Simulations of the role of water in the protein- folding mechanism

  • Rhee Y
  • Sorin E
  • Jayachandran G
 et al. 
  • 18

    Readers

    Mendeley users who have this article in their library.
  • N/A

    Citations

    Citations of this article.

Abstract

There are many unresolved questions regarding the role of water in protein folding. Does water merely induce hydrophobic forces, or does the discrete nature of water play a structural role in folding? Are the nonadditive aspects of water important in determining the folding mechanism? To help to address these questions, we have performed simulations of the folding of a model protein (BBA5) in explicit solvent. Starting 10,000 independent trajectories from a fully unfolded conformation, we have observed numerous folding events, making this work a comprehensive study of the kinetics of protein folding starting from the unfolded state and reaching the folded state and with an explicit solvation model and experimentally validated rates. Indeed, both the raw TIP3P folding rate (4.5 {Â}{\}pm2.5 {Â}µs) and the diffusion-constant corrected rate (7.5 {Â}{\}pm4.2 {Â}µs) are in strong agreement with the experimentally observed rate of 7.5 {Â}{\}pm3.5 {Â}µs. To address the role of water in folding, the mechanism is compared with that predicted from implicit solvation simulations. An examination of solvent density near hydrophobic groups during folding suggests that in the case of BBA5, there are water-induced effects not captured by implicit solvation models, including signs of a {\}tt"concurrent mechanism{\}tt" of core collapse and desolvation.

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document

Authors

  • Young Min Rhee

  • Eric J Sorin

  • Guha Jayachandran

  • Erik Lindahl

  • Vijay S Pande

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free