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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
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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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 Protein Sci.Home page
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]


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