Conservation of metal-coordinating residues.
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.
Kasampalidis
Ioannis N
IN
Department of Informatics, School of Applied Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
Pitas
Ioannis
I
Lyroudia
Kleoniki
K
D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D030562:Databases, Protein; D008667:Metalloproteins / Q000235:genetics* / Q000378:metabolism; D008670:Metals / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D016415:Sequence Alignment; D013329:Structure-Activity Relationship
D008667:Metalloproteins; D008670:Metals