HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Nielsen, J. E. Articles by McCammon, J. A. Search for Related Content PubMed PubMed Citation Articles by Nielsen, J. E. Articles by McCammon, J. A. Social Bookmarking                   What's this?

On the evaluation and optimization of protein X-ray structures for pKa calculations

Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA

Reprint requests to: Jens Erik Nielsen, Department of Chemistry and Biochemistry M/C 0365, UCSD, La Jolla, CA 92093, USA; e-mail: jnielsen{at}mccammon.ucsd.edu; fax: (858) 534-7042.

The calculation of the physical properties of a protein from its X-ray structure is of importance in virtually every aspect of modern biology. Although computational algorithms have been developed for calculating everything from the dynamics of a protein to its binding specificity, only limited information is available on the ability of these methods to give accurate results when used with a particular X-ray structure. We examine the ability of a pKa calculation algorithm to predict the proton-donating residue in the catalytic mechanism of hen egg white lysozyme. We examine the correlation between the ability of the pKa calculation method to obtain the correct result and the overall characteristics of 41 X-ray structures such as crystallization conditions, resolution, and the output of structure validation software. We furthermore examine the ability of energy minimizations (EM), molecular dynamics (MD) simulations, and structure-perturbation methods to optimize the X-ray structures such that these give correct results with the pKa calculation algorithm. We propose a set of criteria for identifying the proton donor in a catalytic mechanism, and demonstrate that the application of these criteria give highly accurate prediction results when using unmodified X-ray structures. More specifically, we are able to successfully identify the proton donor in 85% of the X-ray structures when excluding structures with crystal contacts near the active site. Neither the use of the overall characteristics of the X-ray structures nor the optimization of the structure by EM, MD, or other methods improves the results of the pKa calculation algorithm. We discuss these results and their implications for the design of structure-based energy calculation algorithms in general.

Keywords: pKa calculations; crystal contacts; structural genomics; molecular dynamics; electrostatics; enzymes

Abbreviations: HEWL, hen egg white lysozyme • RMSD, root mean square difference • PDB, Protein Data Bank

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				D. Narzi, K. Winkler, J. Saidowsky, R. Misselwitz, A. Ziegler, R. A. Bockmann, and U. Alexiev Molecular Determinants of Major Histocompatibility Complex Class I Complex Stability: SHAPING ANTIGENIC FEATURES THROUGH SHORT AND LONG RANGE ELECTROSTATIC INTERACTIONS J. Biol. Chem., August 22, 2008; 283(34): 23093 - 23103. [Abstract] [Full Text] [PDF]

				B. M. Tynan-Connolly and J. E. Nielsen Redesigning protein pKa values Protein Sci., February 1, 2007; 16(2): 239 - 249. [Abstract] [Full Text] [PDF]

				P. J. Kundrotas and E. Alexov Electrostatic Properties of Protein-Protein Complexes Biophys. J., September 1, 2006; 91(5): 1724 - 1736. [Abstract] [Full Text] [PDF]

				N. Ishiyama, C. Creuzenet, W. L. Miller, M. Demendi, E. M. Anderson, G. Harauz, J. S. Lam, and A. M. Berghuis Structural Studies of FlaA1 from Helicobacter pylori Reveal the Mechanism for Inverting 4,6-Dehydratase Activity J. Biol. Chem., August 25, 2006; 281(34): 24489 - 24495. [Abstract] [Full Text] [PDF]

				C. P. Toseland, H. McSparron, M. N. Davies, and D. R. Flower PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values Nucleic Acids Res., January 1, 2006; 34(suppl_1): D199 - D203. [Abstract] [Full Text] [PDF]

				J. E. Nielsen and J. A. McCammon Calculating pKa values in enzyme active sites Protein Sci., September 1, 2003; 12(9): 1894 - 1901. [Abstract] [Full Text] [PDF]