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A mathematical model of actin filament turnover for fitting FRAP data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A novel mathematical model of the actin dynamics in living cells under steady-state conditions has been developed for fluorescence recovery after photobleaching (FRAP) experiments. As opposed to other FRAP fitting models, which use the average lifetime of actins in filaments and the actin turnover rate as fitting parameters, our model operates with unbiased actin association/dissociation rate constants and accounts for the filament length. The mathematical formalism is based on a system of stochastic differential equations. The derived equations were validated on synthetic theoretical data generated by a stochastic sim...
Source: European Biophysics Journal : EBJ - November 18, 2009 Category: Physics Authors: Halavatyi AA, Nazarov PV, Al Tanoury Z, Apanasovich VV, Yatskou M, Friederich E Tags: Eur Biophys J Source Type: journals

Expression and structural characterization of peripherin/RDS, a membrane protein implicated in photoreceptor outer segment morphology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Peripherin/RDS is a member of the tetraspanin family of integral membrane proteins and plays a major role in the morphology of photoreceptor outer segments. Peripherin/RDS has a long extracellular loop (hereafter referred to as the LEL domain), which is vital for its function. Point mutations in the LEL domain often lead to impaired photoreceptor formation and function, making peripherin/RDS an important drug target. Being a eukaryotic membrane protein, acquiring sufficient peripherin/RDS for biophysical characterisation represents a significant challenge. Here, we describe the expression and characterisation of periph...
Source: European Biophysics Journal : EBJ - November 18, 2009 Category: Physics Authors: Vos WL, Vaughan S, Lall PY, McCaffrey JG, Wysocka-Kapcinska M, Findlay JB Tags: Eur Biophys J Source Type: journals

Phase transition kinetics of lipid bilayer membranes studied by time-resolved pressure perturbation calorimetry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The relaxation kinetics of aqueous lipid dispersions after a pressure jump (p-jump) was investigated using time-resolved pressure perturbation calorimetry (PPC). Analysis of the calorimetric response curves by deconvolution with the instrumental response function gives information about slow processes connected with the lipid phase transition. The lipid transition from the gel to the liquid-crystalline state was found to be a multi-step process with relaxation constants in the seconds range resolvable by time-resolved PPC and faster processes with relaxation times shorter than ca. 5 s that could not be resolved by the ...
Source: European Biophysics Journal : EBJ - November 17, 2009 Category: Physics Authors: Schiewek M, Blume A Tags: Eur Biophys J Source Type: journals

Kinesin velocity increases with the number of motors pulling against viscoelastic drag.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Although the properties of single kinesin molecular motors are well understood, it is not clear whether multiple motors pulling a single vesicle in a cell cooperate or interfere with one another. To learn how small numbers of motors interact, microtubule gliding assays were carried out with full-length Drosophila kinesin in a novel motility medium containing xanthan, a stiff, water-soluble polysaccharide. At 2 mg/ml xanthan, the zero-shear viscosity of this medium is 1,000 times the viscosity of water, similar to cellular viscosity. To mimic the rheological drag force on the motors when attached to a vesicle in a cell,...
Source: European Biophysics Journal : EBJ - November 17, 2009 Category: Physics Authors: Gagliano J, Walb M, Blaker B, Macosko JC, Holzwarth G Tags: Eur Biophys J Source Type: journals

Quantitative permeability imaging of plant tissues.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A method for mapping tissue permeability based on time-dependent diffusion measurements is presented. A pulsed field gradient sequence to measure the diffusion encoding time dependence of the diffusion coefficients based on the detection of stimulated spin echoes to enable long diffusion times is combined with a turbo spin echo sequence for fast NMR imaging (MRI). A fitting function is suggested to describe the time dependence of the apparent diffusion constant in porous (bio-)materials, even if the time range of the apparent diffusion coefficient is limited due to relaxation of the magnetization. The method is demonst...
Source: European Biophysics Journal : EBJ - November 17, 2009 Category: Physics Authors: Sibgatullin TA, Vergeldt FJ, Gerkema E, Van As H Tags: Eur Biophys J Source Type: journals

Ceramide acyl chain length markedly influences miscibility with palmitoyl sphingomyelin in bilayer membranes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study we investigated the effect of acyl chain composition in ceramides (C4-C24:1) on their miscibility with N-palmitoyl-sphingomyelin (PSM) using differential scanning calorimetry. We found that short-chain (C4 and C8) ceramides induced phase separation and lowered the T (m) and enthalpy of the PSM endotherm. We conclude that short-chain ceramides were more miscible in the fluid-phase than in the gel-phase PSM bilayers. Long-chain ceramides induced apparent heterogeneity in the bilayers. The main PSM endotherm decreased in cooperativity and enthalpy with increasing ceramide concentration. New ceramide-enriched com...
Source: European Biophysics Journal : EBJ - November 12, 2009 Category: Physics Authors: Westerlund B, Grandell PM, Isaksson YJ, Slotte JP Tags: Eur Biophys J Source Type: journals

Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Transient structures in unfolded proteins are important in elucidating the molecular details of initiation of protein folding. Recently, native and non-native secondary structure have been discovered in unfolded A. vinelandii flavodoxin. These structured elements transiently interact and subsequently form the ordered core of an off-pathway folding intermediate, which is extensively formed during folding of this alpha-beta parallel protein. Here, site-directed spin-labelling and paramagnetic relaxation enhancement are used to investigate long-range interactions in unfolded apoflavodoxin. For this purpose, glutamine-48, ...
Source: European Biophysics Journal : EBJ - November 6, 2009 Category: Physics Authors: Nabuurs SM, de Kort BJ, Westphal AH, van Mierlo CP Tags: Eur Biophys J Source Type: journals

On a biophysical and mathematical model of Pgp-mediated multidrug resistance: understanding the "space-time" dimension of MDR.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Multidrug resistance (MDR) is explained by drug transporters with a drug-handling activity. Despite much work, MDR remains multifaceted, and several conditions are required to generate drug resistance. The drug pumping was conceptually described using a kinetic, i.e., temporal, approach. The re-emergence of physical biology has allowed us to take into account new parameters focusing on the notion of space. This, in turn, has given us important clues regarding the process whereby drug and transporter interact. We will demonstrate that the likelihood of drug-transporter meeting (i.e., the affinity) and thus interaction a...
Source: European Biophysics Journal : EBJ - November 4, 2009 Category: Physics Authors: Panagiotopoulou V, Richardson G, Jensen OE, Rauch C Tags: Eur Biophys J Source Type: journals

Rearrangement of erythrocyte band 3 molecules and reversible formation of osmotic holes under hypotonic conditions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The complex phenomenon of rearrangement of band 3 molecules after erythrocyte swelling under hypotonic condition is considered. The rearrangement includes the increase of the mobile fraction and clustering of band 3. The self-associative tendency and the action of the elastic field generated within the lipid membrane after erythrocyte swelling result in equilibration of the number of molecules per cluster and the number of clusters. The local perturbation of the elastic field induces excitation of the cluster in the nearest neighbor and changes its packing state generating changes in the free volume within the cluster....
Source: European Biophysics Journal : EBJ - November 3, 2009 Category: Physics Authors: Pajic-Lijakovic I, Ilic V, Bugarski B, Plavsic M Tags: Eur Biophys J Source Type: journals

Unfolding and refolding properties of S pili on extraintestinal pathogenic Escherichia coli.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
S pili are members of the chaperone-usher-pathway-assembled pili family that are predominantly associated with neonatal meningitis (S(II)) and believed to play a role in ascending urinary tract infections (S(I)). We used force-measuring optical tweezers to characterize the intrinsic biomechanical properties and kinetics of S(II) and S(I) pili. Under steady-state conditions, a sequential unfolding of the layers in the helix-like rod occurred at somewhat different forces, 26 pN for S(II) pili and 21 pN for S(I) pili, and there was an apparent difference in the kinetics, 1.3 and 8.8 Hz. Tests with bacteria defective in a ...
Source: European Biophysics Journal : EBJ - November 3, 2009 Category: Physics Authors: Castelain M, Sjöström AE, Fällman E, Uhlin BE, Andersson M Tags: Eur Biophys J Source Type: journals

Netropsin binding in five duplex-dimer DNA constructs as a function of size and distance between binding sites: circular dichroism and absorption spectroscopy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The optical activity induced on binding the drug netrospin (NET) in the minor groove of DNA is studied in five oligonucleotides (OGNs) as a function of (1) the size of the binding site in (5'-(GC)(2)AATT(GC)(2)-3')(2) (OGN 1a) versus (5'-(GC)(2)AAATTT(GC)(2)-3')(2) (OGN 1b) and (2) the distance between two AATT binding sites in (5'-(GC)(2)AATT(GC)( x )AATT(GC)(2)-3')(2), with x = 1, 2, or 3 (OGNs 2a, b, c, respectively). NET binding is monitored via the induced circular dichroism (CD) at ~315 nm, where the nucleic acids are optically inactive. The CD titrations, fit to a tight binding model, yield lower limits for the ...
Source: European Biophysics Journal : EBJ - October 28, 2009 Category: Physics Authors: Premvardhan L, Maurizot JC Tags: Eur Biophys J Source Type: journals

Structural and dynamic properties of juxta-membrane segments of caveolin-1 and caveolin-2 at the membrane interface.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Caveolins (cav1-3) are essential membrane proteins found in caveolae. The caveolin scaffolding domain of cav-1 includes a short sequence containing a CRAC motif (V94TKYWFYR101) at its C-terminal end. To investigate the role of this motif in the caveolin-membrane interaction at the atomic level, we performed a detailed structural and dynamics characterization of a cav-1(V94-L102) nonapeptide encompassing this motif and including the first residue of cav-1 hydrophobic domain (L102), in dodecylmaltoside (DM) or dodecylphosphocholine (DPC) micelles, as membrane mimics. Cav-1(V94-L102) partitioned better in DPC and in DM/an...
Source: European Biophysics Journal : EBJ - October 21, 2009 Category: Physics Authors: Le Lan C, Gallay J, Vincent M, Neumann JM, de Foresta B, Jamin N Tags: Eur Biophys J Source Type: journals

Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study clearly shows that SAXS profiles obtained from highly flexible proteins can be wrongly interpreted as arising from a rigid structure. In this context, it would be important to identify features from the SAXS data or from the derived structural models that indicate interdomain motions to differentiate between these two scenarios. Features of SAXS data that identify flexible proteins are: (1) general attenuation of fine structure in the scattering profiles, which becomes more dramatic in Kratky representations, and (2) a reduced number of interdomain correlation peaks in p(r) functions that also present large D (m...
Source: European Biophysics Journal : EBJ - October 20, 2009 Category: Physics Authors: Bernadó P Tags: Eur Biophys J Source Type: journals

Membrane microheterogeneity: Förster resonance energy transfer characterization of lateral membrane domains.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Membrane microheterogeneity: Förster resonance energy transfer characterization of lateral membrane domains. Eur Biophys J. 2009 Oct 21; Authors: Loura LM, Fernandes F, Prieto M Lateral membrane heterogeneity, in the form of lipid rafts and microdomains, is currently implicated in cell processes including signal transduction, endocytosis, and cholesterol trafficking. Various biophysical techniques have been used to detect and characterize lateral membrane domains. Among these, Förster resonance energy transfer (FRET) has the crucial advantage of being sensitive to domain sizes smaller than 50-100 nm, ...
Source: European Biophysics Journal : EBJ - October 20, 2009 Category: Physics Authors: Loura LM, Fernandes F, Prieto M Tags: Eur Biophys J Source Type: journals

Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Extradiol dioxygenases facilitate microbial aerobic degradation of catechol and its derivatives by activating molecular dioxygen and incorporating both oxygen atoms into their substrates. Experimental and theoretical studies have focused on the mechanism of the reaction at the active site. However, whether the catalytic rate is limited by O(2) access to the active site has not yet been explored. Here, we choose a recently solved X-ray structure of homoprotocatechuate 2,3-dioxygenase as a typical example to determine potential pathways for O(2) migration from the solvent into the enzyme center. On the basis of the traje...
Source: European Biophysics Journal : EBJ - October 13, 2009 Category: Physics Authors: Xu L, Zhao W, Wang X Tags: Eur Biophys J Source Type: journals

Crystal structures of all-alpha type membrane proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Integral membrane proteins are involved in a wide range of essential biological functions and the determination of their three-dimensional structures plays a central role in understanding their function. This review focuses on the structures of one class of integral membrane proteins: the functionally diverse all-alpha type membrane proteins. It gives an overview of all the structures determined by X-ray crystallography, describing each system and structure in turn. It shows that the structures of all-alpha type membrane proteins have made valuable contributions to understanding structure-function relationships in memb...
Source: European Biophysics Journal : EBJ - October 13, 2009 Category: Physics Authors: McLuskey K, Roszak AW, Zhu Y, Isaacs NW Tags: Eur Biophys J Source Type: journals

Membrane chemical stability and seed longevity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here, we investigate the relationships between the chemical stability of the membrane surface and seed longevity. Dry embryos of long-lived tomato and short-lived onion seeds were labeled with 5-doxyl-stearic acid (5-DS). Temperature-induced loss of the electron spin resonance signal caused by chemical conversion of 5-DS to nonparamagnetic species was used to characterize the membrane surface chemical stability. No difference was found between temperature plots of 5-DS signal intensity in dry onion and tomato below 345 K. Above this temperature, the 5-DS signal remained unchanged in tomato embryos and irreversibly disa...
Source: European Biophysics Journal : EBJ - October 12, 2009 Category: Physics Authors: Golovina EA, Van As H, Hoekstra FA Tags: Eur Biophys J Source Type: journals

Single-channel properties of a stretch-sensitive chloride channel in the human mast cell line HMC-1.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A stretch-activated (SA) Cl(-) channel in the plasma membrane of the human mast cell line HMC-1 was identified in outside-out patch-clamp experiments. SA currents, induced by pressure applied to the pipette, exhibited voltage dependence with strong outward rectification (55.1 pS at +100 mV and an about tenfold lower conductance at -100 mV). The probability of the SA channel being open (P (o)) also showed steep outward rectification and pressure dependence. The open-time distribution was fitted with three components with time constants of tau(1o) = 755.1 ms, tau(2o) = 166.4 ms, and tau(3o) = 16.5 ms at +60 mV. The close...
Source: European Biophysics Journal : EBJ - October 12, 2009 Category: Physics Authors: Wang L, Ding G, Gu Q, Schwarz W Tags: Eur Biophys J Source Type: journals

On computational approaches for size-and-shape distributions from sedimentation velocity analytical ultracentrifugation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sedimentation velocity analytical ultracentrifugation has become a very popular technique to study size distributions and interactions of macromolecules. Recently, a method termed two-dimensional spectrum analysis (2DSA) for the determination of size-and-shape distributions was described by Demeler and colleagues (Eur Biophys J 2009). It is based on novel ideas conceived for fitting the integral equations of the size-and-shape distribution to experimental data, illustrated with an example but provided without proof of the principle of the algorithm. In the present work, we examine the 2DSA algorithm by comparison with ...
Source: European Biophysics Journal : EBJ - October 5, 2009 Category: Physics Authors: Schuck P Tags: Eur Biophys J Source Type: journals

Hydrophobicity as a possible reason for gelation of FG-rich nucleoporins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this work we address the question of whether hydrophobic parts of FG-rich nucleoporins can be the reason for their ability to form a hydro-gel (Frey et al. in Science 314:3, 2006). We focus on the N-terminal fsFG domain of the essential yeast nucleoporin Nsp1p (Hurt in EMBO J 7:4323, 1988) as a nucleoporin model system and on the question of whether a phase transition between a sol and a gel phase exists. The N-terminal fsFG domain comprises 18 regular FSFG repeats and 16 less regular FG repeats. This domain is modeled, and a Metropolis Monte-Carlo algorithm is used to generate equilibrated ensembles of peptide netw...
Source: European Biophysics Journal : EBJ - September 30, 2009 Category: Physics Authors: Diesinger PM, Heermann DW Tags: Eur Biophys J Source Type: journals

Synchrotron X-ray imaging via ultra-small-angle scattering: principles of quantitative analysis and application in studying bone integration to synthetic grafting materials.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Optimized experimental conditions for extracting accurate information at subpixel length scales from analyzer-based X-ray imaging were obtained and applied to investigate bone regeneration by means of synthetic beta-TCP grafting materials in a rat calvaria model. The results showed a 30% growth in the particulate size due to bone ongrowth/ingrowth within the critical size defect over a 1-month healing period. PMID: 19784835 [PubMed - as supplied by publisher] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - September 26, 2009 Category: Physics Authors: Morelhão SL, Coelho PG, Hönnicke MG Tags: Eur Biophys J Source Type: journals

Proteins, membranes and cells: the structure-function nexus-ASB 2008.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19768456 [PubMed - as supplied by publisher] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - September 18, 2009 Category: Physics Authors: Vandenberg JI, Kuchel PW Tags: Eur Biophys J Source Type: journals

Minimal models of electric potential oscillations in non-excitable membranes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sustained oscillations in the membrane potential have been observed in a variety of cellular and subcellular systems, including several types of non-excitable cells and mitochondria. For the plasma membrane, these electrical oscillations have frequently been related to oscillations in intracellular calcium. For the inner mitochondrial membrane, in several cases the electrical oscillations have been attributed to modifications in calcium dynamics. As an alternative, some authors have suggested that the sustained oscillations in the mitochondrial membrane potential induced by some metabolic intermediates depends on the d...
Source: European Biophysics Journal : EBJ - September 17, 2009 Category: Physics Authors: Perdomo G, Hernández JA Tags: Eur Biophys J Source Type: journals

A nonlinear model of ionic wave propagation along microtubules.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19760184 [PubMed - as supplied by publisher] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - September 16, 2009 Category: Physics Authors: Satarić MV, Ilić DI, Ralević N, Tuszynski JA Tags: Eur Biophys J Source Type: journals

Profiling of dynamics in protein-lipid-water systems: a time-resolved fluorescence study of a model membrane protein with the label BADAN at specific membrane depths.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Profiles of lipid-water bilayer dynamics were determined from picosecond time-resolved fluorescence spectra of membrane-embedded BADAN-labeled M13 coat protein. For this purpose, the protein was labeled at seven key positions. This places the label at well-defined locations from the water phase to the center of the hydrophobic acyl chain region of a phospholipid model membrane, providing us with a nanoscale ruler to map membranes. Analysis of the time-resolved fluorescence spectroscopic data provides the characteristic time constant for the twisting motion of the BADAN label, which is sensitive to the local flexibility...
Source: European Biophysics Journal : EBJ - September 15, 2009 Category: Physics Authors: Koehorst RB, Laptenok S, van Oort B, van Hoek A, Spruijt RB, van Stokkum IH, van Amerongen H, Hemminga MA Tags: Eur Biophys J Source Type: journals

Guanidine hydrochloride and urea-induced unfolding of Brugia malayi hexokinase.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Guanidine hydrochloride and urea-induced unfolding of B. malayi hexokinase (BmHk), a tetrameric protein, was examined in detail by using various optical spectroscopic techniques, enzymatic activity measurements, and size-exclusion chromatography. The equilibrium unfolding of BmHk by guanidine hydrochloride (GdmCl) and urea proceeded through stabilization of several unique oligomeric intermediates. In the presence of low concentrations of GdmCl, stabilization of an enzymatically active folded dimer of BmHk was observed. However an enzymatically inactive dimer of BmHk was observed for urea-treated BmHk. This is the first...
Source: European Biophysics Journal : EBJ - September 14, 2009 Category: Physics Authors: Singh AR, Joshi S, Arya R, Kayastha AM, Saxena JK Tags: Eur Biophys J Source Type: journals

Quantification of protein-lipid selectivity using FRET.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Membrane proteins exhibit different affinities for different lipid species, and protein-lipid selectivity regulates the membrane composition in close proximity to the protein, playing an important role in the formation of nanoscale membrane heterogeneities. The sensitivity of Förster resonance energy transfer (FRET) for distances of 10 A up to 100 A is particularly useful to retrieve information on the relative distribution of proteins and lipids in the range over which protein-lipid selectivity is expected to influence membrane composition. Several FRET-based methods applied to the quantification of protein-lipid...
Source: European Biophysics Journal : EBJ - September 3, 2009 Category: Physics Authors: Loura LM, Prieto M, Fernandes F Tags: Eur Biophys J Source Type: journals

NMR studies of p7 protein from hepatitis C virus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The p7 protein of hepatitis C virus (HCV) plays an important role in the viral lifecycle. Like other members of the viroporin family of small membrane proteins, the amino acid sequence of p7 is largely conserved over the entire range of genotypes, and it forms ion channels that can be blocked by a number of established channel-blocking compounds. Its characteristics as a membrane protein make it difficult to study by most structural techniques, since it requires the presence of lipids to fold and function properly. Purified p7 can be incorporated into phospholipid bilayers and micelles. Initial solid-state nuclear magn...
Source: European Biophysics Journal : EBJ - September 1, 2009 Category: Physics Authors: Cook GA, Opella SJ Tags: Eur Biophys J Source Type: journals

Homology modelling and spectroscopy, a never-ending love story.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Homology modelling is normally the technique of choice when experimental structure data are not available but three-dimensional coordinates are needed, for example, to aid with detailed interpretation of results of spectroscopic studies. Herein, the state of the art of homology modelling will be described in the light of a series of recent developments, and an overview will be given of the problems and opportunities encountered in this field. The major topic, the accuracy and precision of homology models, will be discussed extensively due to its influence on the reliability of conclusions drawn from the combination of ...
Source: European Biophysics Journal : EBJ - August 28, 2009 Category: Physics Authors: Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G Tags: Eur Biophys J Source Type: journals

Time-resolved FRET fluorescence spectroscopy of visible fluorescent protein pairs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Förster resonance energy transfer (FRET) is a powerful method for obtaining information about small-scale lengths between biomacromolecules. Visible fluorescent proteins (VFPs) are widely used as spectrally different FRET pairs, where one VFP acts as a donor and another VFP as an acceptor. The VFPs are usually fused to the proteins of interest, and this fusion product is genetically encoded in cells. FRET between VFPs can be determined by analysis of either the fluorescence decay properties of the donor molecule or the rise time of acceptor fluorescence. Time-resolved fluorescence spectroscopy is the technique of ...
Source: European Biophysics Journal : EBJ - August 19, 2009 Category: Physics Authors: Visser AJ, Laptenok SP, Visser NV, van Hoek A, Birch DJ, Brochon JC, Borst JW Tags: Eur Biophys J Source Type: journals

Dehydration stability of amyloid fibrils studied by AFM.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Atomic force microscopy was used to investigate the stability of dehydrated amyloid fibrils formed by human islet polypeptide (IAPP) and Abeta(1-42) peptides. IAPP amyloid fibrils were imaged in liquid (hydrated state) and in air (dehydrated). In addition, fibrils dried on the mica surface were rehydrated and re-examined both in liquid and in air (after consecutive redrying). As reported previously, the initial drying process does not result in any major change in the amyloid appearance and the dimensions of the fibrils are preserved. However, when once-dried samples are rehydrated, fibril stability is lost. The fibril...
Source: European Biophysics Journal : EBJ - August 13, 2009 Category: Physics Authors: Maurstad G, Prass M, Serpell LC, Sikorski P Tags: Eur Biophys J Source Type: journals

Viruses: incredible nanomachines. New advances with filamentous phages.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproduction cycle. The results of the spectroscopic studies conducted in our group compellingly demonstrate a critical role of membrane ...
Source: European Biophysics Journal : EBJ - August 12, 2009 Category: Physics Authors: Hemminga MA, Vos WL, Nazarov PV, Koehorst RB, Wolfs CJ, Spruijt RB, Stopar D Tags: Eur Biophys J Source Type: journals

In vivo magnetic resonance spectroscopy: basic methodology and clinical applications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The clinical use of in vivo magnetic resonance spectroscopy (MRS) has been limited for a long time, mainly due to its low sensitivity. However, with the advent of clinical MR systems with higher magnetic field strengths such as 3 Tesla, the development of better coils, and the design of optimized radio-frequency pulses, sensitivity has been considerably improved. Therefore, in vivo MRS has become a technique that is routinely used more and more in the clinic. In this review, the basic methodology of in vivo MRS is described-mainly focused on (1)H MRS of the brain-with attention to hardware requirements, patient safety,...
Source: European Biophysics Journal : EBJ - August 12, 2009 Category: Physics Authors: van der Graaf M Tags: Eur Biophys J Source Type: journals

Viral membrane proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19672588 [PubMed - as supplied by publisher] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - August 11, 2009 Category: Physics Authors: Fischer WB, Thiel G, Fink RH Tags: Eur Biophys J Source Type: journals

Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Computer simulations were carried out of a number of AEDANS-labeled single cysteine mutants of a small reference membrane protein, M13 major coat protein, covering 60% of its primary sequence. M13 major coat protein is a single membrane-spanning, alpha-helical membrane protein with a relatively large water-exposed region in the N-terminus. In 10-ns molecular dynamics simulations, we analyze the behavior of the AEDANS label and the native tryptophan, which were used as acceptor and donor in previous FRET experiments. The results indicate that AEDANS is a relatively inert environmental probe that can move unhindered thro...
Source: European Biophysics Journal : EBJ - August 10, 2009 Category: Physics Authors: Vos WL, Schor M, Baumgaertner A, Tieleman DP, Hemminga MA Tags: Eur Biophys J Source Type: journals

Conformational studies of peptides representing a segment of TM7 from H(+)-V (O)-ATPase in SDS micelles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The conformation of a transmembrane peptide, sMTM7, encompassing the cytoplasmic hemi-channel domain of the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae solubilized in SDS solutions was studied by circular dichroism (CD) spectroscopy and fluorescence spectroscopy of the single tryptophan residue of this peptide. The results show that the peptide adopts an alpha-helical conformation or aggregated beta-sheet depending on the peptide-to-SDS ratio used. The results are compared with published data about a longer version of the peptide (i.e., MTM7). It is concluded that the bulky, p...
Source: European Biophysics Journal : EBJ - August 10, 2009 Category: Physics Authors: Duarte AM, de Jong ER, Koehorst RB, Hemminga MA Tags: Eur Biophys J Source Type: journals

Calibration of dynamic models of biological systems with KInfer.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Methods for parameter estimation that are robust to experimental uncertainties and to stochastic and biological noise and that require a minimum of a priori input knowledge are of key importance in computational systems biology. The new method presented in this paper aims to ensure an inference model that deduces the rate constants of a system of biochemical reactions from experimentally measured time courses of reactants. This new method was applied to some challenging parameter estimation problems of nonlinear dynamic biological systems and was tested both on synthetic and real data. The synthetic case studies are th...
Source: European Biophysics Journal : EBJ - August 10, 2009 Category: Physics Authors: Lecca P, Palmisano A, Ihekwaba A, Priami C Tags: Eur Biophys J Source Type: journals

Electron spin resonance in membrane research: protein-lipid interactions from challenging beginnings to state of the art.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conventional electron paramagnetic resonance (EPR) spectra of lipids that are spin-labelled close to the terminal methyl end of the acyl chains are able to resolve the lipids directly contacting the protein from those in the fluid bilayer regions of the membrane. This allows determination of both the stoichiometry of lipid-protein interaction (i.e., number of lipid sites at the protein perimeter) and the selectivity of the protein for different lipid species (i.e., association constants relative to the background lipid). Spin-label EPR data are summarised for 20 or more different transmembrane peptides and proteins, an...
Source: European Biophysics Journal : EBJ - August 10, 2009 Category: Physics Authors: Marsh D Tags: Eur Biophys J Source Type: journals

SDSL-ESR-based protein structure characterization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to a...
Source: European Biophysics Journal : EBJ - August 10, 2009 Category: Physics Authors: Strancar J, Kavalenka A, Urbančič I, Ljubetič A, Hemminga MA Tags: Eur Biophys J Source Type: journals

Biophysical studies of the interactions between the phage varphiKZ gp144 lytic transglycosylase and model membranes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The use of naturally occurring lytic bacteriophage proteins as specific antibacterial agents is a promising way to treat bacterial infections caused by antibiotic-resistant pathogens. The opportunity to develop bacterial resistance to these agents is minimized by their broad mechanism of action on bacterial membranes and peptidoglycan integrity. In the present study, we have investigated lipid interactions of the gp144 lytic transglycosylase from the Pseudomonas aeruginosa phage varphiKZ. Interactions with zwitterionic lipids characteristic of eukaryotic cells and with anionic lipids characteristic of bacterial cells w...
Source: European Biophysics Journal : EBJ - August 7, 2009 Category: Physics Authors: Cloutier I, Paradis-Bleau C, Giroux AM, Pigeon X, Arseneault M, Levesque RC, Auger M Tags: Eur Biophys J Source Type: journals

Structure and heterogeneity of gliadin: a hydrodynamic evaluation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A study of the heterogeneity and conformation in solution [in 70% (v/v) aq. ethanol] of gliadin proteins from wheat was undertaken based upon sedimentation velocity in the analytical ultracentrifuge, analysis of the distribution coefficients and ellipsoidal axial ratios assuming quasi-rigid particles, allowing for a range of plausible time-averaged hydration values. All classical fractions (alpha, gamma, omega(slow), omega(fast)) show three clearly resolved components. Based on the weight-average sedimentation coefficient for each fraction and a weight-average molecular weight from sedimentation equilibrium and/or cDNA...
Source: European Biophysics Journal : EBJ - August 7, 2009 Category: Physics Authors: Ang S, Kogulanathan J, Morris GA, Kök MS, Shewry PR, Tatham AS, Adams GG, Rowe AJ, Harding SE Tags: Eur Biophys J Source Type: journals

Biophysical studies on chitosan-coated liposomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Liposomes have been used as delivery vehicles for stabilizing drugs, overcoming barriers to cellular and tissue uptake, and for directing their contents toward specific sites in vivo. Chitosan is a biological macromolecule derived from crustacean shells and has several emerging applications in drug development, obesity control, and tissue engineering. In the present work, the interaction between chitosan and dipalmitoyl phosphatidylcholine (DPPC) liposomes was studied by transmission electron microscopy (TEM), zeta potential, solubilization using the nonionic detergent octylglucoside (OG), as well as Fourier transform ...
Source: European Biophysics Journal : EBJ - August 1, 2009 Category: Physics Authors: Mady MM, Darwish MM, Khalil S, Khalil WM Tags: Eur Biophys J Source Type: journals

On the analysis of sedimentation velocity in the study of protein complexes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe how these effects can be computationally accounted for in SEDFIT and SEDPHAT. PMID: 19644686 [PubMed - as supplied by publisher] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - July 30, 2009 Category: Physics Authors: Brown PH, Balbo A, Schuck P Tags: Eur Biophys J Source Type: journals

Cholesterol modulation of nicotinic acetylcholine receptor surface mobility.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nicotinic acetylcholine receptor (AChR) function and distribution are quite sensitive to cholesterol (Chol) levels in the plasma membrane (reviewed by Barrantes in J Neurochem 103 (suppl 1):72-80, 2007). Here we combined confocal fluorescence recovery after photobleaching (FRAP) and confocal fluorescence correlation spectroscopy (FCS) to examine the mobility of the AChR and its dependence on Chol content at the cell surface of a mammalian cell line. Plasma membrane AChR exhibited limited mobility and only ~55% of the fluorescence was recovered within 10 min after photobleaching. Depletion of membrane Chol by methyl-bet...
Source: European Biophysics Journal : EBJ - July 29, 2009 Category: Physics Authors: Baier CJ, Gallegos CE, Levi V, Barrantes FJ Tags: Eur Biophys J Source Type: journals

Exploring the structure of the N-terminal domain of CP29 with ultrafast fluorescence spectroscopy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A high-throughput Förster resonance energy transfer (FRET) study was performed on the approximately 100 amino acids long N-terminal domain of the photosynthetic complex CP29 of higher plants. For this purpose, CP29 was singly mutated along its N-terminal domain, replacing one-by-one native amino acids by a cysteine, which was labeled with a BODIPY fluorescent probe, and reconstituted with the natural pigments of CP9, chlorophylls and xanthophylls. Picosecond fluorescence experiments revealed rapid energy transfer (~20-70 ps) from BODIPY at amino-acid positions 4, 22, 33, 40, 56, 65, 74, 90, and 97 to Chl a molecul...
Source: European Biophysics Journal : EBJ - July 28, 2009 Category: Physics Authors: Berghuis BA, Spruijt RB, Koehorst RB, van Hoek A, Laptenok SP, van Oort B, van Amerongen H Tags: Eur Biophys J Source Type: journals

Solution NMR mapping of water-accessible residues in the transmembrane beta-barrel of OmpX.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The atomic structure of OmpX, the smallest member of the bacterial outer membrane protein family, has been previously established by X-ray crystallography and NMR spectroscopy. In apparent conflict with electrophysiological studies, the lumen of its transmembrane beta-barrel appears too tightly packed with amino acid side chains to let any solute flow through. In the present study, high-resolution solution NMR spectra were obtained of OmpX kept water-soluble by either amphipol A8-35 or the detergent dihexanoylphosphatidylcholine. Hydrogen/deuterium exchange measurements performed after prolonged equilibration show that...
Source: European Biophysics Journal : EBJ - July 28, 2009 Category: Physics Authors: Catoire LJ, Zoonens M, van Heijenoort C, Giusti F, Guittet E, Popot JL Tags: Eur Biophys J Source Type: journals

Modulating the activity of the channel-forming segment of Vpr protein from HIV-1.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study a short peptide, Vpr(55-83), was shown to exhibit ion-channel-like activity when reconstituted into (1) planar lipid bilayers and (2) lipid bilayers held at the tip of a glass pipette. The two set-ups led to differences in the oligomerization state of the peptide, which was reflected in differences in the conductance levels. Experiments under applied hydrostatic pressure affect the dynamics of the protein within the membrane. PMID: 19629466 [PubMed - as supplied by publisher] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - July 23, 2009 Category: Physics Authors: Chen CP, Kremer C, Henklein P, Schubert U, Fink RH, Fischer WB Tags: Eur Biophys J Source Type: journals

Using a five-state model for fitting amplitude histograms from MaxiK channels: beta-distributions reveal more than expected.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Fast gating of ion channels with rate constants higher than the corner frequency of the recording set-up can be evaluated by fitting so-called beta distributions to measured amplitude histograms. Up to now, this was preferentially done for O-C Markov sub-models with one open and one closed state. Here, a fit of the amplitude histograms from MaxiK (BK) single-channel records was achieved with a five-state model with two open and three closed states including three open-close transitions with rate constants higher than the corner frequency (20 kHz) of the inevitable low-pass filter of the recording system. The numerical ...
Source: European Biophysics Journal : EBJ - July 20, 2009 Category: Physics Authors: Schroeder I, Hansen UP Tags: Eur Biophys J Source Type: journals

Fractal analysis and ionic dependence of endocytotic membrane activity of human breast cancer cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The endocytic membrane activities of two human breast cancer cell lines (MDA-MB-231 and MCF-7) of strong and weak metastatic potential, respectively, were studied in a comparative approach. Uptake of horseradish peroxidase was used to follow endocytosis. Dependence on ionic conditions and voltage-gated sodium channel (VGSC) activity were characterized. Fractal methods were used to analyze quantitative differences in vesicular patterning. Digital quantification showed that MDA-MB-231 cells took up more tracer (i.e., were more endocytic) than MCF-7 cells. For the former, uptake was totally dependent on extracellular Na(+...
Source: European Biophysics Journal : EBJ - July 17, 2009 Category: Physics Authors: Krasowska M, Grzywna ZJ, Mycielska ME, Djamgoz MB Tags: Eur Biophys J Source Type: journals

Electromagnetic field (EMF) effects on channel activity of nanopore OmpF protein.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, the effects of nonionizing electromagnetic fields (EMF; 925 MHz) on the OmpF porin channel have been characterized at the single-channel level. Channel activity was recorded in real time by the voltage clamp method. Our results showed an increase in the frequency of channel gating and voltage sensitivity. The effects of EMF lasted for several milliseconds after the field source was terminated. However, the conductance levels of channels did not change significantly. Thermal effects of EMF on single-channel properties are a possible cause, based on theoretical evaluation of results that were comparable to tho...
Source: European Biophysics Journal : EBJ - July 14, 2009 Category: Physics Authors: Mohammadzadeh M, Mobasheri H, Arazm F Tags: Eur Biophys J Source Type: journals