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Biophysical Journal

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https://www.readbyqxmd.com/read/30309611/modeling-the-axon-as-an-active-partner-with-the-growth-cone-in-axonal-elongation
#1
Rijk de Rooij, Ellen Kuhl, Kyle E Miller
Forces generated by the growth cone are vital for the proper development of the axon and thus brain function. Although recent experiments show that forces are generated along the axon, it is unknown whether the axon plays a direct role in controlling growth cone advance. Here, we use analytic and finite element modeling of microtubule dynamics and the activity of the molecular motors myosin and dynein to investigate mechanical force balance along the length of the axon and its effects on axonal outgrowth. Our modeling indicates that the paradoxical effects of stabilizing microtubules and the consequences of microtubule disassembly on axonal outgrowth can be explained by changes in the passive and active mechanical properties of axons...
October 3, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30322797/rigidity-rules-in-dna-droplets-nucleic-acid-flexibility-affects-model-membraneless-organelles
#2
Alain A M André, Evan Spruijt
No abstract text is available yet for this article.
October 2, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30327139/mapping-the-ligand-binding-landscape
#3
Alex Dickson
The interaction between a ligand and a protein involves a multitude of conformational states. To achieve a particular deeply bound pose, the ligand must search across a rough free-energy landscape with many metastable minima. Creating maps of the ligand binding landscape is a great challenge, as binding and release events typically occur on timescales that are beyond the reach of molecular simulation. The WExplore enhanced sampling method is well suited to build these maps because it is designed to broadly explore free-energy landscapes and is capable of simulating ligand release pathways that occur on timescales as long as minutes...
September 29, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30322796/nanoscale-topography-and-poroelastic-properties-of-model-tissue-breast-gland-basement-membranes
#4
Gloria Fabris, Alessandro Lucantonio, Nico Hampe, Erik Noetzel, Bernd Hoffmann, Antonio DeSimone, Rudolf Merkel
Basement membranes (BMs) are thin layers of condensed extracellular matrix proteins serving as permeability filters, cellular anchoring sites, and barriers against cancer cell invasion. It is believed that their biomechanical properties play a crucial role in determining cellular behavior and response, especially in mechanically active tissues like breast glands. Despite this, so far, relatively little attention has been dedicated to their analysis because of the difficulty of isolating and handling such thin layers of material...
September 29, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30322798/microtubules-provide-a-viscoelastic-resistance-to-myocyte-motion
#5
Matthew Alexander Caporizzo, Christina Yingxian Chen, Alexander Koizumi Salomon, Kenneth B Margulies, Benjamin L Prosser
BACKGROUND: Microtubules (MTs) buckle and bear load during myocyte contraction, a behavior enhanced by post-translational detyrosination. This buckling suggests a spring-like resistance against myocyte shortening, which could store energy and aid myocyte relaxation. Despite this visual suggestion of elastic behavior, the precise mechanical contribution of the cardiac MT network remains to be defined. METHODS: Here we experimentally and computationally probe the mechanical contribution of stable MTs and their influence on myocyte function...
September 28, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30314657/the-i-ks-channel-response-to-camp-is-modulated-by-the-kcne1-kcnq1-stoichiometry
#6
Emely Thompson, Jodene Eldstrom, Maartje Westhoff, Donald McAfee, David Fedida
The delayed potassium rectifier current, IKs, is assembled from tetramers of KCNQ1 and varying numbers of KCNE1 accessory subunits in addition to calmodulin. This channel complex is important in the response of the cardiac action potential to sympathetic stimulation, during which IKs is enhanced. This is likely due to channels opening more quickly, more often, and to greater sublevel amplitudes during adrenergic stimulation. KCNQ1 alone is unresponsive to cyclic adenosine monophosphate (cAMP), and thus KCNE1 is required for a functional effect of protein kinase A phosphorylation...
September 27, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30314656/the-expanding-zoo-of-in-cell-protein-nmr
#7
Samantha S Stadmiller, Gary J Pielak
No abstract text is available yet for this article.
September 26, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30297132/a-plugin-framework-for-extending-the-simulation-capabilities-of-febio
#8
Steve A Maas, Steven A LaBelle, Gerard A Ateshian, Jeffrey A Weiss
The FEBio software suite is a set of software tools for nonlinear finite element analysis in biomechanics and biophysics. FEBio employs mixture theory to account for the multiconstituent nature of biological materials, integrating the field equations for irreversible thermodynamics, solid mechanics, fluid mechanics, mass transport with reactive species, and electrokinetics. This communication describes the development and application of a new "plugin" framework for FEBio. Plugins are dynamically linked libraries that allow users to add new features and to couple FEBio with other domain-specific software applications without modifying the source code directly...
September 26, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30301513/kalman-inversion-stress-microscopy
#9
Vincent Nier, Grégoire Peyret, Joseph d'Alessandro, Shuji Ishihara, Benoit Ladoux, Philippe Marcq
Although mechanical cues are crucial to tissue morphogenesis and development, the tissue mechanical stress field remains poorly characterized. Given traction force time-lapse movies, as obtained by traction force microscopy of in vitro cellular sheets, we show that the tissue stress field can be estimated by Kalman filtering. After validation using numerical data, we apply Kalman inversion stress microscopy to experimental data. We combine the inferred stress field with velocity and cell-shape measurements to quantify the rheology of epithelial cell monolayers in physiological conditions, found to be close to that of an elastic and active material...
September 25, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30314655/stabilizing-effect-of-inherent-knots-on-proteins-revealed-by-molecular-dynamics-simulations
#10
Yan Xu, Shixin Li, Zengshuai Yan, Zhen Luo, Hao Ren, Baosheng Ge, Fang Huang, Tongtao Yue
A growing number of proteins have been identified as knotted in their native structures, with such entangled topological features being expected to play stabilizing roles maintaining both the global fold and the nature of proteins. However, the molecular mechanism underlying the stabilizing effect is ambiguous. Here, we combine unbiased and mechanical atomistic molecular dynamics simulations to investigate how a protein is stabilized by an inherent knot by directly comparing chemical, thermal, and mechanical denaturing properties of two proteins having the same sequence and secondary structures but differing in the presence or absence of an inherent knot...
September 22, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30314654/acoustic-compressibility-of-caenorhabditis-elegans
#11
Thierry Baasch, Peter Reichert, Stefan Lakämper, Nadia Vertti-Quintero, Gamuret Hack, Xavier Casadevall I Solvas, Andrew deMello, Rudiyanto Gunawan, Jürg Dual
The acoustic compressibility of Caenorhabditis elegans is a necessary parameter for further understanding the underlying physics of acoustic manipulation techniques of this widely used model organism in biological sciences. In this work, numerical simulations were combined with experimental trajectory velocimetry of L1 C. elegans larvae to estimate the acoustic compressibility of C. elegans. A method based on bulk acoustic wave acoustophoresis was used for trajectory velocimetry experiments in a microfluidic channel...
September 22, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30297135/effect-of-an-intrinsically-disordered-plant-stress-protein-on-the-properties-of-water
#12
Luisa A Ferreira, Alicyia Walczyk Mooradally, Boris Zaslavsky, Vladimir N Uversky, Steffen P Graether
Dehydrins are plant proteins that are able to protect plants from various forms of dehydrative stress such as drought, cold, and high salinity. Dehydrins can prevent enzymes from losing activity after freeze/thaw treatments. Previous studies had suggested that the dehydrins function by a molecular shield effect, essentially preventing a denatured enzyme from aggregating with another enzyme. Therefore, the larger the dehydrin, the larger the shield and theoretically the more effective the protection. Although this relationship holds for smaller dehydrins, it fails to explain why larger dehydrins are less efficient than would be predicted from their size...
September 22, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30290957/keys-to-amyloid-city-computation-and-nmr-reveal-potential-tdp-43-als-intermediates
#13
W Michael Babinchak, Zhenlu Li, Matthias Buck
No abstract text is available yet for this article.
September 22, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30309612/characterization-of-tdp-43-rrm2-partially-folded-states-and-their-significance-to-als-pathogenesis
#14
Davide Tavella, Jill A Zitzewitz, Francesca Massi
The human protein TDP-43 is a major component of the cellular aggregates found in amyotrophic lateral sclerosis and other neurodegenerative diseases. Insoluble cytoplasmic aggregates isolated from the brain of amyotrophic lateral sclerosis and frontotemporal lobar degeneration patients contain ubiquitinated, hyperphosphorylated, and N-terminally truncated TDP-43. Truncated fragments of TDP-43 identified from patient tissues contain part of the second RNA recognition motif (RRM2) and the disordered C-terminus, indicating that both domains can be involved in aggregation and toxicity...
September 21, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30297134/dynamic-migration-modes-of-collective-cells
#15
Shao-Zhen Lin, Sang Ye, Guang-Kui Xu, Bo Li, Xi-Qiao Feng
Collective cell migration occurs in a diversity of physiological processes such as wound healing, cancer metastasis, and embryonic morphogenesis. In the collective context, cohesive cells may move as a translational solid, swirl as a fluid, or even rotate like a disk, with scales ranging from several to dozens of cells. In this work, an active vertex model is presented to explore the regulatory roles of social interactions of neighboring cells and environmental confinements in collective cell migration in a confluent monolayer...
September 20, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30287110/the-role-of-lipid-interactions-in-simulations-of-the-%C3%AE-hemolysin-ion-channel-forming-toxin
#16
Nicholas B Guros, Arvind Balijepalli, Jeffery B Klauda
Molecular dynamics simulations were performed to describe the function of the ion-channel-forming toxin α-hemolysin (αHL) in lipid membranes that were composed of either 1,2-diphytanoyl-sn-glycero-3-phospho-choline or 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline. The simulations highlight the importance of lipid type in maintaining αHL structure and function, enabling direct comparison to experiments for biosensing applications. We determined that although the two lipids studied are similar in structure, 1,2-diphytanoyl-sn-glycero-3-phospho-choline membranes better match the hydrophobic thickness of αHL compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline membranes...
September 18, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30297133/accurate-in-silico-modeling-of-asymmetric-bilayers-based-on-biophysical-principles
#17
Milka Doktorova, Harel Weinstein
Technological advances in the last decade have enabled the study of ever more complex and physiologically relevant model membranes to help dispel the mystery surrounding the role of plasma membrane asymmetry in various cellular processes. The slowly accumulating body of experimental data is fueling renewed interest in and the need for computational methods to support interpretations and address a wide range of problems that are still not amenable to direct experimental study. The specific appeal of molecular dynamics simulations for this purpose lies in their ability to access information at atomic resolution, which is useful for the formulation of testable mechanistic hypotheses...
September 15, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30301514/effect-of-dsdna-on-the-assembly-pathway-and-mechanical-strength-of-sv40-vp1-virus-like-particles
#18
Mariska G M van Rosmalen, Chenglei Li, Adam Zlotnick, Gijs J L Wuite, Wouter H Roos
Simian virus 40 (SV40) is a possible vehicle for targeted drug delivery systems because of its low immunogenicity, high infectivity, and high transfection efficiency. To use SV40 for biotechnology applications, more information is needed on its assembly process to efficiently incorporate foreign materials and to tune the mechanical properties of the structure. We use atomic force microscopy to determine the effect of double-stranded DNA packaging, buffer conditions, and incubation time on the morphology and strength of virus-like particles (VLPs) composed of SV40 VP1 pentamers...
September 13, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30287111/internal-tensile-force-and-a2-domain-unfolding-of-von-willebrand-factor-multimers-in-shear-flow
#19
Michael Morabito, Chuqiao Dong, Wei Wei, Xuanhong Cheng, Xiaohui F Zhang, Alparslan Oztekin, Edmund Webb
Using Brownian molecular dynamics simulations, we examine the internal dynamics and biomechanical response of von Willebrand factor (vWF) multimers subject to shear flow. The coarse grain multimer description employed here is based on a monomer model in which the A2 domain of vWF is explicitly represented by a nonlinear elastic spring whose mechanical response was fit to experimental force/extension data from vWF monomers. This permits examination of the dynamic behavior of hydrodynamic forces acting on A2 domains as a function of shear rate and multimer length, as well as position of an A2 domain along the multimer contour...
September 13, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30274829/a-hidden-markov-model-for-detecting-confinement-in-single-particle-tracking-trajectories
#20
Paddy J Slator, Nigel J Burroughs
State-of-the-art single-particle tracking (SPT) techniques can generate long trajectories with high temporal and spatial resolution. This offers the possibility of mechanistically interpreting particle movements and behavior in membranes. To this end, a number of statistical techniques have been developed that partition SPT trajectories into states with distinct diffusion signatures, allowing a statistical analysis of diffusion state dynamics and switching behavior. Here, we develop a confinement model, within a hidden Markov framework, that switches between phases of free diffusion and confinement in a harmonic potential well...
September 13, 2018: Biophysical Journal
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