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

Autor: Williams SL; Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093-0365, USA. swilliam@mccammon.ucsd.edu, Blachly PG, McCammon JA
Jazyk: angličtina
Zdroj: Proteins [Proteins] 2011 Dec; Vol. 79 (12), pp. 3381-8. Date of Electronic Publication: 2011 Aug 30.
DOI: 10.1002/prot.23136
Abstrakt: 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.
(Copyright © 2011 Wiley-Liss, Inc.)
Databáze: MEDLINE
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