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

TitleStudying the role of cooperative hydration in stabilizing folded protein states.
Publication TypeJournal Article
Year of Publication2016
AuthorsHuggins DJ
JournalJ Struct Biol
Volume196
Issue3
Pagination394-406
Date Published2016 12
ISSN1095-8657
KeywordsAmino Acid Sequence, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Molecular Dynamics Simulation, Peptide Fragments, Protein Folding, Protein Stability, Protein Structure, Tertiary, Proteins, Salts, Thermodynamics, Water
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.

DOI10.1016/j.jsb.2016.09.003
Alternate JournalJ Struct Biol
PubMed ID27633532
PubMed Central IDPMC5131609
Grant ListMR/L007266/1 / / Medical Research Council / United Kingdom