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.affiliation: Freiburg Institute for Advanced Studies, School of Soft Matter Research, Albertstrasse 19, 79104 Freiburg im Breisgau, Germany.
authors.forename: Cheng
authors.initials: C
authors.lastname: Lu
authors.affiliation: Freiburg Institute for Advanced Studies, School of Soft Matter Research, Albertstrasse 19, 79104 Freiburg im Breisgau, Germany.
authors.forename: Diego
authors.initials: D
authors.lastname: Prada-Gracia
authors.affiliation: Freiburg Institute for Advanced Studies, School of Soft Matter Research, Albertstrasse 19, 79104 Freiburg im Breisgau, Germany.
authors.forename: Francesco
authors.initials: F
authors.lastname: Rao
mesh_terms: D006860:Hydrogen Bonding; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D010455:Peptides; D012997:Solvents; D014867:Water