Exploring the origins of binding specificity through the computational redesign of calmodulin

Julia M. Shifman, Stephen L. Mayo*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

95 Scopus citations


Calmodulin (CaM) is a second messenger protein that has evolved to bind tightly to a variety of targets and, as such, exhibits low binding specificity. We redesigned CaM by using a computational protein design algorithm to improve its binding specificity for one of its targets, smooth muscle myosin light chain kinase (smMLCK). Residues in or near the CaM/smMLCK binding interface were optimized; CaM interactions with alternative targets were not directly considered in the optimization. The predicted CaM sequences were constructed and tested for binding to a set of eight targets including smMLCK. The best CaM variant, obtained from a calculation that emphasized intermolecular interactions, showed up to a 155-fold increase in binding specificity. The increase in binding specificity was not due to improved binding to smMLCK, but due to decreased binding to the alternative targets. This finding is consistent with the fact that the sequence of wild-type CaM is nearly optimal for interactions with numerous targets.

Original languageAmerican English
Pages (from-to)13274-13279
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number23
StatePublished - 11 Nov 2003
Externally publishedYes


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