The interplay between protein dynamics and frustration of non-bonded interactions as revealed by molecular dynamics simulations
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One of the fundamental challenges of physical biology is to understand the relationship between protein dynamics and function. At physiological temperatures, functional motions arise from the complex interplay of thermal motions of proteins and their envir ...
This work examines the conformational ensemble involved in beta-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, an ...
Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...
In this paper, the efficacy of structured and unstructured parameterisations of the degree of freedom within a predictive control algorithm is investigated. While several earlier papers investigated the enlargement of the region of attraction using structu ...
The biological function of a protein is strongly tied to the ensemble of three-dimensional conformations populated at physiological temperature, and dynamically transforming into each other. Experimental techniques such as nuclear magnetic resonance spectr ...
It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to pro ...
Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by comb ...
We study the equilibrium liquid structure and dynamics of dilute and concentrated bovine eye lens alpha-crystallin solutions, using small-angle X-ray scattering, static and dynamic light scattering, viscometry, molecular dynamics simulations, and mode-coup ...
Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...
The dynamics of peptide α-helices have been studied extensively for many years, and the kinetic mechanism of the helix-coil dynamics has been discussed controversially. Recent experimental results have suggested that equilibrium helix-coil dynamics are gov ...