Paper Citing NAMD - Abstract
Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery
Multibody correlations in the hydrophobic solvation of glycine peptides
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D525, DEC 14 2014
Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (Delta G(vdw)) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that G(vdw), as well as its attractive (Delta G(att)) and repulsive (Delta G(rep)) components, was not simply a linear function of A. We found that the surface tensions, gamma(rep), gamma(att), and gamma(vdw), gotten from Delta G(rep), G(att), and Delta G(vdw) against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of gamma(rep). Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the gamma(rep) for the intact decaglycines. Finally, gamma(att) for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of gamma(vdw) (-74 and -56 cal/mol/angstrom(2) for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that Delta G(vdw) favors extended rather than compact structures for decaglycine. We find that Delta G(rep) and Delta G(vdw) have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms. (C) 2014 AIP Publishing LLC.
