A polarizable coarse-grained protein model for dissipative particle dynamics

Phys Chem Chem Phys. 2015 Oct 7;17(37):24452-61. doi: 10.1039/c5cp03479e. Epub 2015 Sep 4.

Abstract

We present a new coarse-grained polarizable protein model for dissipative particle dynamics (DPD) method. This method allows large timesteps in particle-based systems and speeds up sampling by many orders of magnitude. Our new model is based on the electrostatic polarization of the protein backbone and a detailed representation of the sidechains in combination with a polarizable water model. We define our model parameters using the experimental structures of two proteins, TrpZip2 and TrpCage. Backmapping and subsequent short replica-exchange molecular dynamics runs verify our approach and show convergence to the experimental structures on the atomistic level. We validate our model on five different proteins: GB1, the WW-domain, the B-domain of Protein A, the peripheral binding subunit and villin headpiece.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Particle Size
  • Proteins / chemistry*
  • Surface Properties
  • Water / chemistry

Substances

  • Proteins
  • Water