Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study

✍ Scribed by Sarah L. Williams; Patrick G. Blachly; J. Andrew McCammon

• Book ID: 105358304
• Publisher: John Wiley and Sons
• Year: 2011
• Tongue: English
• Weight: 618 KB
• Volume: 79
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/prot.23136

✦ Synopsis

A constant pH molecular dynamics method has been used in the blind prediction of p__K__~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 p__K__~a~ of solvent-exposed residues. For residues in the protein interior, the CpHMD method encounters some difficulties in reaching convergence and predicting the p__K__~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 p__K__~a~ values consistent with experimental results.