Functionally specified protein signatures distinctive for each of the different blue copper proteins.
BACKGROUND
Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance of using patterns or signatures to retrieve out related sequences. Blue copper proteins are found in the electron transport chain of prokaryotes and eukaryotes. The signatures already existing in the databases like the type 1 copper blue, multiple copper oxidase, cyt b/b6, photosystem 1 psaA&B, psaG&K, and reiske iron sulphur protein are not specified signatures for blue copper proteins as the name itself suggests. Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. This work describes the signatures designed based on the copper metal binding motifs in blue copper proteins. The common feature in all blue copper proteins is a trigonal planar arrangement of two nitrogen ligands [each from histidine] and one sulphur containing thiolate ligand [from cysteine], with strong interactions between the copper center and these ligands.


RESULTS
Sequences that share such conserved motifs are crucial to the structure or function of the protein and this could provide a signature of family membership. The blue copper proteins chosen for the study were plantacyanin, plastocyanin, cucumber basic protein, stellacyanin, dicyanin, umecyanin, uclacyanin, cusacyanin, rusticyanin, sulfocyanin, halocyanin, azurin, pseudoazurin, amicyanin and nitrite reductase which were identified in both eukaryotes and prokaryotes. ClustalW analysis of the protein sequences of each of the blue copper proteins was the basis for designing protein signatures or peptides. The protein signatures and peptides identified in this study were designed involving the active site region involving the amino acids bound to the copper atom. It was highly specific for each kind of blue copper protein and the false picks were minimized. The set of signatures designed specifically for the BCP's was entirely different from the existing broad spectrum signatures as mentioned in the background section.


CONCLUSIONS
These signatures can be very useful for the annotation of uncharacterized proteins and highly specific to retrieve blue copper protein sequences of interest from the non redundant databases containing a large deposition of protein sequences.
Giri
Anuradha Vivekanandan
AV
Centre for Biotechnology, Anna University, Chennai 600 025, India. anuvivek15@yahoo.com
Anishetty
Sharmila
S
Gautam
Pennathur
P
D000595:Amino Acid Sequence; D001400:Azurin / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D002352:Carrier Proteins / Q000737:chemistry* / Q000502:physiology*; D003300:Copper / Q000378:metabolism*; D030562:Databases, Protein; D008667:Metalloproteins / Q000737:chemistry / Q000502:physiology; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology; D010970:Plastocyanin / Q000737:chemistry / Q000502:physiology
D001426:Bacterial Proteins; D002352:Carrier Proteins; D008667:Metalloproteins; D010940:Plant Proteins; C023548:copper-binding protein; C012543:rusticyanin; C002054:umecyanin; D001400:Azurin; C072144:CBP protein, Cucumis sativus; D003300:Copper; D010970:Plastocyanin