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Comparative Study
. 2002 Nov 12;99(23):14764-71.
doi: 10.1073/pnas.222508899. Epub 2002 Nov 4.

Finding important sites in protein sequences

Peter J Bickel  1 , Katherina J Kechris, Philip C Spector, Gary J Wedemayer, Alexander N Glazer
Affiliations
Comparative Study

Finding important sites in protein sequences

Peter J Bickel et al. Proc Natl Acad Sci U S A. .

Abstract

By using sequence information from an aligned protein family, a procedure is exhibited for finding sites that may be functionally or structurally critical to the protein. Features based on sequence conservation within subfamilies in the alignment and associations between sites are used to select the sites. The sites are subject to statistical evaluation correcting for phylogenetic bias in the collection of sequences. This method is applied to two families: the phycobiliproteins, light-harvesting proteins in cyanobacteria, red algae, and cryptomonads, and the globins that function in oxygen storage and transport. The sites identified by the procedure are located in key structural positions and merit further experimental study.

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Figures

Fig 1.
Fig 1.
An example illustrating the strong-motif algorithm.
Fig 2.
Fig 2.
An example of an aligned phycobiliprotein sequence from Rhodella violacea PE-β subunit (A) and an aligned Mb sequence from Physeter catodon (sperm whale) (B).
Fig 3.
Fig 3.
The amino acid environment of residue 110 within biliprotein α and β subunits. (A–D) The 110 residue in α subunits of AP (A), C-PC (B), PEC (C), and B-PE (D). (E–H) The 110 residue in the corresponding β subunits. All bonds and van der Waals contacts with interatomic separations between 2.7 and 4.0 Å are shown as dotted lines; for hydrogen bonds, this is the separation distance between donor and acceptor atoms. Each image is labeled on the lower right with the respective protein and subunit. The residues found at position 110 are particularly noteworthy, because they participate in several strong motifs: Tyr-110 is conserved in all PC and PEC-α subunits, Trp-110 is found in all C-, B-, and R-PE-α subunits, Ile-110 is conserved in all AP-α subunits, and Arg-110 occurs in all biliprotein β subunits. In C (PEC-α), the internal cavity lies behind Tyr-A110; in G (PEC-β), the internal cavity lies below and to the right of Arg-B110; in D (B-PE-α), the internal cavity is behind Trp-C110; and in H (B-PE-β), the internal cavity lies above Arg-B110.
See this image and copyright information in PMC

References

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