The dynamics of inter-residue distances in bovine pancreatic trypsin inhibitor

Abstract

Time series for the distance between selected residues surrounding the active site in bovine pancreatic trypsin inhibitor (BPTI) protein are analyzed using a one-dimensional Langevin-type stochastic difference equation. The time series are extracted from molecular dynamics simulations performed on the protein in vacuum and water. The deterministic and stochastic contributions to the time series show interesting behavior for certain residue pairs only, and only in solvated molecular dynamics simulations.