Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution

J Chem Theory Comput. 2016 Sep 13;12(9):4390-9. doi: 10.1021/acs.jctc.6b00507. Epub 2016 Aug 29.

Abstract

An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.

MeSH terms

  • Amino Acids / chemistry
  • Capsid Proteins / chemistry
  • Capsid Proteins / metabolism
  • Dimerization
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Proteins / chemistry*
  • Proteins / metabolism
  • Static Electricity
  • Viral Proteins / chemistry
  • West Nile virus / metabolism

Substances

  • Amino Acids
  • Capsid Proteins
  • Proteins
  • Viral Proteins