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Conservation of metal‐coordinating residues
Author(s) -
Kasampalidis Ioannis N.,
Pitas Ioannis,
Lyroudia Kleoniki
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21384
Subject(s) - metal , residue (chemistry) , protein function , chemistry , binding site , protein structure , conserved sequence , computational biology , crystallography , biology , biochemistry , peptide sequence , organic chemistry , gene
As a result of rapid advances in genome sequencing, the pace of discovery of new protein sequences has surpassed that of structure and function determination by orders of magnitude. This is also true for metal‐binding proteins, that is, proteins that bind one or more metal atoms necessary for their biological function. While metal binding site geometry and composition have been extensively studied, no large scale investigation of metal‐coordinating residue conservation has been pursued so far. In pursuing this analysis, we were able to corroborate anecdotal evidence that certain residues are preferred to others for binding to certain metals. The conservation of most metal‐coordinating residues is correlated with residue preference in a statistically significant manner. Additionally, we also established a statistically significant difference in conservation between metal‐coordinating and noncoordinating residues. These results could be useful for providing better insight to functional importance of metal‐coordinating residues, possibly aiding metal binding site prediction and design, metal‐protein complex structure prediction, drug discovery, as well as model fitting to electron‐density maps produced by X‐ray crystallography. Proteins 2007. © 2007 Wiley‐Liss, Inc.