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Nucleic Acids Research 2006 34(Web Server issue):W48-W51; doi:10.1093/nar/gkl192
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

pKD: re-designing protein pKa values

Barbara M. Tynan-Connolly and Jens Erik Nielsen*

School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin Belfield, Dublin 4, Ireland

*To whom correspondence should be addressed. Tel: +353 1 716 6724; Fax: +353 1 716 6898; Email: Jens.Nielsen{at}UCD.IE

Received February 14, 2006. Revised March 21, 2006. Accepted March 21, 2006.

The pKa values in proteins govern the pH-dependence of protein stability and enzymatic activity. A large number of mutagenesis experiments have been carried out in the last three decades to re-engineer the pH-activity and pH-stability profile of enzymes and proteins. We have developed the pKD webserver (http://polymerase.ucd.ie/pKa_Design), which predicts sets of point mutations that will change the pKa values of a set of target residues in a given direction, thus allowing for targeted re-design of the pH-dependent characteristics of proteins. The server provides the user with an interactive experience for re-designing pKa values by pre-calculating {Delta}pKa values from all feasible point mutations. Design solutions are found in less than 10 min for a typical design job for a medium-sized protein. Mutant {Delta}pKa values calculated by the pKD web server are in close agreement with those produced by comparing results from full-fledged pKa calculation methods.


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