Zinc binding in proteins and solution: a simple but accurate nonbonded representation.
Force field parameters that use a combination of Lennard-Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 beta all-atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer-range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc-containing systems.
Stote
R H
RH
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA.
Karplus
M
M
D001665:Binding Sites; D002256:Carbonic Anhydrases / Q000737:chemistry / Q000378:metabolism; D002268:Carboxypeptidases / Q000737:chemistry / Q000378:metabolism; D043422:Carboxypeptidases A; D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D055585:Physical Phenomena; D010825:Physics; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012996:Solutions; D014867:Water; D015032:Zinc / Q000737:chemistry / Q000378:metabolism*
D011506:Proteins; D012996:Solutions; D014867:Water; D002268:Carboxypeptidases; D043422:Carboxypeptidases A; D002256:Carbonic Anhydrases; D015032:Zinc