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19 records returned

Amplitude distribution of stochastic oscillations in biochemical networks due to intrinsic noiseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Intrinsic noise is a common phenomenon in biochemical reaction networks and may affect the occurence and amplitude of sustained oscillations in the states of the network. To evaluate properties of such oscillations in the time domain, it is usually required to conduct long-term stochastic simulations, using for example the Gillespie algorithm. In this paper, we present a new method to compute the amplitude distribution of the oscillations without the need for long-term stochastic simulations. By the derivation of the method, we also gain insight into the structural features underlying the stochastic oscillations. The metho...
Source: PMC Biophysics - November 17, 2009 Category: Physics Authors: Moritz LangSteffen WaldherrFrank Allgower Source Type: journals

Two-dimensional nanosecond electric field mapping based on cell electropermeabilizationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nanosecond, megavolt-per-meter electric pulses cause permeabilization of cells to small molecules, programmed cell death (apoptosis) in tumor cells, and are under evaluation as a treatment for skin cancer. We use nanoelectroporation and fluorescence imaging to construct two-dimensional maps of the electric field associated with delivery of 15 ns, 10 kV pulses to monolayers of the human prostate cancer cell line PC3 from three different electrode configurations: single-needle, five-needle, and flat-cut coaxial cable. Influx of the normally impermeant fluorescent dye YO-PRO-1 serves as a sensitive indicator of membrane perme...
Source: PMC Biophysics - November 11, 2009 Category: Physics Authors: Meng-Tse ChenChunqi JiangP. Thomas VernierYu-Hsuan WuMartin Gundersen Source Type: journals

Simple modeling of FtsZ polymers on flat and curved surfaces: correlation with experimental in vitro observationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
FtsZ is a GTPase that assembles at midcell into a dynamic ring that constricts the membrane to induce cell division in the majority of bacteria,in many archea and several organelles. In vitro, FtsZ polymerizes in a GTP-dependent manner forming a variety of filamentous flexible structures. Based on data derived from the measurement of the in vitro polymerization of Escherichia coli FtsZ cell division protein we have formulated a model in which the fine balance between curvature, flexibility and lateral interactions accounts for structural and dynamic properties of the FtsZ polymers observed with AFM. The experimental result...
Source: PMC Biophysics - October 21, 2009 Category: Physics Authors: Alfonso PaezPablo Mateos-GilInes HorgerJesus MingoranceGerman RivasMiguel VicenteMarisela VelezPedro Tarazona Source Type: journals

The influence of membrane physical properties on microvesicle release in human erythrocytesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study tested the hypothesis that microvesicle release depends on microscopic membrane physical properties such as lipid order, fluidity, and composition. Membrane properties were manipulated by varying the experimental temperature, membrane cholesterol content, and the activity of the trans-membrane phospholipid transporter, scramblase. Microvesicle release was enhanced by increasing the experimental temperature. Reduction in membrane cholesterol content by treatment with methyl-beta-cyclodextrin also facilitated vesicle shedding. Inhibition of scramblase with R5421 impaired vesicle release. These data were interprete...
Source: PMC Biophysics - August 23, 2009 Category: Physics Authors: Laurie GonzalezElizabeth GibbonsRachel BaileyJeremy FairbournThaothanh NguyenSamantha SmithKatrina BestJennifer NelsonAllan JuddJohn Bell Source Type: journals

Zwanzig-Mori projection operators and EEG dynamics: deriving a simple equation of motionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a macroscopic theory of electroencephalogram (EEG) dynamics based on the laws of motion that govern atomic and molecular motion. The theory is an application of Zwanzig-Mori projection operators. The result is a simple equation of motion that has the form of a generalized Langevin equation (GLE), which requires knowledge only of macroscopic properties. The macroscopic properties can be extracted from experimental data by one of two possible variational principles. These variational principles are our principal contribution to the formalism. Potential applications are discussed, including applications to the theo...
Source: PMC Biophysics - July 12, 2009 Category: Physics Authors: David HsuMurielle Hsu Source Type: journals

Structural and functional implications of p53 missense cancer mutationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, the stabilities of all core domain missense mutations are predicted and are used to infer their likely inactivation mechanisms. Overall, 47.0% non-PRO/GLY mutants are stable (ΔΔG < 1.0 kT) and 36.3% mutants are unstable (ΔΔG > 3.0 kT), 12.2% mutants are with 1.0 kT < ΔΔG < 3.0 kT. Only 4.5% mutants are with no conclusive predictions. Certain types of either stable or unstable mutations are found not to depend on their local structures. Y, I, C, V, F and W (W, R and F) are the most common residues before (after) mutation in unstable mutants. Q, N, K, D, A, S and T (I, T, L and V) are the most common res...
Source: PMC Biophysics - June 25, 2009 Category: Physics Authors: Yuhong TanRay Luo Source Type: journals

Structural and functional implications of p53 missense cancer mutationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, the stabilities of all core domain missense mutations are predicted and are used to infer their likely inactivation mechanisms. Overall, 47.0% non-PRO/GLY mutants are stable (DeltaDeltaG < 1.0kT) and 36.3% mutants are unstable (DeltaDeltaG > 3.0kT), 12.2% mutants are with 1.0kT < DeltaDeltaG < 3.0kT. Only 4.5% mutants are with no conclusive predictions. Certain types of either stable or unstable mutations are found not to depend on their local structures. Y, I, C, V, F and W (W, R and F) are the most common residues before (after) mutation in unstable mutants. Q, N, K, D, A, S and T (I, T, L and V) are the m...
Source: PMC Biophysics - June 25, 2009 Category: Physics Authors: Yuhong TanRay Luo Source Type: journals

Three-dimensional studies of pathogenic peptides from the c-terminal of Trypanosoma cruzi ribosomal P proteins and their interaction with a monoclonal antibody structural modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The acidic C-terminal peptides from Trypanosoma cruzi ribosomal P proteins are the major target of the antibody response in patients suffering Chagas's chronic heart disease. It has been proposed that the disease is triggered by the cross-reaction of these antibodies with the second extra cellular loop of the beta1-adrenoreceptor, brought about by the molecular mimicry between the acidic C-terminal peptides and the receptor's loop. To improve the understanding of the structural basis of the autoimmune response against heart receptors, the 3-dimensional structure of the C-terminal peptides of Trypanosoma cruzi ribosomal pro...
Source: PMC Biophysics - May 27, 2009 Category: Physics Authors: Osvaldo MartinMyriam VillegasCarlos Aguilar Source Type: journals

Three-dimensional studies of pathogenic peptides from the c-terminal of Trypanosoma cruziribosomal P proteins and their interaction with a monoclonal antibody structural modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The acidic C-terminal peptides from Trypanosoma cruzi ribosomal P proteins are the major target of the antibody response in patients suffering Chagas chronic heart disease. It has been proposed that the disease is triggered by the cross-reaction of these antibodies with the second extra cellular loop of the β1-adrenoreceptor, brought about by the molecular mimicry between the acidic C-terminal peptides and the receptor's loop. To improve the understanding of the structural basis of the autoimmune response against heart receptors, the 3-dimensional structure of the C-terminal peptides of Trypanosoma cruzi ribosomal protein...
Source: PMC Biophysics - May 26, 2009 Category: Physics Authors: Osvaldo MartinMyriam VillegasCarlos Aguilar Source Type: journals

The multiple faces of self-assembled lipidic systemsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lipids, the building blocks of cells, common to every living organisms, have the propensity to self-assemble into well-defined structures over short and long-range spatial scales. The driving forces have their roots mainly in the hydrophobic effect and electrostatic interactions. Membranes in lamellar phase are ubiquitous in cellular compartments and can phase-separate upon mixing lipids in different liquid-crystalline states. Hexagonal phases and especially cubic phases can be synthesized and observed in vivo as well. Membrane often closes up into a vesicle whose shape is determined by the interplay of curvature, area dif...
Source: PMC Biophysics - April 17, 2009 Category: Physics Authors: Guillaume Tresset Source Type: journals

An effective all-atom potential for proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy lands...
Source: PMC Biophysics - April 8, 2009 Category: Physics Authors: Anders Irback, Simon Mitternacht and Sandipan Mohanty Source Type: journals

Membrane protein dynamics: limited lipid controlEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Correlation of lipid disorder with membrane protein dynamics has been studied with infrared spectroscopy, by combining data characterizing lipid phase, protein structure and, via hydrogen-deuterium (H/D) exchange, protein dynamics. The key element was a new measuring scheme, by which the combined effects of time and temperature on the H/D exchange could be separated. Cyanobacterial and plant thylakoid membranes, mammalian mitochondria membranes, and for comparison, lysozyme were investigated. In dissolved lysozyme, as a function of temperature, H/D exchange involved only reversible movements (the secondary structure did no...
Source: PMC Biophysics - February 6, 2009 Category: Physics Authors: Balazs Szalontai Source Type: journals

Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectivesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Finding the global probabilistic nature of a non-equilibrium circadian clock is essential for addressing important issues of robustness and function. We have uncovered the underlying potential energy landscape of a simple cyanobacteria biochemical network, and the corresponding flux which is the driving force for the oscillation. We found that the underlying potential landscape for the oscillation in the presence of small statistical fluctuations is like an explicit ring valley or doughnut shape in the three dimensional protein concentration space. We found that the barrier height separating the oscillation ring and other ...
Source: PMC Biophysics - December 30, 2008 Category: Physics Authors: Jin Wang, Li Xu and Erkang Wang Source Type: journals

Resolution of complex fluorescence spectra of lipids and nicotinic acetylcholine receptor by multivariate analysis reveals protein-mediated effects on the receptor's immediate lipid microenvironmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Analysis of fluorescent spectra from complex biological systems containing various fluorescent probes with overlapping emission bands is a challenging task. Valuable information can be extracted from the full spectra, however, by using multivariate analysis (MA) of measurements at different wavelengths. We applied MA to spectral data of purified Torpedo nicotinic acetylcholine receptor (AChR) protein reconstituted into liposomes made up of dioleoylphosphatidic acid (DOPA) and dioleoylphosphatidylcholine (DOPC) doped with two extrinsic fluorescent probes (NBD-cholesterol/pyrene-PC). Forster resonance energy transfer (FRET) ...
Source: PMC Biophysics - December 18, 2008 Category: Physics Authors: Jorge J. Wenz and Francisco J. Barrantes Source Type: journals

Stochastic reconstruction of protein structures from effective connectivity profilesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity'', which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors of the contact map of the target structure. The structural profile is used to bias a search of the conformational space towards the target structure in a Monte Carlo scheme operating on a C_alpha-chain of uniform, finite thickness. Structure information thus enters the folding dynamics via the effective connectivity, but the interaction is not restricted to pairs of amino acids that for...
Source: PMC Biophysics - November 26, 2008 Category: Physics Authors: Katrin Wolff, Michele Vendruscolo and Markus Porto Source Type: journals

The debut of PMC BiophysicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Welcome to PMC Biophysics, an international, peer-reviewed, open access journal devoted to biological physics in all its myriad forms. The journal has been launched in response to two significant trends in publishing and research. (Source: PMC Biophysics)
Source: PMC Biophysics - November 5, 2008 Category: Physics Authors: Huan-Xiang Zhou Source Type: journals

On the electrostatic component of protein-protein binding free energyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Calculations of electrostatic properties of protein-protein complexes are usually done within framework of a model with a certain set of parameters. In this paper we present a comprehensive statistical analysis of the sensitivity of the electrostatic component of binding free energy (DDGel) with respect with different force fields (Charmm, Amber, and OPLS), different values of the internal dielectric constant, and different presentations of molecular surface (different values of the probe radius). The study was done using the largest so far set of entries comprising 260 hetero and 2148 homo protein-protein complexes extrac...
Source: PMC Biophysics - November 5, 2008 Category: Physics Authors: Kemper Talley, Carmen Ng, Michael Shoppell, Petras Kundrotas and Emil Alexov Source Type: journals

ATR-FTIR spectroscopy detects alterations induced by organotin(IV) carboxylates in MCF-7 cells at sub-cytotoxic/-genotoxic concentrationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The environmental impact of metal complexes such as organotin(IV) compounds is of increasing concern. Genotoxic effects of organotin(IV) compounds (0.01 microg/ml, 0.1 microg/ml or 1.0 microg/ml) were measured using the alkaline single-cell gel electrophoresis (comet) assay to measure DNA single-strand breaks (SSBs) and the cytokinesis-block micronucleus (CBMN) assay to determine micronucleus formation. Biochemical-cell signatures were also ascertained using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. In the comet assay, organotin(IV) carboxylates induced significantly-elevated levels of...
Source: PMC Biophysics - November 5, 2008 Category: Physics Authors: Muhammad S Ahmad, Bushra Mirza, Mukhtiar Hussain, Muhammad Hanif, Saqib J Ali, Michael J Walsh and Francis L Martin Source Type: journals

Label-free electrical quantification of the dielectrophoretic response of DNAEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution by measuring the capacitance between planar microelectrodes. Concentrations of DNA in the ng/mL range have been used in samples of 1 microL volume. The method has been applied to the characterisation of the dielectrophoretic response of DNA without the need for any chemical modifications. The influence of electrical parameters like duty cycle, voltage and frequency has been investigated. The results are in good agreement with data from dielectrophoretic studies on fluorescently labelled DNA. Extension of the meth...
Source: PMC Biophysics - November 5, 2008 Category: Physics Authors: Anja Henning, Jorg Henkel, Frank F Bier and Ralph Holzel Source Type: journals