Detection of gene duplication signals of Ig folds from their amino acid sequences

Proteins: Structure, Function and Genetics

Volumn 68, Issue 1, 2007, Pages 267-272

  Huang, Yanzhao ^a   Xiao, Yi ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

( )8 barrel; Internal repeat; Pearson correlation; Similarity matrix; Structural symmetry

Indexed keywords

IMMUNOGLOBULIN;

AMINO ACID SEQUENCE; ARTICLE; GENE DUPLICATION; GENE FUSION; PRIORITY JOURNAL; PROTEIN FOLDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; GENE DUPLICATION; IMMUNOGLOBULINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING;

EID: 34249867707     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21330     Document Type: Article

References (22)

1. Söding J, Lupas AN. More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 2003;25:837-846.
2. Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion. Science 2000;289:1546-1550.
3. Höcker B, Beismann-Driemeyer S, Hettwer S, Lustig A, Sterner R. Dissection of a (αβ)8-barrel enzyme into two folded halves. Nature Struct Bio 2001;8:32-36.
4. McLachlan AD. Repeating sequences and gene duplication in proteins. J Mol Biol 1972;64:417-437.
5. McLachlan AD. Gene duplication and the origin of repetitive protein structures. Quant Bio 1987;17:411-420. Cold Spring Harbor Symposium.
6. McLachlan AD. Evidence for gene duplication in collagen. J Mol Biol 1976;107:159-174.
7. McLachlan AD, Stewart M, Smillie LB. Sequence repeats in alphatropomyosin. J Mol Biol 1975;98:281-291.
8. McLachlan AD. Repeated helical pattern in apolipoprotein-A-I. Nature 1977;267:465-466.
9. McLachlan AD. Analysis of gene duplication repeats in the myosin rod. J Mol Biol 1983;169:15-30.
10. McLachlan AD. Three-fold structural pattern in the soybean trypsin inhibitor (Kunitz). J Mol Biol 1979;133:557-563.
11. McLachlan AD. Repeated folding pattern in copper-zinc superoxide dismutase. Nature 1980;285:267-268.
12. McLachlan AD, Bloomer AC, Butler PJ. Structural repeats and evolution of tobacco mosaic virus coat protein and RNA. J Mol Biol 1980;136:203-224.
13. Rackovsky S. "Hidden" sequence periodicities and protein architecture. Proc Natl Acad Sci USA 1998;95:8580-8584.
14. Salem GM, Hutchinson EG, Orengo CA. Correlation of observed fold frequency with the occurrence of local structural motifs. J Mol Biol 1999;287:969-981.
15. Xu R, Xiao Y. A common sequence-associated physicochemical feature for proteins of beta-trefoil family. Comput Biol Chem 2005;29:79-82.
16. Shih ESC, Hwang MJ. Alternative alignments from comparison of protein structures. Proteins 2004;56:519-527. Available at http://gln.ibms.sinica.edu. tw/product/repeat/.
17. Giuliani A, Benigni R, Zbilut JP, Weber CL, Sirabella P, Colosimo A. Nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships. Chem Rev 2002;102:1471-1491.
18. Turutina VP, Laskin AA, Kudryashov NA, Skryabin KG, Korotkov EV. Identification of amino acid latent periodicity within 94 protein families. J Comput Biol 2006;13:946-964.
19. Heger A, Holm L. Many large proteins have evolved by internal duplication and many internal sequence repeats. Proteins 2000;41:224-237. Available at www.ebi.ac.uk/Radar/.
20. Szklarczyk R, Heringa J. Tracking repeats using significance and transitivity, Part 26. Bioinformatics 2004;20:1311-1317. Available at http://ibivu.cs.vu.nl/programs/trustwww.
21. Mount DW. Bioinformatics: Sequences and Genome Analysis. New York: Cold Spring Harbor; 2001. 428 pp.
22. Sweet RM, Eisenberg D. Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol 1983;171:479-488.