Repository logo
 

Studying the role of cooperative hydration in stabilizing folded protein states.

Published version
Peer-reviewed

Change log

Authors

Huggins, David J 

Abstract

Understanding and modelling protein folding remains a key scientific and engineering challenge. Two key questions in protein folding are (1) why many proteins adopt a folded state and (2) how these proteins transition from the random coil ensemble to a folded state. In this paper we employ molecular dynamics simulations to address the first of these questions. Computational methods are well-placed to address this issue due to their ability to analyze systems at atomic-level resolution. Traditionally, the stability of folded proteins has been ascribed to the balance of two types of intermolecular interactions: hydrogen-bonding interactions and hydrophobic contacts. In this study, we explore a third type of intermolecular interaction: cooperative hydration of protein surface residues. To achieve this, we consider multiple independent simulations of the villin headpiece domain to quantify the contributions of different interactions to the energy of the native and fully extended states. In addition, we consider whether these findings are robust with respect to the protein forcefield, the water model, and the presence of salt. In all cases, we identify many cooperatively hydrated interactions that are transient but energetically favor the native state. Whilst further work on additional protein structures, forcefields, and water models is necessary, these results suggest a role for cooperative hydration in protein folding that should be explored further. Rational design of cooperative hydration on the protein surface could be a viable strategy for increasing protein stability.

Description

Keywords

Hydration, Molecular dynamics, Protein folding, Amino Acid Sequence, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Molecular Dynamics Simulation, Peptide Fragments, Protein Folding, Protein Stability, Protein Structure, Tertiary, Proteins, Salts, Thermodynamics, Water

Journal Title

J Struct Biol

Conference Name

Journal ISSN

1047-8477
1095-8657

Volume Title

196

Publisher

Elsevier BV
Sponsorship
Medical Research Council (MR/L007266/1)
Work in DJH’s lab was supported by the Medical Research Council (MRC) under grant ML/L007266/1. We thank Arno Proeme for porting the Solvaware package to ARCHER as part of the EPSRC embedded computational science and engineering grant eCSE03-3.