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https://www.readbyqxmd.com/read/29135465/thermally-activated-trp-channels-molecular-sensors-for-temperature-detection
#1
Karen Castillo, Ignacio Diaz-Franulic, Jonathan Canan, Fernando Gonzalez-Nilo, Ramon Latorre
Temperature sensing is one of the most ancient capabilities of living organisms and is essential to sustain life, because failures in avoiding extreme noxious temperatures can result in tissue damage or death. A subset of members of the transient receptor potential (TRP) ion channel family is finely tuned to detect temperatures ranging from extreme cold to noxious heat, giving rise to thermoTRP channels. Structural and functional experiments have shown that thermoTRP channels are allosteric proteins, containing different domains that sense changes in temperature, among other stimuli, triggering pore opening...
November 14, 2017: Physical Biology
https://www.readbyqxmd.com/read/29116056/excess-area-dependent-scaling-behavior-of-nano-sized-membrane-tethers
#2
Ramakrishnan Natesan, K K Sreeja, Arpita Roychoudhuri, David M Eckmann, Portonovo S Ayyaswamy, Tobias Baumgart, Thomas Pucadyil, Shivprasad Vitthal Patil, Valerie M Weaver, Ravi Radhakrishnan
Thermal fluctuations in cell membranes manifest as an excess area (Aex) which governs a multitude of physical process at the sub-micron scale. We present a theoretical framework, based on an in silico tether pulling method, which may be used to reliably estimate Aex in live cells. We perform our simulations in two different thermodynamic ensembles: (i) the constant projected area and (ii) the constant frame tension ensembles and show the equivalence of our results in the two. The tether forces estimated from our simulations compare well with our experimental measurements for tethers extracted from ruptured GUVs and HeLa cells...
November 8, 2017: Physical Biology
https://www.readbyqxmd.com/read/29116053/elastic-strain-and-twist-analysis-of-protein-structural-data-and-allostery-of-the-transmembrane-channel-kcsa
#3
Michael Robert Mitchell, Stanislas Leibler
The abundance of available protein static structural data makes more effective analysis and interpretation of this data a valuable tool to supplement experimental study of protein mechanics. Structural displacements can be difficult to analyze and interpret. Previously, we showed that strains provide a more natural and interpretable representation of protein deformations, revealing mechanical coupling between spatially distinct sites of allosteric proteins. Here, we demonstrate that other transformations of displacements yield additional insights...
November 8, 2017: Physical Biology
https://www.readbyqxmd.com/read/29091050/bottom-up-synthetic-biology-modular-design-for-making-artificial-platelets
#4
Sagardip Majumder, Allen P Liu
Engineering artificial cells to mimic one or multiple fundamental cell biological functions is an emerging area of synthetic biology. Reconstituting functional modules from biological components in vitro is a challenging yet an important essence of bottom-up synthetic biology. Here we describe the concept of building artificial platelets using bottom-up synthetic biology and the four functional modules that together could enable such an ambitious effort.
November 1, 2017: Physical Biology
https://www.readbyqxmd.com/read/29091048/role-of-contact-inhibition-of-locomotion-and-junctional-mechanics-in-epithelial-collective-responses-to-injury
#5
Luke Coburn, Hender Lopez, Irin-Maya Schouwenaar, Alpha Yap, Vladimir Lobaskin, Guillermo Gomez
Epithelial tissues form physically integrated barriers against the external environment protecting organs from infection and invasion. Within each tissue, epithelial cells respond to different challenges that can potentially compromise tissue integrity. In particular, cells collectively respond to injuries by reorganizing their cell-cell junctions and migrating directionally towards the sites of damage. Notwithstanding, the mechanisms that drive collective responses in epithelial aggregates remain poorly understood...
November 1, 2017: Physical Biology
https://www.readbyqxmd.com/read/29058683/cooperative-mechanosensitivity-and-allostery-of-focal-adhesion-clusters
#6
Darryl C W Foo, Eugene Terentjev
We analyse a role of cooperative interaction between neighbouring adhesion-mechanosensor complexes by constructing an Ising-like Hamiltonian describing the free energy of cell adhesion on a substrate as a lattice of 3-state mechanosensing sites involving focal adhesion kinase (FAK). We use Monte Carlo stochastic algorithm to find equilibrium configurations of these mechanosensors in two representative geometries: on a 1D ring representing the rim of a cell on flat surface, and a 2D bounded surface representing the whole area of cell contact with flat surface...
October 23, 2017: Physical Biology
https://www.readbyqxmd.com/read/29035272/binding-stability-of-peptides-on-major-histocompatibility-complex-class-i-proteins-role-of-entropy-and-dynamics
#7
Ahmet Gul, Burak Erman
Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: Peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies...
October 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28980528/a-passive-physical-model-for-dnak-chaperoning
#8
Lionel Uhl, Sam Dukan, Audrey Dumont
Almost all living organisms use protein chaperones with a view to preventing proteins from misfolding or aggregation either spontaneously or during cellular stress. This work uses a reaction-diffusion stochastic model to describe the dynamic localization of the Hsp70 chaperone DnaK in E. coli cells during transient proteotoxic collapse characterized by the accumulation of insoluble proteins. In the model, misfolded ("abnormal") proteins are produced during alcoholic stress and have the propensity to aggregate with a polymerization like kinetics...
October 5, 2017: Physical Biology
https://www.readbyqxmd.com/read/28976365/cellular-reprogramming-dynamics-follow-a-simple-one-dimensional-reaction-coordinate
#9
Sai Teja Pusuluri, Alex H Lang, Pankaj Mehta, Horacio Castillo
Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an open problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple one-dimensional reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used...
October 4, 2017: Physical Biology
https://www.readbyqxmd.com/read/28976363/physical-root-soil-interactions
#10
Evelyne Kolb, Valérie Legue, Marie-Béatrice Bogeat-Triboulot
Plant root system development is highly modulated by the physical properties of the soil and especially by its mechanical resistance to penetration. The interplay between the mechanical stresses exerted by the soil and root growth is of particular interest for many communities, in agronomy and soil science as well as in biomechanics and plant morphogenesis. In contrast to shoots, roots apices must exert a growth pressure to penetrate strong soils and reorient their growth trajectory to cope with obstacles like stones or hardpans or to follow the tortuous paths of the soil porosity...
October 4, 2017: Physical Biology
https://www.readbyqxmd.com/read/28976354/exciton-transport-in-the-pe545-complex-insight-from-atomistic-qm-mm-based-quantum-master-equations-and-elastic-network-models
#11
Sima Pouyandeh, Stefano Iubini, Sandro Jurinovich, Yasser Omar, Benedetta Mennucci, Francesco Piazza
In this paper we work out a parameterization of the environment noise within the Haken-Strobl-Reinenker (HSR) model for the PE545 light-harvesting complex based on atomic-level quantum mechanics/molecular mechanics (QM/MM) simulations. We use this approach to investigate the role of different auto- and cross-correlations in the HSR noise tensor, confirming that site-energy autocorrelations (pure dephasing) terms dominate the noise-induced exciton mobility enhancement, followed by site energy-coupling cross-correlations for specific triplets of pigments...
October 4, 2017: Physical Biology
https://www.readbyqxmd.com/read/28944767/reply-to-comment-on-the-cancer-warburg-effect-may-be-a-testable-example-of-the-minimum-entropy-production-rate-principle
#12
Bartolome Sabater, Dolores Marín
We point that the minimum rate theorem [3] refers to internal entropy production (ΔSi), here calculated for the chemical reaction in the open cell system. We also point that In the steady-state open system the constant supply of glucose makes equivalent the minimum rate of entropy production per unit of time to the minimum rate of production of entropy per mole of glucose.
September 25, 2017: Physical Biology
https://www.readbyqxmd.com/read/28944760/comment-on-the-cancer-warburg-effect-may-be-a-testable-example-of-the-minimum-entropy-production-rate-principle
#13
Mostafa Sadeghi Ghuchani
Marín and Sabater have estimated the entropy production of cancer cells and compared it to that of normal cells. They estimated that cancer cells produce 10 percent less entropy per mole of glucose in comparison to normal cells and concluded that it may accomplish the minimum entropy production theorem of Prigogine. However, according to previously published papers, it seems that there are two errors both in the method of estimation and conclusion. .
September 25, 2017: Physical Biology
https://www.readbyqxmd.com/read/28914615/apoptosis-generates-mechanical-forces-that-close-the-lens-vesicle-in-the-chick-embryo
#14
Alina Oltean, Larry A Taber
During the initial stages of eye development, optic vesicles grow laterally outward from both sides of the forebrain and come into contact with the surrounding surface ectoderm (SE). Within the region of contact, these layers then thicken locally to create placodes and invaginate to form the optic cup (primitive retina) and lens vesicle (LV), respectively. This paper examines the biophysical mechanisms involved in LV formation, which consists of three phases: (1) lens placode formation; (2) invagination to create the lens pit (LP); and (3) closure to form a complete ellipsoidally shaped LV...
September 15, 2017: Physical Biology
https://www.readbyqxmd.com/read/28862157/modelling-the-collective-response-of-heterogeneous-cell-populations-to-stationary-gradients-and-chemical-signal-relay
#15
Miguel Pineda, Raluca Eftimie
The directed motion of cell aggregates toward a chemical source occurs in many relevant biological processes. Understanding the mechanisms that control this complex behavior is of great relevance for our understanding of developmental biological processes and many diseases. In this paper, we consider a self-propelled particle model for the movement of heterogeneous subpopulations of chemically interacting cells towards an imposed stable chemical gradient. Our simulations show explicitly how self-organisation of cell populations (which could lead to engulfment or complete cell segregation) can arise from the heterogeneity of chemotactic responses alone...
September 1, 2017: Physical Biology
https://www.readbyqxmd.com/read/28862154/stalk-length-dependence-of-the-contractility-of-i-vorticella-convallaria-i
#16
Eun Gul Chung, Sangjin Ryu
<i>Vorticella convallaria</i> is a sessile protozoan of which the spasmoneme contracts on a millisecond timescale. Because this contraction is induced and powered by the binding of calcium ions (Ca<sup>2+</sup>), the spasmoneme showcases Ca<sup>2+</sup>-powered cellular motility. Because the isometric tension of <i>V. convallaria</i> increases linearly with its stalk length, it is hypothesized that the contractility of <i>V. convallaria</i> during unhindered contraction depends on the stalk length...
September 1, 2017: Physical Biology
https://www.readbyqxmd.com/read/29098989/an-application-of-the-krylov-fsp-ssa-method-to-parameter-fitting-with-maximum-likelihood
#17
Khanh N Dinh, Roger B Sidje
Monte Carlo methods such as the stochastic simulation algorithm (SSA) have traditionally been employed in gene regulation problems. However, there has been increasing interest to directly obtain the probability distribution of the molecules involved by solving the chemical master equation (CME). This requires addressing the curse of dimensionality that is inherent in most gene regulation problems. The finite state projection (FSP) seeks to address the challenge and there have been variants that further reduce the size of the projection or that accelerate the resulting matrix exponential...
November 3, 2017: Physical Biology
https://www.readbyqxmd.com/read/28825411/luria-delbr%C3%A3-ck-revisited-the-classic-experiment-does-not-rule-out-lamarckian-evolution
#18
Caroline M Holmes, Mahan Ghafari, Anzar Abbas, Varun Saravanan, Ilya Nemenman
We re-examined data from the classic Luria-Delbrück fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms (as would happen for bacteria with CRISPR-Cas immunity). Analysis of the combined model was not performed in the original 1943 paper...
August 21, 2017: Physical Biology
https://www.readbyqxmd.com/read/28698411/estimation-of-turgor-pressure-through-comparison-between-single-plant-cell-and-pressurized-shell-mechanics
#19
P Durand-Smet, E Gauquelin, N Chastrette, A Boudaoud, A Asnacios
While plant growth is well known to rely on turgor pressure, it is challenging to quantify the contribution of turgor pressure to plant cell rheology. Here we used a custom-made micro-rheometer to quantify the viscoelastic behavior of isolated plant cells while varying their internal turgor pressure. To get insight into how plant cells adapt their internal pressure to the osmolarity of their medium, we compared the mechanical behavior of single plant cells to that of a simple, passive, pressurized shell: a soccer ball...
August 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28675379/non-steady-state-mass-action-dynamics-without-rate-constants-dynamics-of-coupled-reactions-using-chemical-potentials
#20
William R Cannon, Scott E Baker
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants...
August 16, 2017: Physical Biology
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