Abstract
To predict the protein binding domain or active site residues of an enzyme always helps offering useful information for protein and enzyme researches.A strategy called “Evolutionary Trace Method (denoted to ET)” is developed by Lichtarge et al. (1996). We try to use ET to investigate TIM barrel glycosidase superfamily. The diversity within the samples is so enormous that many gaps occur during MSA. To handle this problem, we modify Evolutionary Trace by tracing consensus of protein groups belonged to “the same ancestor” by each level of tree instead of according “PICs”, partition identity cutoffs (PICs) that are used to define partitions. Our Evolutionary Trace Method is compared to traditional one by repeat experiment made by Mathew E. Sowa et al. . Six residues with PDEγ effects identified by Mathew E. Sowa et al. are identified on branch 12 in our studies, too. No false negative result occurs in our study. Then we investigate beta-glycanases TIM-barrel in glycosidases superfamily. Among 313 residues of Cellulose/Xylan Specificity of the beta-1,4-Glycanase Cex from Cellulomonas fimi[1exp], we can eliminate 281 unnecessary residues from 313 residues of Cellulose/Xylan Specificity of the beta-1,4- Glycanase Cex from ellulomonas fimi and pick up 32 critical residues on branch 39. Ten of picked up residues are considered to play a role in hydrolase activities. In contrast, traditional Evolutionary Trace can get no information.

This is helpful to biologists, and they can save a lot of time and money. This is the contribution of our modified Evolutionary Trace Method.

Reference
[1]Farber,G.K. (1993) An tim barrel full of evolutionary trouble. Current Opinion in Structural Biology, 3, 409-412.
[2]Henrissat,B. and Davies,G. (1997) Current Opinion in Structural Biology, 7, 637-644.
[3]Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
[4]Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method de.nes binding surfaces common to protein families. J Mol Biol 1996;257:342–358.
[5]Higgins D., Thompson J., Gibson T. Thompson J. D., Higgins D. G., Gibson T.J.(1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
[6]Mathew E.Sowa, Wei He et al. (2000) A regulator of G protein signaling interaction surface linked to effector specificity. PNAS. Vol.97 no.4 :1483-1488
[7]Umesh R Desai, Ph.D.Associate. School of Pharmacy, Virginia Commonwealth University, Richmond, VA http://www.people.vcu.edu/~urdesai/
[8]Biocatalysis page. Wageningen University 2001 http://www.ftns.wau.nl/oc/research/biocatalysis/glycosidase/glycosidasepage.htm
[9]Chothia, C. & Lesk, A. M. (1986). The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823–826.
[10]Zvelebil, M. J., Barton, G. J., Taylor, W. R. & Sternberg, M. J. (1987). Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol. 195, 957–961.
[11]Shunyi Zhu, Isabelle Huys et al.(2004) Evolutionary Trace Analysis of Scorpion Toxins Specific for K-Channels. PROTEINS: Structure, Function, and Bioinformatics 54:361-370
[12]Wang, J., Ducret, A. T. Y., Kozasa, T., Aebersold, R. & Ross, E. M. (1998) J. Biol. Chem. 273, 26014–26025.
[13]Hepler, J. R., Berman, D. M., Gilman, A. G. & Kozasa, T. (1997) Proc. Natl. Acad. Sci. USA 94, 428–432.
[14]O’Neill, G., Goh, S. H., Warren, R. A. J., Kilburn, D. G., and Miller, R. C., Jr. (1986) Gene 44, 325.
[15]A.White, D.Tull, et al.(1996).Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase. Nat Struct Biol. Feb;3(2):149-54.