Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides

J Chem Theory Comput. 2022 Jul 12;18(7):4070-4076. doi: 10.1021/acs.jctc.1c01172. Epub 2022 Jun 10.

Abstract

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 five peptides. These results illustrate that these models are not usefully predictive in this context. These peptides provide a useful test set for simulation methods.

MeSH terms

  • Computer Simulation
  • Lysine*
  • Molecular Dynamics Simulation
  • Peptides* / chemistry
  • Protein Structure, Secondary
  • Solvents / chemistry
  • Thermodynamics

Substances

  • Peptides
  • Solvents
  • Lysine