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Published November 3, 2003 | Published
Journal Article Open

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


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.

Additional Information

© 2003 by The National Academy of Sciences of the USA. Edited by Peter G. Wolynes, University of California at San Diego, La Jolla, CA and approved September 10, 2003 (received for review July 9, 2003) This paper was submitted directly (Track II) to the PNAS office. We thank K. Beckingham for providing a plasmid containing wild-type calmodulin, P. Huang for providing the program PRPCR used for primer design, P. Shah for help with construction of some of the CaM mutants, and M. Ary for assistance with the manuscript. This work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, an IBM Shared University research grant (to S.L.M.), a National Institutes of Health postdoctoral fellowship, and the Caltech Initiative in Computational Molecular Biology, awarded by the Burroughs Wellcome Fund (to J.M.S.).

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