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Title: Structure and dynamics of water in crowded environments slows down peptide conformational changes

Abstract

The concentration of macromolecules inside the cell is high with respect to conventional in vitro experiments or simulations. In an effort to characterize the effects of crowding on the thermodynamics and kinetics of disordered peptides, molecular dynamics simulations were run at different concentrations by varying the number of identical weakly interacting peptides inside the simulation box. We found that the presence of crowding does not influence very much the overall thermodynamics. On the other hand, peptide conformational dynamics was found to be strongly affected, resulting in a dramatic slowing down at larger concentrations. The observation of long lived water bridges between peptides at higher concentrations points to a nontrivial role of the solvent in the altered peptide kinetics. Our results reinforce the idea for an active role of water in molecular crowding, an effect that is expected to be relevant for problems influenced by large solvent exposure areas like in intrinsically disordered proteins.

Authors:
; ;  [1]
  1. Freiburg Institute for Advanced Studies, School of Soft Matter Research, Albertstrasse 19, 79104 Freiburg im Breisgau (Germany)
Publication Date:
OSTI Identifier:
22419970
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 141; Journal Issue: 4; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; IN VITRO; KINETICS; MOLECULAR DYNAMICS METHOD; PEPTIDES; SIMULATION; SOLVENTS

Citation Formats

Lu, Cheng, Prada-Gracia, Diego, and Rao, Francesco, E-mail: francesco.rao@frias.uni-freiburg.de. Structure and dynamics of water in crowded environments slows down peptide conformational changes. United States: N. p., 2014. Web. doi:10.1063/1.4891465.
Lu, Cheng, Prada-Gracia, Diego, & Rao, Francesco, E-mail: francesco.rao@frias.uni-freiburg.de. Structure and dynamics of water in crowded environments slows down peptide conformational changes. United States. doi:10.1063/1.4891465.
Lu, Cheng, Prada-Gracia, Diego, and Rao, Francesco, E-mail: francesco.rao@frias.uni-freiburg.de. Mon . "Structure and dynamics of water in crowded environments slows down peptide conformational changes". United States. doi:10.1063/1.4891465.
@article{osti_22419970,
title = {Structure and dynamics of water in crowded environments slows down peptide conformational changes},
author = {Lu, Cheng and Prada-Gracia, Diego and Rao, Francesco, E-mail: francesco.rao@frias.uni-freiburg.de},
abstractNote = {The concentration of macromolecules inside the cell is high with respect to conventional in vitro experiments or simulations. In an effort to characterize the effects of crowding on the thermodynamics and kinetics of disordered peptides, molecular dynamics simulations were run at different concentrations by varying the number of identical weakly interacting peptides inside the simulation box. We found that the presence of crowding does not influence very much the overall thermodynamics. On the other hand, peptide conformational dynamics was found to be strongly affected, resulting in a dramatic slowing down at larger concentrations. The observation of long lived water bridges between peptides at higher concentrations points to a nontrivial role of the solvent in the altered peptide kinetics. Our results reinforce the idea for an active role of water in molecular crowding, an effect that is expected to be relevant for problems influenced by large solvent exposure areas like in intrinsically disordered proteins.},
doi = {10.1063/1.4891465},
journal = {Journal of Chemical Physics},
number = 4,
volume = 141,
place = {United States},
year = {Mon Jul 28 00:00:00 EDT 2014},
month = {Mon Jul 28 00:00:00 EDT 2014}
}
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