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Published online before print December 22, 2006, 10.1110/ps.062538707
Protein Science (2007), 16:239-249. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Redesigning protein pKa values

Barbara Mary 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

(RECEIVED September 4, 2006; FINAL REVISION November 14, 2006; ACCEPTED November 15, 2006)

The ability to re-engineer enzymatic pH-activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re-engineering enzymatic pH-activity profiles by changing active site pKa values using point mutations. We calculate the maximum achievable {Delta}pKa values for 141 target titratable groups in seven enzymes by introducing conservative net-charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10Å can change pKa values up to two units, but that the introduction of a requirement to keep other pKa values constant reduces the magnitude of the achievable {Delta}pKa. The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server at http://enzyme.ucd.ie/pKD.

Keywords: enzymes; computational analysis of protein structure; pH-activity profile; pKa calculations; protein electrostatics


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