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Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water?
journal contribution
posted on 2019-12-11, 16:48 authored by Shuting Zhang, Reinhard Schweitzer-Stenner, Brigita UrbancWe examine the ability of six molecular dynamics (MD)
force fields
(Amber ff14SB, Amber ff99SBnmr1, Amber ff03ws, OPLS-AA/L, OPLS-AA/M,
and CHARMM36) to reproduce conformational ensembles of the central
alanine in GAG and AAA in a way that is consistent with five (GAG)
or six (AAA) J coupling constants and amide I′
profiles. MD-derived Ramachandran plots for all six force fields under
study differ from those obtained by the Gaussian fit to experimental
data in three major ways: (i) the polyproline II (pPII) basin in the
Ramachandran plot is too concentrated, (ii) the antiparallel β
(aβ) basin is overpopulated, and (iii) the transitional β
(βt) basin is underpopulated. Amber ff14SB outperforms the other
five MD force fields and yields the highest pPII populations of the
central alanine residue in GAG (55%) and AAA (63%), in good agreement
with the predictions of the Gaussian model (59 and 76%). The analysis
of the hydration layer around the central alanine residue reveals
considerable reorientation of water molecules and reduction in both
the average number of water molecules and the average number of water–water
hydrogen bonds when glycines (in GAG) are replaced by alanines (in
AAA), elucidating water-mediated nearest neighbor effects on alanine’s
conformational dynamics.