Intrinsic Conformational Dynamics of Glycine and Alanine in Polarizable Molecular Dynamics Force Fields: Comparison to Spectroscopic Data.

ABSTRACT: Molecular dynamics (MD) is a great tool for elucidating conformational dynamics of proteins and peptides in water at the atomistic level that often surpasses the level of detail available experimentally. Structure predictions, however, are limited by the accuracy of the underlying MD force field. This limitation is particularly stark in the case of intrinsically disordered peptides and proteins, which are characterized by solvent-accessible and disordered peptide regions and domains. Recent studies show that most additive MD force fields, including CHARMM36m, do not reproduce the intrinsic conformational distributions of guest amino acid residues x in cationic GxG peptides in water in line with experimental data. Positing that a lack of polarizability in additive MD force fields may be the

SUBMITTER: Andrews B 

PROVIDER: S-EPMC11215781 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature