Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields

J Phys Chem B. 2015 Jun 25;119(25):7975-84. doi: 10.1021/acs.jpcb.5b03440. Epub 2015 Jun 15.

Abstract

Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli
  • Fluorescence Resonance Energy Transfer
  • Humans
  • Intrinsically Disordered Proteins / chemistry*
  • Models, Chemical*
  • Molecular Dynamics Simulation
  • Monte Carlo Method
  • Nuclear Pore Complex Proteins / chemistry*
  • Nuclear Pore Complex Proteins / genetics
  • Protein Conformation
  • Scattering, Small Angle
  • Solutions
  • Water / chemistry
  • X-Ray Diffraction

Substances

  • Intrinsically Disordered Proteins
  • NUP153 protein, human
  • Nuclear Pore Complex Proteins
  • Solutions
  • Water