title: Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study.
abstract: A constant pH molecular dynamics method has been used in the blind prediction of pK(a) values of titratable residues in wild type and mutated structures of the Staphylococcal nuclease (SNase) protein. The predicted values have been subsequently compared to experimental values provided by the laboratory of García-Moreno. CpHMD performs well in predicting the pK(a) of solvent-exposed residues. For residues in the protein interior, the CpHMD method encounters some difficulties in reaching convergence and predicting the pK(a) values for residues having strong interactions with neighboring residues. These results show the need to accurately and sufficiently sample conformational space in order to obtain pK(a) values consistent with experimental results.
authors.affiliation: Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093-0365, USA. swilliam@mccammon.ucsd.edu
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Williams
authors.forename: Patrick G
authors.initials: PG
authors.lastname: Blachly
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D008836:Micrococcal Nuclease / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011522:Protons; D055672:Static Electricity
chemical_list: D011522:Protons; D008836:Micrococcal Nuclease
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