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Advances in molecular simulations of protein mechanical properties and function

Abstract (Expand)

Single-molecule force spectroscopy and classical molecular dynamics are natural allies. Recent advances in both experiments and simulations have increasingly facilitated a direct comparison of SMFS and … MD data, most importantly by closing the gap between time scales, which has been traditionally at least 5 orders of magnitudes wide. In this review, we will explore these advances chiefly on the computational side. We focus on protein dynamics under force and highlight recent studies that showcase how lower loading rates and more statistics help to better interpret previous experiments and to also motivate new ones. At the same time, steadily increasing system sizes are used to mimic more closely the mechanical environment in the biological context. We showcase some of these advances on atomistic and coarse-grained scale, from asymmetric membrane tension to larger (multidomain/multimeric) protein assemblies under force.

Authors: Florian Franz, Csaba Daday, Frauke Gräter

Date Published: 1st Apr 2020

Publication Type: Journal

Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins

Abstract

Not specified

Authors: Benedikt Rennekamp, Fabian Kutzki, Agnieszka Obarska-Kosinska, Christopher Zapp, Frauke Gräter

Date Published: 16th Jan 2020

Publication Type: Journal

The plakin domain of C. elegans VAB-10/plectin acts as a hub in a mechanotransduction pathway to promote morphogenesis

Abstract

Not specified

Authors: Shashi Kumar Suman, Csaba Daday, Teresa Ferraro, Thanh Vuong-Brender, Saurabh Tak, Sophie Quintin, François Robin, Frauke Gräter, Michel Labouesse

Date Published: 13th Dec 2019

Publication Type: Journal

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.

Abstract (Expand)

Networks describe how parts associate with each other to form integrated systems which often have modular and hierarchical structure. In biology, network growth involves two processes, one that unifies … and the other that diversifies. Here, we propose a biphasic (bow-tie) theory of module emergence. In the first phase, parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are often selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In the second phase, variants of the modules diversify and become new parts for a new generative cycle of higher level organization. The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels. Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism, elementary functionomes, and protein domain organization.

Authors: Gustavo Caetano-Anollés, M Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés

Date Published: 5th Sep 2019

Publication Type: Journal

A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data

Abstract

Not specified

Authors: Yuwei Zhang, Kelin Xia, Zexing Cao, Frauke Gräter, Fei Xia

Date Published: 15th May 2019

Publication Type: Journal

Molecular Dynamics Simulations of Molecules in Uniform Flow

Abstract (Expand)

Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of … flow on molecules, we present uniform-flow molecular dynamics simulations at atomic level. The pull module of the GRoningen MAchine for Chemical Simulations package was extended to be able to force-group atoms within a defined layer of the simulation box. Application of this external enforcement to explicit water molecules, together with the coupling to a thermostat, led to a uniform terminal velocity of the solvent water molecules. We monitored the density of the whole system to establish the conditions under which the simulated flow is well-behaved. A maximal velocity of 1.3 m/s can be generated if a pull slice of 8 nm is used, and high velocities would require larger pull slices to still maintain a stable density. As expected, the target velocity increases linearly with the total external force applied. Finally, we suggest an appropriate setup to stretch a protein by uniform flow, in which protein extensions depend on the flow conditions. Our implementation provides an efficient computational tool to investigate the effect of the flow at the molecular level.

Authors: Ana M. Herrera-Rodríguez, Vedran Miletić, Camilo Aponte-Santamaría, Frauke Gräter

Date Published: 1st May 2019

Publication Type: Journal

How Fast Is Too Fast in Force-Probe Molecular Dynamics Simulations?

Abstract

Not specified

Authors: Steven Sheridan, Frauke Gräter, Csaba Daday

Date Published: 19th Apr 2019

Publication Type: Journal

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