title: Molecular dynamics simulation accurately predicts the experimentally-observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions.
abstract: A molecular dynamics simulation of the operator binding domain of the lambda repressor protein has been carried out. The protein was embedded in explicit waters, Na(+) and CL(-) ions. The Amber 4.1 computer package and the Cornell et al. Force field were used for energy-minimization and molecular dynamics simulation. We find that the atoms distributions in the environment of waters and Na(+) ions are in excellent agreement with those derived from the analysis of water molecules in crystal structures and ion-binding proteins. We also find that, on the whole, both distributions are similar to each other.
authors.affiliation: Department of Chemistry & Molecular Biophysics Program, Hall-Atwater Laboratory, Wesleyan University, Middletown, Connecticut 06457, USA.
authors.forename: D C
authors.initials: DC
authors.lastname: Kombo
authors.forename: M A
authors.initials: MA
authors.lastname: Young
authors.forename: D L
authors.initials: DL
authors.lastname: Beveridge
mesh_terms: D002244:Carbon / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry; D046911:Macromolecular Substances; D008958:Models, Molecular; D009010:Monte Carlo Method; D009584:Nitrogen / Q000737:chemistry*; D010100:Oxygen / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; D014867:Water / Q000737:chemistry*
chemical_list: D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D014867:Water; D002244:Carbon; D009584:Nitrogen; D010100:Oxygen