Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.

ABSTRACT: In protein simulation or structure refinement based on values of observable quantities measured in (aqueous) solution, solvent (water) molecules may be explicitly treated, omitted, or represented by a potential of mean-solvation-force term, depending on protein coordinates only, in the force field used. These three approaches are compared for hen egg white lysozyme (HEWL). This 129-residue non-spherical protein contains a variety of secondary-structure elements, and ample experimental data are available: 1630 atom-atom Nuclear Overhauser Enhancement (NOE) upper distance bounds, 213 ³ J-couplings and 200 S² order parameters. These data are used to compare the performance of the three approaches. It is found that a molecular dynamics (MD) simulation in explicit water ap

SUBMITTER: Pechlaner M 

PROVIDER: S-EPMC9035012 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature