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. 2010 Feb 7;53(1):52–60. doi: 10.1007/s11426-010-0011-5

Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering

YanYi Chen 1, ShengHui Xue 1, YuBin Zhou 1, Jenny Jie Yang 1,✉
PMCID: PMC2926812  NIHMSID: NIHMS226085  PMID: 20802784

Abstract

Ca2+ plays a pivotal role in the physiology and biochemistry of prokaryotic and mammalian organisms. Viruses also utilize the universal Ca2+ signal to create a specific cellular environment to achieve coexistence with the host, and to propagate. In this paper we first describe our development of a grafting approach to understand site-specific Ca2+ binding properties of EF-hand proteins with a helix-loop-helix Ca2+ binding motif, then summarize our prediction and identification of EF-hand Ca2+ binding sites on a genome-wide scale in bacteria and virus, and next report the application of the grafting approach to probe the metal binding capability of predicted EF-hand motifs within the streptococcal hemoprotein receptor (Shr) of Streptococcus pyrogenes and the nonstructural protein 1 (nsP1) of Sindbis virus. When methods such as the grafting approach are developed in conjunction with prediction algorithms we are better able to probe continuous Ca2+-binding sites that have been previously underrepresented due to the limitation of conventional methodology.

Keywords: Ca2+, EF-hand calcium binding pockets, protein grafting approach, Streptococcus pyrogenes, Sindbis virus

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