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

Shifman, Julia M. and Mayo, Stephen L. (2003) Exploring the origins of binding specificity through the computational redesign of calmodulin. Proceedings of the National Academy of Sciences of the United States of America, 100 (23). pp. 13274-13279. ISSN 0027-8424. PMCID PMC263780. doi:10.1073/pnas.2234277100.

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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.

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Mayo, Stephen L.0000-0002-9785-5018
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.).
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Ralph M. Parsons FoundationUNSPECIFIED
NIH Postdoctoral FellowshipUNSPECIFIED
Caltech Initiative in Computational Molecular BiologyUNSPECIFIED
Burroughs Wellcome FundUNSPECIFIED
Issue or Number:23
PubMed Central ID:PMC263780
Record Number:CaltechAUTHORS:SHIpnas03
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:649
Deposited By: Archive Administrator
Deposited On:09 Sep 2005
Last Modified:01 Jun 2023 23:12

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