The gramicidin channel ion permeation free-energy profile: direct and indirect effects of CHARMM force field improvements

Interdiscip Sci. 2009 Jun;1(2):113-27. doi: 10.1007/s12539-009-0025-3.

Abstract

A revised CHARMM force field for tryptophan residues is studied as well as a new grid-based correction algorithm, called CMAP, using molecular dynamics simulations of gramicidin A (1JNO) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl or KCl saline solution. The conformational stability of the interfacial side chains is studied, which shows good stability on the 10 ns time scale. The revised force field for the tryptophan side chain produces, in the decomposition, a Na(+) PMF(Trp) profile that is consonant with the prediction from the experimental results, analyzed with rate theory by Durrant et al. (2006), but in stark contrast to the prediction of the original CHARMM force field, version 22. However, the effect is diluted in the PMF profile due to indirect effects mediated by other components of the system (polypeptide, lipid molecules, ions, and water molecules). CMAP corrections to the L-amino acids help reduce the excessive translocation barrier. Decomposition demonstrates that this effect is due to effects on the K(+) PMF(H(2)O) profile rather than on the K(+) PMF(gA) profile. The results have been confirmed to be robust using an alternative umbrella-potential method. Further force field balancing efforts (direct and indirect) are required for future studies to evaluate whether these effects give rise to predictions that are consistent with those observables extracted from real experiments.

Keywords: CMAP; Highly occupied site; Independent transport coordinate; NPAT; Potential of mean force; Relative transport coordinate; Torsion angles.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Amino Acids / chemistry
  • Biophysics / methods
  • Cations
  • Computer Simulation
  • Gramicidin / chemistry*
  • Ions*
  • Models, Molecular
  • Models, Statistical
  • Molecular Conformation
  • Sodium / chemistry
  • Software
  • Stress, Mechanical
  • Tryptophan / chemistry

Substances

  • Amino Acids
  • Cations
  • Ions
  • Gramicidin
  • Tryptophan
  • Sodium