Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20.

摘要: Here, we perform structural, thermodynamic, and kinetics tests of the Kirkwood-Buff-derived force field, KBFF20, for peptides proteins developed in previous article. The physical/structural measure ability KBFF20 to capture experimental J-couplings small peptides, keep globular monomeric oligomeric folded, produce experimentally relevant expanded conformational ensembles intrinsically disordered proteins. thermodynamic-based probe KBFF20's quantify preferential interactions sodium chloride around native β-lactoglobulin urea lysozyme, reproduce melting curves helix- sheet-based fold Trp-cage Villin. kinetics-based how well can match contact formation rates small, repeat-sequence variable lengths rotational diffusion coefficients results suggest that is naturally able properties both folded proteins, which attribute use Kirkwood-Buff theory as foundation field's development. However, show tends lose some well-defined secondary structural elements increases percentage coil regions, indicating perfect balance all remains elusive. Nevertheless, argue an improvement over recently modified fields require ad hoc interventions prevent collapse