Top 8 Biorxiv Papers Today in Biophysics


2.016 Mikeys
#1. GPCRmd uncovers the dynamics of the 3D-GPCRome
Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, Johanna K.S. Tiemann, David Aranda-García, Juan Manuel Ramírez-Anguita, Tomasz Maciej Stepniewski, Nathalie Worp, Alejandro Varela-Rial, Adrián Morales-Pastor, Brian Medel Lacruz, Gáspár Pándy-Szekeres, Eduardo Mayol, Rasmus Fonseca, Toni Giorgino, Jens Carlsson, Xavier Deupi, Slawomir Filipek, José Carlos Gómez-Tamayo, Angel Gonzalez, Hugo Gutierrez-de-Teran, Mireia Jimenez, Willem Jespers, Jon Kapla, Peter Kolb, Dorota Latek, Maria Marti-Solano, Pierre Matricon, Minos-Timotheos Matsoukas, Przemyslaw Miszta, Mireia Olivella, Laura Perez-Benito, Santiago Ríos, Iván Rodríguez-Torrecillas, Jessica Sallander, Agnieszka Sztyler, Silvana Vasile, Peter W. Hildebrand, Gianni De Fabritiis, David E. Gloriam, Arnau Cordomi, Ramon Guixà-González, Jana Selent
G protein-coupled receptors (GPCRs) are involved in numerous physiological processes and the most frequent targets of approved drugs. The striking explosion in the number of new 3D molecular structures of GPCRs (3D-GPCRome) during the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. While experimentally-resolved structures undoubtedly provide valuable snapshots of specific GPCR conformational states, they give only limited information on their flexibility and dynamics associated with function. Molecular dynamics (MD) simulations have become a widely established technique to explore the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations requires efficient storage resources and specialized software, hence limiting the dissemination of these data to specialists in the field. Here we present the GPCRmd, an online platform with web-based visualization capabilities and a comprehensive analysis toolbox that...
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GPCRmd: RT @biorxivpreprint: GPCRmd uncovers the dynamics of the 3D-GPCRome https://t.co/aRaJBthnEL #bioRxiv
giorginolab: RT @biorxivpreprint: GPCRmd uncovers the dynamics of the 3D-GPCRome https://t.co/aRaJBthnEL #bioRxiv
Github

System building protocol for GPCRmd molecular dynamics

Repository: MD-protocol
User: GPCRmd
Language: Rich Text Format
Stargazers: 2
Subscribers: 1
Forks: 0
Open Issues: 0
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Authors: 42
Total Words: 8860
Unqiue Words: 2710

2.009 Mikeys
#2. Effects of coral colony morphology on turbulent flow dynamics
MD MONIR HOSSAIN, ANNE E. STAPLES
Local flow dynamics play a central role in physiological processes like respiration and nutrient uptake in coral reefs. Despite the importance of corals as hosts to a quarter of all marine life, and the pervasive threats currently facing corals, little is known about the detailed hydrodynamics of branching coral colonies. Here, in order to investigate the effects of the colony branch density and surface roughness on the local flow field, three-dimensional simulations were performed using immersed boundary, large-eddy simulations for four different colony geometries under low and high unidirectional oncoming flow conditions. The first two colonies were from the Pocillopora genus, one with a densely branched geometry, and one with a comparatively loosely branched geometry. The second pair of colony geometries were derived from a scan of a single Montipora capitata colony, one with the verrucae covering the surface intact, and one with the verrucae removed. We found that the mean velocity profiles in the densely branched colony...
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biorxivpreprint: Effects of coral colony morphology on turbulent flow dynamics https://t.co/cfFmjp8NjW #bioRxiv
biorxiv_biophys: Effects of coral colony morphology on turbulent flow dynamics https://t.co/Dk7FmiX1pI #biorxiv_biophys
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Sample Sizes : [6]
Authors: 2
Total Words: 11714
Unqiue Words: 2834

2.006 Mikeys
#3. Uncovering patterns of atomic interactions in static and dynamic structures of proteins
A. J. Venkatakrishnan, Rasmus Fonseca, Anthony K Ma, Scott A Hollingsworth, Augustine Chemparathy, Daniel Hilger, Albert J. Kooistra, Ramin Ahmari, M. Madan Babu, Brian K. Kobilka, Ron Dror
The number of structures and molecular dynamics simulations of proteins is exploding owing to dramatic advances in cryo-electron microscopy, crystallography, and computing. One of the most powerful ways to analyze structural information involves comparisons of interatomic interactions across different structures or simulations of the same protein or related proteins from the same family (e.g. different GPCRs). Such comparative analyses are of interest to a wide range of researchers but currently prove challenging for all but a few. To facilitate comparative structural analyses, we have developed tools for (i) rapidly computing and comparing interatomic interactions and (ii) interactively visualizing interactions to enable structure-based interpretations. Using these tools, we have developed the Contact Comparison Atlas, a web-based resource for the comparative analysis of interactions in structures and simulations of proteins. Using the Contact Comparison Atlas and our tools, we have identified patterns of interactions with...
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kentgorday: RT @biorxiv_biophys: Uncovering patterns of atomic interactions in static and dynamic structures of proteins https://t.co/UF57MBlqgj #bior…
dkumar02: RT @biorxiv_biophys: Uncovering patterns of atomic interactions in static and dynamic structures of proteins https://t.co/UF57MBlqgj #bior…
FonsecaRasmus: RT @biorxivpreprint: Uncovering patterns of atomic interactions in static and dynamic structures of proteins https://t.co/s9upQ0PwdB #bioR…
Premkumar009: RT @biorxiv_biophys: Uncovering patterns of atomic interactions in static and dynamic structures of proteins https://t.co/UF57MBlqgj #bior…
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2.0 Mikeys
#4. Visualization of the HIV-1 Env Glycan Shield Across Scales
Zachary T Berndsen, Srirupa Chakraborty, Xiaoning Wang, Christopher A Cottrell, Jonathan L Torres, Jolene K Diedrich, Cesar Lopez, John Robert Yates, Marit J van-Gils, James C. Paulson, S. Gnanakaran, Andrew B Ward
The dense array of N-linked glycans on the HIV-1 Envelope Glycoprotein (Env), known as the "glycan shield", is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure-function analysis. Here we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM) and computational modeling to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of inter-glycan interactions and drive higher-order structuring within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and provides a mapping of potentially immunogenic sites on Env. Analysis of the same Env across a range of glycosylation states revealed that subtle changes in glycan occupancy, composition, and dynamics can impact glycan shield structure and epitope accessibility. We also performed site-specific mass-spectrometry analysis on the same samples and show how cryo-EM can complement such studies. Finally, we...
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Tweets
biorxivpreprint: Visualization of the HIV-1 Env Glycan Shield Across Scales https://t.co/bIy1FLIKGB #bioRxiv
biorxiv_biophys: Visualization of the HIV-1 Env Glycan Shield Across Scales https://t.co/h5GTvvyn39 #biorxiv_biophys
cryoEM_Papers: Visualization of the HIV-1 Env Glycan Shield Across Scales https://t.co/N7kctihx0M
chrashwood: RT @biorxivpreprint: Visualization of the HIV-1 Env Glycan Shield Across Scales https://t.co/bIy1FLIKGB #bioRxiv
TomislavCaval: RT @biorxivpreprint: Visualization of the HIV-1 Env Glycan Shield Across Scales https://t.co/bIy1FLIKGB #bioRxiv
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1.998 Mikeys
#5. Adhesion modulates cell morphology and migration within dense fibrous networks
Maurício Moreira-Soares, Susana P Cunha, José Rafael Bordin, Rui D M Travasso
One of the most fundamental abilities required for the sustainability of complex life forms is active cell migration, since it is essential in diverse processes from morphogenesis to leukocyte chemotaxis in immune response. The movement of a cell is the result of intricate mechanisms, that involve the coordination between mechanical forces, biochemical regulatory pathways and environmental cues. In particular, epithelial cancer cells have to employ mechanical strategies in order to migrate through the tissue's basement membrane and infiltrate the bloodstream during the invasion stage of metastasis. In this work we explore how mechanical interactions such as spatial restriction and adhesion affect migration of a self-propelled droplet in dense fibrous media. We have performed a systematic analysis using a phase-field model and we propose a novel approach to simulate cell migration with Dissipative Particle Dynamics (DPD) modelling. With this purpose we have measured the cell's velocity and quantified its morphology as a function of...
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biorxivpreprint: Adhesion modulates cell morphology and migration within dense fibrous networks https://t.co/DXDg1PNYC7 #bioRxiv
biorxiv_biophys: Adhesion modulates cell morphology and migration within dense fibrous networks https://t.co/akXfI7VRVK #biorxiv_biophys
1stDarwin: RT @biorxivpreprint: Adhesion modulates cell morphology and migration within dense fibrous networks https://t.co/DXDg1PNYC7 #bioRxiv
maurice_moreira: RT @biorxivpreprint: Adhesion modulates cell morphology and migration within dense fibrous networks https://t.co/DXDg1PNYC7 #bioRxiv
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Authors: 4
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1.998 Mikeys
#6. Proposed mechanism of kinesin backstepping
Algirdas Toleikis, Nicholas John Carter, Robert Anthony Cross
Kinesins are molecular motors that walk along microtubules, hauling cargo through the crowded cytoplasm of eukaryotic cells. At low load, kinesins almost always step towards microtubule plus ends, but at high load, forward stepping slows down and backsteps appear. Current models envisage that backsteps occur by directional reversal of the forwards walking mechanism. Here we report to the contrary, that at substall forces, kinesin steps back using a rescued detachment mechanism. We show (1) that dwell times for forward steps are shorter, on average, than dwell times for backsteps or detachments (2) that dwell times for backsteps and detachments are indistinguishable and (3) that the balance of backsteps and detachments can be tilted dramatically, without affecting forward steps. All three points hold not only for kinesin stepping on brain GDP-taxol MTs, but also for brain GDP MTs, brain GMPCPP-epothilone MTs, S. pombe GMPCPP-epothilone MTs and subtilisin-treated GDP-taxol MTs. Our data establish that forward steps originate from a...
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Authors: 3
Total Words: 6074
Unqiue Words: 1784

1.997 Mikeys
#7. Computational analysis of filament polymerization dynamics in cytoskeletal networks
Paul Caldas, Philipp Radler, Christoph Sommer, Martin Loose
The polymerization-depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a non-biased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living...
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ma63713534: RT @biorxivpreprint: Computational analysis of filament polymerization dynamics in cytoskeletal networks https://t.co/3JRN4ohw8W #bioRxiv
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1.997 Mikeys
#8. Same Equilibrium. Different Kinetics. Protein Functional Consequences.
Sonja Schmid, Thorsten Hugel
In a living cell, protein function is regulated in several ways, including post-translational modifications (PTMs), protein-protein interaction, or by the global environment, e.g. by crowding or phase separation. While site-specific PTMs act very locally on the protein, specific protein interactions typically affect larger (sub-)domains, and global changes affect the whole protein non-specifically. Herein, we directly observe protein regulation with three different degrees of localization, and present the effect on the Hsp90 chaperone system on the level of conformational equilibria, kinetics and protein function. Interestingly, we find by single-molecule FRET that similar functional and conformational steady-state observations are caused by completely different underlying kinetics. Solving the complete kinetic rate model allows us to disentangle specific and non-specific effects controlling Hsp90's ATPase function, which has remained puzzling up to date. Lastly, we introduce a new mechanistic concept: functional stimulation...
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