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J Gen Physiol. 2014 Jul;144(1):105-14. doi: 10.1085/jgp.201311140. Epub 2014 Jun 16.

Calmodulation meta-analysis: predicting calmodulin binding via canonical motif clustering.

Author information

1
Department of Biochemistry and Molecular Pharmacology and Programs in Chemical Biology and Neuroscience, and.
2
Department of Scientific and Research Computing, University of Massachusetts Medical School, Worcester, MA 01605.
3
Department of Biochemistry and Molecular Pharmacology and Programs in Chemical Biology and Neuroscience, and william.kobertz@umassmed.edu.

Abstract

The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator to this meta-analysis resulted in a tool that identifies potential CaM-binding domains within a given sequence. To allow users to search for CaM-binding motifs within a protein of interest, perform the meta-analysis, and then compare the results to target peptide-CaM structures deposited in the Protein Data Bank, we created a website and online database. The availability of these tools and analyses will facilitate the design of CaM-related studies of ion channels and membrane transport proteins.

PMID:
24935744
PMCID:
PMC4076516
DOI:
10.1085/jgp.201311140
[Indexed for MEDLINE]
Free PMC Article

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