Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides.
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ABSTRACT:
SUBMITTER: Lang EJM
PROVIDER: S-EPMC9281390 | biostudies-literature | 2022 Jul
REPOSITORIES: biostudies-literature
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Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of <i>De Novo</i> Designed Glu/Lys Peptides.
Lang Eric J M EJM Baker Emily G EG Woolfson Derek N DN Mulholland Adrian J AJ
Journal of chemical theory and computation 20220610 7
We test a range of standard generalized Born (GB) models and protein force fields for a set of five experimentally characterized, designed peptides comprising alternating blocks of glutamate and lysine, which have been shown to differ significantly in α-helical content. Sixty-five combinations of force fields and GB models are evaluated in >800 μs of molecular dynamics simulations. GB models generally do not reproduce the experimentally observed α-helical content, and none perform well for all f ...[more]
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