Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach
- 1 May 1985
- journal article
- research article
- Published by Wiley in Biopolymers
- Vol. 24 (5) , 843-865
- https://doi.org/10.1002/bip.360240509
Abstract
The stochastic boundary molecular‐dynamics approach for studying chemical events in liquids is extended to proteins. A method for simulating the localized dynamics of a portion of a protein is developed and illustrated by an application to the bovine pancreatic trypsin inhibitor (BPTI). The dynamics of the aromatic ring atoms of Tyr 21 of BPTI are targeted as the “active site,” and the results from several different localized models are compared with those from a simulation of the entire molecule. The most consistent results are obtained with a model that consists of a buffer region composed of harmonically constrained Langevin atoms surrounding the active site region whose atoms are treated by molecular dynamics. Possible applications of the model are discussed.Keywords
This publication has 22 references indexed in Scilit:
- Deformable stochastic boundaries in molecular dynamicsThe Journal of Chemical Physics, 1983
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983
- Molecular dynamics of ferrocytochrome c: Time dependence of the atomic displacementsBiopolymers, 1983
- Generalized Langevin models and condensed-phase chemical reaction dynamicsThe Journal of Physical Chemistry, 1982
- Proton nuclear Overhauser effects and protein dynamicsJournal of the American Chemical Society, 1981
- Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Å resolutionJournal of Molecular Biology, 1981
- Simulation of Protein DynamicsAnnual Review of Physical Chemistry, 1980
- Dynamics of ligand binding to heme proteinsJournal of Molecular Biology, 1979
- The hinge-bending mode in lysozymeNature, 1976
- Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolutionActa Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 1975