Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins

J Chem Theory Comput. 2017 Mar 14;13(3):1454-1461. doi: 10.1021/acs.jctc.6b01153. Epub 2017 Feb 15.

Abstract

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

MeSH terms

  • Intrinsically Disordered Proteins / chemistry*
  • Molecular Dynamics Simulation*
  • Protein Aggregates*
  • Protein Conformation
  • Protein Multimerization

Substances

  • Intrinsically Disordered Proteins
  • Protein Aggregates