New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage

Proteins: Structure, Function and Genetics

Volumn 68, Issue 4, 2007, Pages 915-921

  Chiang, Yih Shien ^a   Gelfand, Tatiana I ^b   Kister, Alexander E ^a   Gelfand, Israel M ^b  

^a State University of New Jersey   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

sandwich proteins; Protein folding; Protein structure classification; Protein structure prediction; Supersecondary structure

Indexed keywords

AMINO ACID; BETA SANDWICH LIKE PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE;

DATABASES, PROTEIN; HYDROGEN BONDING; IMAGE PROCESSING, COMPUTER-ASSISTED; KINETICS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 34548787257     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21473     Document Type: Article

References (26)

1. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
2. He J, Hu HJ, Harrison R, Tai PC, Pan Y. Rule generation for protein secondary structure prediction with support vector machines and decision tree. IEEE Trans Nanobiosci 2006;5:46-53.
3. Aydin Z, Altunbasak Y, Borodovsky M. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinformatics 2006;7:178.
4. Lin K, Simossis VA, Taylor WR, Heringa J. A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 2005;21:152-159.
5. Crooks GE, Brenner SE. Protein secondary structure: entropy, correlations and prediction. Bioinformatics 2004;20:1603-1611.
6. Pollastri G, McLysaght A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 2005;21: 1719-1720.
7. Richardson JS. Handedness of crossover connections in β-sheets. Proc Natl Acad Sci USA 1976;173:2619-2623.
8. Cohen FE, Sternberg MJE, Taylor WR. Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins. J Mol Biol 1982;156:821-862.
9. Taylor WR, Green NM. The predicted secondary structures of the nucleotide-binding sites of six cation-transporting ATPases lead to a probable tertiary fold. Eur J Biochem 1989;179:241-248.
10. Clark DA, Shirazi J, Rawlings CJ. Protein topology prediction through constraint-based search and the evaluation of topological folding rules. Protein Eng 1991;4:751-760.
11. Woolfson DN, Evans PA, Hutchinson EG, Thornton JM. Topological and stereochemical restrictions in β-sandwich protein structures. Prot Eng 1993;6:461-470.
12. Ruczinski I, Kooperberg C, Bonneau R, Baker D. Distributions of β sheets in proteins with application to structure prediction. Proteins 2002;48:85-97
13. Eidhammer I, Jonassen I, Taylor WR. Structure comparison and structure patterns. J Comp Biol 2000;7:685-716.
14. Kister A, Finkelstein A, Gelfand I. Common sequence and structural features in sandwich-like proteins. Proc Natl Acad Sci USA 2002;99:14137-14141.
15. Kister AE, Fokas AS, Papatheodorou TS, Gelfand IM. Strict rules determine arrangements of strands in sandwich proteins. Proc Natl Acad Sci USA 2006;103:4107-4110.
16. Andreeva A, Howorth D, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acid Res 2004;32:D226-D229.
17. Laskowski RA, Chistyakov VV, Thornton JM. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 2005;33:D266-D26S.
18. Chothia C. One thousand families for the molecular biologist. Nature 1992;357:543-544.
19. Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C. The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res 2005;33:D247-D251.
20. Levitt M, Chothia C. Structural patterns in globular proteins. Nature 1976;261:552-558.
21. Sternberg MJE, Thornton JM. On the conformation of proteins: the handedness of the β-strand-α-helix-β-strand unit. J Mol Biol 1976; 105:367-382.
22. Cohen FE, Sternberg MJE, Taylor WR. Analysis of the tertiary structure of protein β-sheet sandwiches. J Mol Biol 1981;148:253-272.
23. Michalopoulos I, Torrance GM, Gilbert DR, Westhead DR. TOPS: an enhanced database of protein structural topology. Nucleic Acids Res 2004;32:D251-D254.
24. McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994;238:777-793.
25. Chothia C, Finkelstein AV. The classification and origins of protein folding patterns. Annu Rev Biochem 1990;59:1007-1039.
26. Richardson JS. β-Sheet topology and the relatedness of proteins. Nature, 268, 1997;495-500.