Biophysical Journal

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Biophysical Journal RSS feed. Cell Press was chosen by the Biophysical Society to publish its premier journal, beginning in January 2009. Published semimonthly, the Biophysical Journal presents original articles, letters and reviews on the most important developments in modern biophysics, emphasizing the molecular and cellular aspects of biology.Topics covered include:Channels, Receptors, and Electrical SignalingProteins Biophysical Theory and ModelingCell BiophysicsPhotobiophysicsMembranesSpectroscopy, Imaging, Other TechniquesMuscle and ContractilitySupramolecular AssembliesBioenergeticsNucleic AcidsElectrophysiology
Updated: 1 year 50 weeks ago

Discrimination of Kinetic Models by a Combination of Microirradiation and Fluorescence Photobleaching

Mon, 10/19/2015 - 23:00
Fluorescence recovery after photobleaching (FRAP) is an excellent tool to measure the chemical rate constants of fluorescently labeled proteins in living cells. Usually FRAP experiments are conducted with the protein concentrations being in a steady state, i.e., when the association and dissociation of the proteins are equilibrated. This is a strong limitation because situations in which rate constants change with time are of great scientific interest. In this study, we present an approach in which FRAP is used shortly after DNA damage introducing laser microirradiation, which results in the recruitment of the DNA clamp protein proliferating cell nuclear antigen (PCNA) to DNA lesions.
Categories: Journal Articles

Secondary Structure Analysis of a Functional Construct of Caveolin-1 Reveals a Long C-Terminal Helix

Mon, 10/19/2015 - 23:00
Caveolin-1 is an integral membrane protein that is the primary component of cell membrane invaginations called caveolae. While caveolin-1 is known to participate in a myriad of vital cellular processes, structural data on caveolin-1 of any kind is severely limited. In order to rectify this dearth, secondary structure analysis of a functional construct of caveolin-1, containing the intact C-terminal domain, was performed using NMR spectroscopy in lyso-myristoylphosphatidylglycerol micelles. Complete backbone assignments of caveolin-1 (residues 62–178) were made, and it was determined that residues 62–79 were dynamic; residues 89–107, 111–128, and 132–175 were helical; and residues 80–88, 108–110, and 129–131 represent unstructured breaks between the helices.
Categories: Journal Articles

The Effect of Membrane Lipid Composition on the Formation of Lipid Ultrananodomains

Mon, 10/19/2015 - 23:00
Some lipid mixtures form membranes containing submicroscopic (nanodomain) ordered lipid domains (rafts). Some of these nanodomains are so small (radius <5 nm) that they cannot be readily detected with Förster resonance energy transfer (FRET)-labeled lipid pairs with large Ro. We define such domains as ultrananodomains. We studied the effect of lipid structure/composition on the formation of ultrananodomains in lipid vesicles using a dual-FRET-pair approach in which only one FRET pair had Ro values that were sufficiently small to detect the ultrananodomains.
Categories: Journal Articles

Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?

Mon, 10/19/2015 - 23:00
G-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane’s cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency.
Categories: Journal Articles

Mapping the Processivity Determinants of the Kinesin-3 Motor Domain

Mon, 10/19/2015 - 23:00
Kinesin superfamily members play important roles in many diverse cellular processes, including cell motility, cell division, intracellular transport, and regulation of the microtubule cytoskeleton. How the properties of the family-defining motor domain of distinct kinesins are tailored to their different cellular roles remains largely unknown. Here, we employed molecular-dynamics simulations coupled with energetic calculations to infer the family-specific interactions of kinesin-1 and kinesin-3 motor domains with microtubules in different nucleotide states.
Categories: Journal Articles

Theory of Triplet Excitation Transfer in the Donor-Oxygen-Acceptor System: Application to Cytochrome f

Mon, 10/19/2015 - 23:00
Theoretical consideration is presented of the triplet excitation dynamics in donor-acceptor systems in conditions where the transfer is mediated by an oxygen molecule. It is demonstrated that oxygen may be involved in both real and virtual intramolecular triplet-singlet conversions in the course of the process under consideration. Expressions describing a superexchange donor-acceptor coupling owing to a participation of the bridging twofold degenerate oxygen’s virtual singlet state are derived and the transfer kinetics including the sequential (hopping) and coherent (distant) routes are analyzed.
Categories: Journal Articles

Active Biochemical Regulation of Cell Volume and a Simple Model of Cell Tension Response

Mon, 10/19/2015 - 23:00
Active contractile forces exerted by eukaryotic cells play significant roles during embryonic development, tissue formation, and cell motility. At the molecular level, small GTPases in signaling pathways can regulate active cell contraction. Here, starting with mechanical force balance at the cell cortex, and the recent discovery that tension-sensitive membrane channels can catalyze the conversion of the inactive form of Rho to the active form, we show mathematically that this active regulation of cellular contractility together with osmotic regulation can robustly control the cell size and membrane tension against external mechanical or osmotic shocks.
Categories: Journal Articles

Critical Timing without a Timer for Embryonic Development

Mon, 10/19/2015 - 23:00
Timing of embryonic development is precisely controlled, but the mechanisms underlying biological timers are still unclear. Here, a validated model for timing under control of Sonic Hedgehog is revisited and generalized to an arbitrary number of genes. The developmental dynamics where a temporal sequence of gene expression recapitulates a steady-state spatial pattern can be realized through a simple network close to criticality, controlled by the duration of exposure to a morphogen. Criticality simultaneously accounts for many observed biological properties, such as timing, multistability, and canalization of genetic expression.
Categories: Journal Articles

Local Crystalline Structure in an Amorphous Protein Dense Phase

Mon, 10/19/2015 - 23:00
Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumin precipitate particles salted out with ammonium sulfate.
Categories: Journal Articles

Dipole-Potential-Mediated Effects on Ion Pump Kinetics

Mon, 10/19/2015 - 23:00
The kinetics of conformational changes of P-type ATPases necessary for the occlusion or deocclusion of transported ions are known to be sensitive to the composition of the surrounding membrane, e.g., phospholipid content, mole percentage of cholesterol, and the presence of lipid-bound anions. Research has shown that many membrane components modify the dipole potential of the lipid head-group region. Based on the observation that occlusion/deocclusion reactions of ion pumps perturb the membrane surrounding the protein, a mechanism is suggested whereby dipole potential modifiers induce preferential stabilization or destabilization of occluded or nonoccluded states of the protein, leading to changes in the forward and backward rate constants for the transition.
Categories: Journal Articles

A Thermodynamic Model for Genome Packaging in Hepatitis B Virus

Mon, 10/19/2015 - 23:00
Understanding the fundamentals of genome packaging in viral capsids is important for finding effective antiviral strategies and for utilizing benign viral particles for gene therapy. While the structure of encapsidated genomic materials has been routinely characterized with experimental techniques such as cryo-electron microscopy and x-ray diffraction, much less is known about the molecular driving forces underlying genome assembly in an intracellular environment and its in vivo interactions with the capsid proteins.
Categories: Journal Articles

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Mon, 10/19/2015 - 23:00
As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters.
Categories: Journal Articles

Nucleosome Core Particle Disassembly and Assembly Kinetics Studied Using Single-Molecule Fluorescence

Mon, 10/19/2015 - 23:00
The stability of the nucleosome core particle (NCP) is believed to play a major role in regulation of gene expression. To understand the mechanisms that influence NCP stability, we studied stability and dissociation and association kinetics under different histone protein (NCP) and NaCl concentrations using single-pair Förster resonance energy transfer and alternating laser excitation techniques. The method enables distinction between folded, unfolded, and intermediate NCP states and enables measurements at picomolar to nanomolar NCP concentrations where dissociation and association reactions can be directly observed.
Categories: Journal Articles

Factors that Influence the Formation and Stability of Thin, Cryo-EM Specimens

Tue, 09/15/2015 - 23:00
Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. Here we first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. We then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated.
Categories: Journal Articles

A Reminiscence about Early Times of Vitreous Water in Electron Cryomicroscopy

Mon, 09/07/2015 - 23:00
A white blackbird is not an issue, until you see one. I saw it in an article by Taylor and Glaeser (1) presenting frozen delicate biological specimens with high contrast and exquisite details. I am still unsure of what really happened with this specimen but, what is certain, is that frozen water was present and that the unstained biological material was more beautiful than anything I had seen before. For me, the path was marked and chance helped.
Categories: Journal Articles