computational methods. Grand canonical Monte Carlo and molecular dynamics simulations were used to stably insert water molecules in both proteins, showing the presence of a water-filled pathway composed of ∼100 water molecules. This provides a structural basis for passive water permeation that is difficult to r... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378145 Wed, 19 Oct 2011 04:00:00 +0100 5378145 http://www.medworm.com/index.php?rid=5378140&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004743%26dopt%3DAbstract Authors: Fibich A, Apell HJ Abstract An open membrane preparation containing SR Ca-ATPase was prepared from sarcoplasmic-reticulum vesicles to study the ion binding kinetics in the P-E(2) conformation. Because Ca(2+) and H(+) binding are electrogenic reactions, fluorescent styryl dyes could be used to determine changes in the binding site occupation in equilibrium titration experiments and time-resolved relaxation processes triggered by a pH jump. By photo release from caged proton the pH of the electrolyte could be decreased in a step of 0.1 pH units by a single ultraviolet-laser flash. Analysis of the pH-jump induced relaxation process in the P-E(2) conformation showed that three Ca-ATPase-specific processes could be identified, fast H(+) binding (τ < 100 μs) and pH-insen... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378140 Wed, 19 Oct 2011 04:00:00 +0100 5378140 http://www.medworm.com/index.php?rid=5378136&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004744%26dopt%3DAbstract Authors: Willenbring D, Liu LT, Mowrey D, Xu Y, Tang P Abstract Pentameric ligand-gated ion channels are targets of general anesthetics. Although the search for discrete anesthetic binding sites has achieved some degree of success, little is known regarding how anesthetics work after the events of binding. Using the crystal structures of the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC), which is sensitive to a variety of general anesthetics, we performed multiple molecular dynamics simulations in the presence and absence of the general anesthetic isoflurane. Isoflurane bound to several locations within GLIC, including the transmembrane pocket identified crystallographically, the extracellular (EC) domain, and the interface of the EC and transmembrane d... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378136 Wed, 19 Oct 2011 04:00:00 +0100 5378136 http://www.medworm.com/index.php?rid=5378132&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004745%26dopt%3DAbstract Authors: Ursell T, Agrawal A, Phillips R Abstract Electrophysiology is a central tool for measuring how different driving forces (e.g., ligand concentration, transmembrane voltage, or lateral tension) cause a channel protein to gate. Upon formation of the high resistance seal between a lipid bilayer and a glass pipette, the so-called "giga-seal", channel activity can be recorded electrically. In this article, we explore the implications of giga-seal formation on the mechanical state of a lipid bilayer patch. We use a mechanical model for the free energy of bilayer geometry in the presence of glass-bilayer adhesion to draw three potentially important conclusions. First, we use our adhesion model to derive an explicit relationship between applied pressure and patch shape that is co... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378132 Wed, 19 Oct 2011 04:00:00 +0100 5378132 http://www.medworm.com/index.php?rid=5378130&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004746%26dopt%3DAbstract Authors: Hale JP, Winlove CP, Petrov PG Abstract We investigate the effect of oxidative stress on red blood cell membrane mechanical properties in vitro using detailed analysis of the membrane thermal fluctuation spectrum. Two different oxidants, the cytosol-soluble hydrogen peroxide and the membrane-soluble cumene hydroperoxide, are used, and their effects on the membrane bending elastic modulus, surface tension, strength of confinement due to the membrane skeleton, and 2D shear elastic modulus are measured. We find that both oxidants alter significantly the membrane elastic properties, but their effects differ qualitatively and quantitatively. While hydrogen peroxide mainly affects the elasticity of the membrane protein skeleton (increasing the membrane shear modulus), cumene hy... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378130 Wed, 19 Oct 2011 04:00:00 +0100 5378130 http://www.medworm.com/index.php?rid=5378129&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004747%26dopt%3DAbstract Authors: Almeida PF, Best A, Hinderliter A Abstract Lipid domain formation induced by annexin was investigated in mixtures of phosphatidylcholine (PC), phosphatidylserine (PS), and cholesterol (Chol), which were selected to mimic the inner leaflet of a eukaryotic plasma membrane. Annexins are ubiquitous and abundant cytoplasmic, peripheral proteins, which bind to membranes containing PS in the presence of calcium ions (Ca(2+)), but whose function is unknown. Prompted by indications of interplay between the presence of cholesterol in PS/PC mixtures and the binding of annexins, we used Monte Carlo simulations to investigate protein and lipid domain formation in these mixtures. The set of interaction parameters between lipids and proteins was assigned by matching experimental observab... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378129 Wed, 19 Oct 2011 04:00:00 +0100 5378129 http://www.medworm.com/index.php?rid=5378128&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004748%26dopt%3DAbstract This study should serve as a general guide for selecting the appropriate mixed surfactant systems to stabilize membrane proteins for biophysical analysis. PMID: 22004748 [PubMed - in process] (Source: Biophysical Journal) Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378128 Wed, 19 Oct 2011 04:00:00 +0100 5378128 http://www.medworm.com/index.php?rid=5378127&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004749%26dopt%3DAbstract Authors: Prakash A, Janosi L, Doxastakis M Abstract GxxxG motifs are common in transmembrane domains of membrane proteins and are often introduced to artificial peptides to inhibit or promote association to stable structures. The transmembrane domain of ErbB2 presents two separate such motifs that are proposed to be connected to stability and activity of the dimer. Using molecular simulations, we show that these sequences play a critical role during the recognition stage, forming transient complexes that lead to stable dimers. In pure phospholipid bilayers association occurs by contacts formed at the C-terminus promoted by the presence of phenylalanine residues. Helices subsequently rotate to eventually pack at short separations favored by lipid entropic contributions. In contrast... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378127 Wed, 19 Oct 2011 04:00:00 +0100 5378127 http://www.medworm.com/index.php?rid=5378126&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004750%26dopt%3DAbstract Authors: Nyholm TK, van Duyl B, Rijkers DT, Liskamp RM, Killian JA Abstract The aim of this study was to gain insight into how interactions between proteins and lipids in membranes are sensed at the protein-lipid interface. As a probe to analyze this interface, we used deuterium-labeled acyl chains that were covalently linked to a model transmembrane peptide. First, a perdeuterated palmitoyl chain was coupled to the Trp-flanked peptide WALP23 (Ac-CGWW(LA)(8)LWWA-NH(2)), and the deuterium NMR spectrum was analyzed in di-C18:1-phosphatidylcholine (PC) bilayers. We found that the chain order of this peptide-linked chain is rather similar to that of a noncovalently coupled perdeuterated palmitoyl chain, except that it exhibits a slightly lower order. Similar results were obtained when ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378126 Wed, 19 Oct 2011 04:00:00 +0100 5378126 http://www.medworm.com/index.php?rid=5378125&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004751%26dopt%3DAbstract Authors: Karsai A, Kellermayer MS, Harris SP Abstract Cardiac myosin-binding protein-C (cMyBP-C) is a thick-filament-associated protein that performs regulatory and structural roles within cardiac sarcomeres. It is a member of the immunoglobulin (Ig) superfamily of proteins consisting of eight Ig- and three fibronectin (FNIII)-like domains, along with a unique regulatory sequence referred to as the M-domain, whose structure is unknown. Domains near the C-terminus of cMyBP-C bind tightly to myosin and mediate the association of cMyBP-C with thick (myosin-containing) filaments, whereas N-terminal domains, including the regulatory M-domain, bind reversibly to myosin S2 and/or actin. The ability of MyBP-C to bind to both myosin and actin raises the possibility that cMyBP-C cross-links ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378125 Wed, 19 Oct 2011 04:00:00 +0100 5378125 http://www.medworm.com/index.php?rid=5378124&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004752%26dopt%3DAbstract Authors: Stahl SW, Puchner EM, Alexandrovich A, Gautel M, Gaub HE Abstract As more and more recent investigations point out, force plays an important role in cellular regulation mechanisms. Biological responses to mechanical stress are often based on force-induced conformational changes of single molecules. The force sensor, titin kinase, is involved in a signaling complex that regulates protein turnover and transcriptional adaptation in striated muscle. The structural architecture of such a force sensor determines its response to force and must assure both activity and mechanical integrity, which are prerequisites for its function. Here, we use single-molecule force-clamp spectroscopy to show that titin kinase is organized in such a way that the regulatory domains have to unfold b... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378124 Wed, 19 Oct 2011 04:00:00 +0100 5378124 http://www.medworm.com/index.php?rid=5378123&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004753%26dopt%3DAbstract Authors: Lech CJ, Cheow Lim JK, Wen Lim JM, Amrane S, Heddi B, Phan AT Abstract Understanding the fundamentals of G-quadruplex formation is important both for targeting G-quadruplexes formed by natural sequences and for engineering new G-quadruplexes with desired properties. Using a combination of experimental and computational techniques, we have investigated the effects of site-specific substitution of a guanine with C8-modified guanine derivatives, including 8-bromo-guanine, 8-O-methyl-guanine, 8-amino-guanine, and 8-oxo-guanine, within a well-defined (3 + 1) human telomeric G-quadruplex platform. The effects of substitutions on the stability of the G-quadruplex were found to depend on the type and position of the modification among different guanines in the structure. An inter... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378123 Wed, 19 Oct 2011 04:00:00 +0100 5378123 http://www.medworm.com/index.php?rid=5378122&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004754%26dopt%3DAbstract Authors: Ettig R, Kepper N, Stehr R, Wedemann G, Rippe K Abstract The nucleosome complex of DNA wrapped around a histone protein octamer organizes the genome of eukaryotes and regulates the access of protein factors to the DNA. We performed molecular dynamics simulations of the nucleosome in explicit water to study the dynamics of its histone-DNA interactions. A high-resolution histone-DNA interaction map was derived that revealed a five-nucleotide periodicity, in which the two DNA strands of the double helix made alternating contacts. On the 100-ns timescale, the histone tails mostly maintained their initial positions relative to the DNA, and the spontaneous unwrapping of DNA was limited to 1-2 basepairs. In steered molecular dynamics simulations, external forces were applied to t... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378122 Wed, 19 Oct 2011 04:00:00 +0100 5378122 http://www.medworm.com/index.php?rid=5378121&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004755%26dopt%3DAbstract Authors: Cao Y, Li H Abstract Many proteins in living cells require cofactors to carry out their biological functions. To reach their functional states, these proteins need to fold into their unique three-dimensional structures in the presence of their cofactors. Two processes, folding of the protein and binding of cofactors, intermingle with each other, making the direct elucidation of the folding mechanism of proteins in the presence of cofactors challenging. Here we use single-molecule atomic force microscopy to directly monitor the folding and cofactor binding dynamics of an engineered metal-binding protein G6-53 at the single-molecule level. Using the mechanical stability of different conformers of G6-53 as sensitive probes, we directly identified different G6-53 conformers (u... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378121 Wed, 19 Oct 2011 04:00:00 +0100 5378121 http://www.medworm.com/index.php?rid=5378120&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004756%26dopt%3DAbstract Authors: Saito K, Ishikita H Abstract The primary electron donor P700 in photosystem I is composed of two chlorophylls, P(A) and P(B). P700 forms the cationic [P(A)/P(B)](•+) state as a result of light-induced electron transfer. We obtained a P(A)(•+)/P(B)(•+) ratio of 28:72 and a spin distribution of 22:78 for the entire PSI protein-pigment complex. By considering the influence of the protein components on the redox potential for one-electron oxidation of P(A)/P(B) monomers, we found that the following three factors significantly contributed to a large P(B)(•+) population relative to P(A)(•+): 1), Thr-A743 forming a H-bond with P(A); 2), P(A) as a chlorophyll a epimer; and 3), a conserved PsaA/PsaB pair, the Arg-A750/Ser-B734 residue. In addition, 4), the methyl-ester gr... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378120 Wed, 19 Oct 2011 04:00:00 +0100 5378120 http://www.medworm.com/index.php?rid=5378119&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004757%26dopt%3DAbstract Authors: Pereverzev YV, Prezhdo E, Sokurenko EV Abstract Catch-binding is a counterintuitive phenomenon in which the lifetime of a receptor/ligand bond increases when a force is applied to break the bond. Several mechanisms have been proposed to rationalize catch-binding. In the two-pathway model, the force drives the system away from its native dissociation pathway into an alternative pathway involving a higher energy barrier. Here, we analyze an allosteric model suggesting that a force applied to the complex alters the distribution of receptor conformations, and as a result, induces changes in the ligand-binding site. The model assumes explicitly that the allosteric transitions govern the properties of the ligand site. We demonstrate that the dynamics of the ligand is described b... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378119 Wed, 19 Oct 2011 04:00:00 +0100 5378119 http://www.medworm.com/index.php?rid=5378118&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004758%26dopt%3DAbstract This study underscores the usefulness of deuteration-assisted SANS, which can provide quantitative information not only on the molecular sizes and shapes of homooligomeric proteins, but also on their kinetic properties. PMID: 22004758 [PubMed - in process] (Source: Biophysical Journal) Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378118 Wed, 19 Oct 2011 04:00:00 +0100 5378118 http://www.medworm.com/index.php?rid=5378117&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004759%26dopt%3DAbstract Authors: Zhou H, Skolnick J Abstract An accurate scoring function is a key component for successful protein structure prediction. To address this important unsolved problem, we develop a generalized orientation and distance-dependent all-atom statistical potential. The new statistical potential, generalized orientation-dependent all-atom potential (GOAP), depends on the relative orientation of the planes associated with each heavy atom in interacting pairs. GOAP is a generalization of previous orientation-dependent potentials that consider only representative atoms or blocks of side-chain or polar atoms. GOAP is decomposed into distance- and angle-dependent contributions. The DFIRE distance-scaled finite ideal gas reference state is employed for the distance-dependent component of ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378117 Wed, 19 Oct 2011 04:00:00 +0100 5378117 http://www.medworm.com/index.php?rid=5378116&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004760%26dopt%3DAbstract Authors: Morrone A, Giri R, Toofanny RD, Travaglini-Allocatelli C, Brunori M, Daggett V, Gianni S Abstract The folding pathway of the small α/β protein GB1 has been extensively studied during the past two decades using both theoretical and experimental approaches. These studies provided a consensus view that the protein folds in a two-state manner. Here, we reassessed the folding of GB1, both by experiments and simulations, and detected the presence of an on-pathway intermediate. This intermediate has eluded earlier experimental characterization and is distinct from the collapsed state previously identified using ultrarapid mixing. Failure to identify the presence of an intermediate affects some of the conclusions that have been drawn for GB1, a popular model for protein folding ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378116 Wed, 19 Oct 2011 04:00:00 +0100 5378116 http://www.medworm.com/index.php?rid=5378115&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004761%26dopt%3DAbstract Authors: Virtanen JJ, Makowski L, Sosnick TR, Freed KF Abstract Small-/wide-angle x-ray scattering (SWAXS) experiments can aid in determining the structures of proteins and protein complexes, but success requires accurate computational treatment of solvation. We compare two methods by which to calculate SWAXS patterns. The first approach uses all-atom explicit-solvent molecular dynamics (MD) simulations. The second, far less computationally expensive method involves prediction of the hydration density around a protein using our new HyPred solvation model, which is applied without the need for additional MD simulations. The SWAXS patterns obtained from the HyPred model compare well to both experimental data and the patterns predicted by the MD simulations. Both approaches exhibit ad... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378115 Wed, 19 Oct 2011 04:00:00 +0100 5378115 http://www.medworm.com/index.php?rid=5378114&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004762%26dopt%3DAbstract Authors: Rawle RJ, van Lengerich B, Chung M, Bendix PM, Boxer SG Abstract Synaptic transmission is achieved by exocytosis of small, synaptic vesicles containing neurotransmitters across the plasma membrane. Here, we use a DNA-tethered freestanding bilayer as a target architecture that allows observation of content transfer of individual vesicles across the tethered planar bilayer. Tethering and fusion are mediated by hybridization of complementary DNA-lipid conjugates inserted into the two membranes, and content transfer is monitored by the dequenching of an aqueous content dye. By analyzing the diffusion profile of the aqueous dye after vesicle fusion, we are able to distinguish content transfer across the tethered bilayer patch from vesicle leakage above the patch. PMID: 2200... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5378114 Wed, 19 Oct 2011 04:00:00 +0100 5378114 http://www.medworm.com/index.php?rid=5294860&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961581%26dopt%3DAbstract Authors: Nicol-Benoit F, Amon A, Vaillant C, le Goff P, le Dréan Y, Pakdel F, Flouriot G, Valotaire Y, Michel D Abstract Transcriptional memory of transient signals can be imprinted on living systems and influence their reactivity to repeated stimulations. Although they are classically ascribed to structural chromatin rearrangements in eukaryotes, such behaviors can also rely on dynamic memory circuits with sustained self-amplification loops. However, these phenomena are either of finite duration, or conversely associated to sustained phenotypic changes. A mechanism is proposed, in which only the responsiveness of the target gene is durably reset at a higher level after primary stimulation, using the celebrated but still puzzling vitellogenesis memory effect. The basic ingredient... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294860 Wed, 05 Oct 2011 04:00:00 +0100 5294860 http://www.medworm.com/index.php?rid=5294858&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961582%26dopt%3DAbstract Authors: Geisel N, Gerland U Abstract Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. Although studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the quantitative characteristics of protein-DNA interactions, no such principles are known for the cooperative interactions between DNA-binding proteins. We consider a simple theoretical model for two interacting transcription factor (TF) species, searching for and binding to two adjacent target sites hidden in the genomic background. We study the kinetic competition of a dimer search pathway and a monomer search pathway, as well as the steady-state regulation function mediated by the two TFs over a broad range of TF-T... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294858 Wed, 05 Oct 2011 04:00:00 +0100 5294858 http://www.medworm.com/index.php?rid=5294856&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961583%26dopt%3DAbstract We report acidification time constants of 500 ms to 1 s. The rate of acidification increased with increasing extravesicular concentrations of ATP and glutamate. These data provide an upper and a lower bound for vesicle acidification and indicate that vesicle readiness can be regulated by changes in energy and transmitter availability. PMID: 21961583 [PubMed - in process] (Source: Biophysical Journal) Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294856 Wed, 05 Oct 2011 04:00:00 +0100 5294856 http://www.medworm.com/index.php?rid=5294854&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961584%26dopt%3DAbstract We present a general model of reversible protein modification networks and demonstrate that a single protein modified by several enzymes is capable of integrating multiple signals into robust digital decisions by switching between multiple forms that can activate distinct cellular processes. First we consider two competing protein modification cycles and show that in the saturated regime, the protein is concentrated into a single form determined by the enzyme activities. We generalize this to protein modification networks with tree structure controlled by multiple enzymes that can be characterized by their phase diagram, which is a partition of the space of enzyme activities into regions corresponding to different dominant forms. We show that the phase diagram can be obtained analytically ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294854 Wed, 05 Oct 2011 04:00:00 +0100 5294854 http://www.medworm.com/index.php?rid=5294851&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961585%26dopt%3DAbstract Authors: Kim T, Hwang W, Kamm RD Abstract We develop a computational model to compare the relative importance of unbinding and unfolding of actin cross-linking proteins (ACPs) in the dynamic properties of the actin cytoskeleton. We show that in the strain-stiffening regime with typical physiological and experimental strain rates, unbinding events are predominant with negligible unfolding. ACPs unbound by greater forces experience larger displacements, with a tendency to rebind to different filaments. At constant strain, stress relaxes to physiological levels by unbinding only-not unfolding-of ACPs, which is consistent with experiments. Also, rebinding of ACPs dampens full relaxation of stress. When the network is allowed to return to a stress-free state after shear deformation, pla... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294851 Wed, 05 Oct 2011 04:00:00 +0100 5294851 http://www.medworm.com/index.php?rid=5294848&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961586%26dopt%3DAbstract Authors: Basu H, Dharmadhikari AK, Dharmadhikari JA, Sharma S, Mathur D Abstract Tank-treading (TT) motion is established in optically trapped, live red blood cells (RBCs) held in shear flow and is systematically investigated under varying shear rates, temperature (affecting membrane viscosity), osmolarity (resulting in changes in RBC shape and cytoplasmic viscosity), and viscosity of the suspending medium. TT frequency is measured as a function of membrane and cytoplasmic viscosity, the former being four times more effective in altering TT frequency. TT frequency increases as membrane viscosity decreases, by as much as 10% over temperature changes of only 4°C at a shear rate of ∼43 s(-1). A threshold shear rate (1.5 ± 0.3 s(-1)) is observed below which the TT frequency drops ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294848 Wed, 05 Oct 2011 04:00:00 +0100 5294848 http://www.medworm.com/index.php?rid=5294833&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961587%26dopt%3DAbstract Authors: Barber AF, Liang Q, Amaral C, Treptow W, Covarrubias M Abstract Several voltage-gated ion channels are modulated by clinically relevant doses of general anesthetics. However, the structural basis of this modulation is not well understood. Previous work suggested that n-alcohols and inhaled anesthetics stabilize the closed state of the Shaw2 voltage-gated (Kv) channel (K-Shaw2) by directly interacting with a discrete channel site. We hypothesize that the inhibition of K-Shaw2 channels by general anesthetics is governed by interactions between binding and effector sites involving components of the channel's activation gate. To investigate this hypothesis, we applied Ala/Val scanning mutagenesis to the S4-S5 linker and the post-PVP S6 segment, and conducted electrophysiologic... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294833 Wed, 05 Oct 2011 04:00:00 +0100 5294833 http://www.medworm.com/index.php?rid=5294811&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961588%26dopt%3DAbstract Authors: Furini S, Domene C Abstract The NaK channel is a cation selective channel with similar permeability for K(+) and Na(+). The available crystallographic structure of wild-type (WT) NaK is usually associated with a conductive state of the channel. Here, potential of mean force for complete conduction events of Na(+) and K(+) ions through NaK show that: i), large energy barriers prevent the passage of ions through the WT NaK structure, ii), the barriers are correlated to the presence of a hydrogen bond between Asp-66 and Asn-68, and iii), the structure of NaK mutated to mimic cyclic nucleotide-gated channels conducts Na(+) and K(+). These results support the hypothesis that the filter of cation selective channels can adopt at least two different structures: a conductive one, r... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294811 Wed, 05 Oct 2011 04:00:00 +0100 5294811 http://www.medworm.com/index.php?rid=5294810&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961589%26dopt%3DAbstract Authors: Castro BM, de Almeida RF, Goormaghtigh E, Fedorov A, Prieto M Abstract To comprehend the molecular processes that lead to the Fas death receptor clustering in lipid rafts, a 21-mer peptide corresponding to its single transmembrane domain (TMD) was reconstituted into mammalian raft model membranes composed of an unsaturated glycerophospholipid, sphingomyelin, and cholesterol. The peptide membrane lateral organization and dynamics, and its influence on membrane properties, were studied by steady-state and time-resolved fluorescence techniques and by attenuated total reflection Fourier transformed infrared spectroscopy. Our results show that Fas TMD is preferentially localized in liquid-disordered membrane regions and undergoes a strong reorganization as the membrane composit... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294810 Wed, 05 Oct 2011 04:00:00 +0100 5294810 http://www.medworm.com/index.php?rid=5294809&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961590%26dopt%3DAbstract Authors: Siegel AP, Kimble-Hill A, Garg S, Jordan R, Naumann CA Abstract Distinct lipid environments, including lipid rafts, are increasingly recognized as a crucial factor affecting membrane protein function in plasma membranes. Unfortunately, an understanding of their role in membrane protein activation and oligomerization has remained elusive due to the challenge of characterizing these often small and transient plasma membrane heterogeneities in live cells. To address this difficulty, we present an experimental model membrane platform based on polymer-supported lipid bilayers containing stable raft-mimicking domains (type I) and homogeneous cholesterol-lipid mixtures (type II) into which transmembrane proteins are incorporated (α(v)β(3) and α(5)β(1) integrins). These flexib... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294809 Wed, 05 Oct 2011 04:00:00 +0100 5294809 http://www.medworm.com/index.php?rid=5294808&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961591%26dopt%3DAbstract Authors: Mueller V, Ringemann C, Honigmann A, Schwarzmann G, Medda R, Leutenegger M, Polyakova S, Belov VN, Hell SW, Eggeling C Abstract Details about molecular membrane dynamics in living cells, such as lipid-protein interactions, are often hidden from the observer because of the limited spatial resolution of conventional far-field optical microscopy. The superior spatial resolution of stimulated emission depletion (STED) nanoscopy can provide new insights into this process. The application of fluorescence correlation spectroscopy (FCS) in focal spots continuously tuned down to 30 nm in diameter distinguishes between free and anomalous molecular diffusion due to, for example, transient binding of lipids to other membrane constituents, such as lipids and proteins. We compared STED... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294808 Wed, 05 Oct 2011 04:00:00 +0100 5294808 http://www.medworm.com/index.php?rid=5294807&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961592%26dopt%3DAbstract Authors: Palmer BM, Sadayappan S, Wang Y, Weith AE, Previs MJ, Bekyarova T, Irving TC, Robbins J, Maughan DW Abstract We investigated the influence of cardiac myosin binding protein-C (cMyBP-C) and its constitutively unphosphorylated status on the radial and longitudinal stiffnesses of the myofilament lattice in chemically skinned myocardial strips of the following mouse models: nontransgenic (NTG), effective null for cMyBP-C (t/t), wild-type cMyBP-C expressed into t/t (WT(t/t)), and constitutively unphosphorylated cMyBP-C (AllP-(t/t)). We found that the absence of cMyBP-C in the t/t and the unphosphorylated cMyBP-C in the AllP-(t/t) resulted in a compressible cardiac myofilament lattice induced by rigor not observed in the NTG and WT(t/t). These results suggest that the presence a... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294807 Wed, 05 Oct 2011 04:00:00 +0100 5294807 http://www.medworm.com/index.php?rid=5294806&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961593%26dopt%3DAbstract Authors: Collepardo-Guevara R, Schlick T Abstract Eukaryotic gene activation requires selective unfolding of the chromatin fiber to access the DNA for processes such as DNA transcription, replication, and repair. Mutation/modification experiments of linker histone (LH) H1 suggest the importance of dynamic mechanisms for LH binding/dissociation, but the effects on chromatin's unfolding pathway remain unclear. Here we investigate the stretching response of chromatin fibers by mesoscale modeling to complement single-molecule experiments, and present various unfolding mechanisms for fibers with different nucleosome repeat lengths (NRLs) with/without LH that are fixed to their cores or bind/unbind dynamically with different affinities. Fiber softening occurs for long compared to short N... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294806 Wed, 05 Oct 2011 04:00:00 +0100 5294806 http://www.medworm.com/index.php?rid=5294805&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961594%26dopt%3DAbstract Authors: Shammas SL, Waudby CA, Wang S, Buell AK, Knowles TP, Ecroyd H, Welland ME, Carver JA, Dobson CM, Meehan S Abstract The molecular chaperone αB-crystallin is a small heat-shock protein that is upregulated in response to a multitude of stress stimuli, and is found colocalized with Aβ amyloid fibrils in the extracellular plaques that are characteristic of Alzheimer's disease. We investigated whether this archetypical small heat-shock protein has the ability to interact with Aβ fibrils in vitro. We find that αB-crystallin binds to wild-type Aβ(42) fibrils with micromolar affinity, and also binds to fibrils formed from the E22G Arctic mutation of Aβ(42). Immunoelectron microscopy confirms that binding occurs along the entire length and ends of the fibrils. Investigations ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294805 Wed, 05 Oct 2011 04:00:00 +0100 5294805 http://www.medworm.com/index.php?rid=5294804&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961595%26dopt%3DAbstract Authors: Fahmy A, Wagner G Abstract Computational determination of optimal side-chain conformations in protein structures has been a long-standing and challenging problem. Solving this problem is important for many applications including homology modeling, protein docking, and for placing small molecule ligands on protein-binding sites. Programs available as of this writing are very fast and reasonably accurate, as measured by deviations of side-chain dihedral angles; however, often due to multiple atomic clashes, they produce structures with high positive energies. This is problematic in applications where the energy values are important, for example when placing small molecules in docking applications; the relatively small binding energy of the small molecule is drowned by the la... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294804 Wed, 05 Oct 2011 04:00:00 +0100 5294804 http://www.medworm.com/index.php?rid=5294803&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961596%26dopt%3DAbstract Authors: Dee DR, Myers B, Yada RY Abstract The pepsin folding mechanism involves a prosegment (PS) domain that catalyzes folding, which is then removed, resulting in a kinetically trapped native state. Although native pepsin (Np) is kinetically stable, it is irreversibly denatured due to a large folding barrier, and in the absence of the PS it folds to a more thermodynamically stable denatured state, termed refolded pepsin (Rp). This system serves as a model to understand the nature of kinetic barriers and folding transitions between compact states. Quasielastic neutron scattering (QENS) was used to characterize and compare the flexibility of Np, as a kinetically trapped state, with that of Rp, as a thermodynamically stable fold. Additionally, the dynamics of Np were compared with ... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294803 Wed, 05 Oct 2011 04:00:00 +0100 5294803 http://www.medworm.com/index.php?rid=5294802&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961597%26dopt%3DAbstract Authors: Milles S, Lemke EA Abstract Nucleoporins (Nups), which are intrinsically disordered, form a selectivity filter inside the nuclear pore complex, taking a central role in the vital nucleocytoplasmic transport mechanism. These Nups display a complex and nonrandom amino-acid architecture of phenylalanine glycine (FG)-repeat clusters and intra-FG linkers. How such heterogeneous sequence composition relates to function and could give rise to a transport mechanism is still unclear. Here we describe a combined chemical biology and single-molecule fluorescence approach to study the large human Nup153 FG-domain. In order to obtain insights into the properties of this domain beyond the average behavior, we probed the end-to-end distance (R(E)) of several ∼50-residues long FG-repeat... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294802 Wed, 05 Oct 2011 04:00:00 +0100 5294802 http://www.medworm.com/index.php?rid=5294801&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961598%26dopt%3DAbstract Authors: Jain N, Bhattacharya M, Mukhopadhyay S Abstract Natively unfolded or intrinsically disordered proteins (IDPs) are under intense scrutiny due to their involvement in both normal biological functions and abnormal protein misfolding disorders. Polypeptide chain collapse of amyloidogenic IDPs is believed to play a key role in protein misfolding, oligomerization, and aggregation leading to amyloid fibril formation, which is implicated in a number of human diseases. In this work, we used bovine κ-casein, which serves as an archetypal model protein for amyloidogenic IDPs. Using a variety of biophysical tools involving both prediction and spectroscopic techniques, we first established that monomeric κ-casein adopts a collapsed premolten-globule-like conformational ensemble under... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294801 Wed, 05 Oct 2011 04:00:00 +0100 5294801 http://www.medworm.com/index.php?rid=5294800&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961599%26dopt%3DAbstract Authors: Pieniazek SN, Hingorani MM, Beveridge DL Abstract The multidomain protein Thermus aquaticus MutS and its prokaryotic and eukaryotic homologs recognize DNA replication errors and initiate mismatch repair. MutS actions are fueled by ATP binding and hydrolysis, which modulate its interactions with DNA and other proteins in the mismatch-repair pathway. The DNA binding and ATPase activities are allosterically coupled over a distance of ∼70 Å, and the molecular mechanism of coupling has not been clarified. To address this problem, all-atom molecular dynamics simulations of ∼150 ns including explicit solvent were performed on two key complexes-ATP-bound and ATP-free MutS⋅DNA(+T bulge). We used principal component analysis in fluctuation space to assess ATP ligand-induced... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294800 Wed, 05 Oct 2011 04:00:00 +0100 5294800 http://www.medworm.com/index.php?rid=5294799&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961600%26dopt%3DAbstract Authors: Bradshaw MJ, Smith ML Abstract The extracellular matrix contains components with remarkable mechanical properties, including fibronectin (Fn) fibers with extensibilities of >700% strain. We utilized what we consider a novel technique to quantify the extent of molecular unfolding that contributes to Fn fiber extension, and we compared this behavior with stochastic models of Fn fibers with different molecular arrangements. In vitro unfolding as a function of strain was measured by fluorescently labeling cysteines in modules FnIII7 and III15 in artificial Fn fibers. A calibration technique we also consider novel made it possible to demonstrate that 44% of cysteines in these modules were exposed in Fn fibers strained to 421% extension, up from 8% exposure without strain. I... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294799 Wed, 05 Oct 2011 04:00:00 +0100 5294799 http://www.medworm.com/index.php?rid=5294798&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961601%26dopt%3DAbstract Authors: Sule SV, Sukumar M, Weiss WF, Marcelino-Cruz AM, Sample T, Tessier PM Abstract Monoclonal antibodies are typically monomeric and nonviscous at low concentrations, yet they display highly variable associative and viscous behavior at elevated concentrations. Although measurements of antibody self-association are critical for understanding this complex behavior, traditional biophysical methods are not capable of characterizing such concentration-dependent self-association in a high-throughput manner. Here we describe a nanoparticle-based method, termed self-interaction nanoparticle spectroscopy, that is capable of rapidly measuring concentration-dependent self-interactions for three human monoclonal antibodies with unique solution behaviors. We demonstrate that gold nanoparti... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294798 Wed, 05 Oct 2011 04:00:00 +0100 5294798 http://www.medworm.com/index.php?rid=5294797&cid=s_35858_75_f&fid=35858&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21961602%26dopt%3DAbstract Authors: Sarkar A, Zhou C, Meklemburg R, Wintrode PL Abstract Neuroserpin is a regulator of neuronal growth and plasticity. Like other members of the serpin family, neuroserpin undergoes a large conformational change as part of its function. Unlike other serpins such as α(1)-antitrypsin, wild-type neuroserpin will polymerize under near-physiological conditions, and will spontaneously transition to the latent state. To probe the origins of this conformational lability, we have performed hydrogen exchange measurements and molecular-dynamics simulations on human neuroserpin. Hydrogen exchange indicates that neuroserpin has greater flexibility in the breach region and in β-strand 1C compared with α(1)-antitrypsin. Molecular-dynamics simulations show that the distance between the top... Biophysical Journal journals http://www.medworm.com/rss/comments.php?id=5294797 Wed, 05 Oct 2011 04:00:00 +0100 5294797