Template-based recognition of protein fold within the midnight and twilight zones of protein sequence similarity

Journal of Molecular Recognition

Volumn 18, Issue 3, 2005, Pages 203-212

  Pirun, Mono ^a   Babnigg, Gyorgy ^b   Stevens, Fred J ^b  

^a University of Illinois at Chicago   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Evolution; Fold recognition; Homology; Statistical insignificance

Indexed keywords

AZURIN; BRCA2 PROTEIN; IMMUNOGLOBULIN; LECTIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; HUMAN; MOLECULAR GENETICS; PROTEIN DATABASE; PROTEIN FOLDING; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; AZURIN; BRCA2 PROTEIN; DATABASES, PROTEIN; HUMANS; IMMUNOGLOBULINS; LECTINS, C-TYPE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 18944397862     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.728     Document Type: Article

References (43)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25: 3389-3402.
2. Altschul SF, Koonin EV. 1998. Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem. Sci. 23: 444-447.
3. Anfinsen CB. 1973. Principles that govern the folding of protein chains. Science 181: 223-230.
4. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2003. GenBank. Nucl. Acids Res. 31: 23-27.
5. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucl. Acids Res. 28: 235-242.
6. Bowie JU, Luthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170.
7. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. 2001. Live-Bench-2: large-scale automated evaluation of protein structure prediction servers. Proteins 5(Suppl.): 184-191.
8. Curtis TP, Sloan WT. 2004. Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr. Opin. Microbiol. 7: 221-226.
9. Curtis TP, Sloan WT, Scannell JW. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA 99: 10494-10499.
10. Doolittle RF. 1981. Similar amino acid sequences: chance or common ancestry? Science 214: 149-159.
11. Doolittle RF. 1992. Stein and Moore Award address. Reconstructing history with amino acid sequences. Protein Sci. 1: 191-200.
12. Elofsson A, Le Grand SM, Eisenberg D. 1995. Local moves: an efficient algorithm for simulation of protein folding. Proteins 23: 73-82.
13. Friedberg I, Kaplan T, Margalit H. 2000. Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold. Proceedings of International Conference on Intelligent Systems and Molecular Evolution, Vol. 8; 162-170.
14. Hadley C, Jones DT. 1999. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Struct. Fold. Des. 7: 1099-1112.
15. Hagler AT, Honig B. 1978. On the formation of protein tertiary structure on a computer. Proc. Natl Acad. Sci. USA 75: 554-558.
16. Hilbert M, Bohm G, Jaenicke R. 1993. Structural relationships of homologous proteins as a fundamental principle in homology modeling. Proteins 17: 138-151.
17. Holm L, Sander C. 1995. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20: 478-480.
18. Holm L, Sander C. 1997. Dali/FSSP classification of three-dimensional protein folds. Nucl. Acids Res. 25: 231-234.
19. Honig B, Cohen FE. 1996. Adding backbone to protein folding: why proteins are polypeptides. Fold. Des. 1: R17-20.
20. Kelley LA, MacCallum RM, Sternberg MJ. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299: 499-520.
21. Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Grana O, Pazos F, Valencia A, Sali A, et al. 2003. EVA: evaluation of protein structure prediction servers. Nucl. Acids Res. 31: 3311-3315.
22. Levitt M, Warshel A. 1975. Computer simulation of protein folding. Nature 253: 694-698.
23. Metlas R, Veljkovic V, Paladini RD, Pongor S. 1991. Protein and DNA-sequence homologies between the V3-loop of human immunodeficiency virus type I envelope protein gp120 and immunoglobulin variable regions. Biochem. Biophys. Res. Commun. 179: 1056-1062.
24. Metlas R, Skerl V, Veljkovic V, Colombatti A, Pongor S. 1994. Immunoglobulin-like domain of HIV-1 envelope glycoprotein gp120 encodes putative internal image of some common human proteins. Viral Immunol. 7: 215-219.
25. Metlas R, Skerl V, Veljkovic V, Pongor S. 1995. Further evidence for the relationship of HIV-1 gp120 V3 loops with Ig superfamily members: similarity with the putative CDR3 region of T-cell receptor delta-chains. Immunol. Lett. 47: 25-28.
26. Murzin AG, Brenner SE, 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.
27. Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. 1998. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284: 1201-1210.
28. Pedersen JT, Moult J. 1996. Genetic algorithms for protein structure prediction. Curr. Opin. Struct. Biol. 6: 227-231.
29. Reaka-Kudla M, Wilson D, Wilson E. 1997. Biodiversity II: Understanding and Protecting our Biological Resources. Joseph Henry Press: Washington, DC.
30. Rost B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12: 85-94.
31. Rost B. 2001. Review: protein secondary structure prediction continues to rise. J. Struct. Biol. 134: 204-218.
32. Rost B, O'Donoghue S. 1997. Sisyphus and prediction of protein structure. Comput. Appl. Biosci. 13: 345-356.
33. Rost B, Sander C. 1996. Bridging the protein sequence-structure gap by structure predictions. A. Rev. Biophys. Biomol. Struct. 25: 113-136.
34. Sander C, Schneider R. 1991. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 56-68.
35. Sippl MJ. 1995. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5: 229-235.
36. Srinivasan R, Rose GD. 1995. LINUS: a hierarchic procedure to predict the fold of a protein. Proteins 22: 81-99.
37. Stevens FJ. 2004. Efficient recognition of protein fold in the twilight and midnight zones by conservative application of Psi-BLAST: validation. J. Mol. Recognit. (in press).
38. Stevens F, Kemmel C, Babnigg G, Collart F. 2004. Efficient recognition of protein fold in the twilight and midnight zones by conservative application of Psi-BLAST: application. J. Mol. Recognit. (in press).
39. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22: 4673-4680.
40. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
41. Wise EL, Rayment I. 2004. Understanding the importance of protein structure to nature's routes for divergent evolution in TIM barrel enzymes. Acc. Chem. Res. 37: 149-158.
42. Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I. 2002. Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5′-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry 41: 3861-3869.
43. Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y, Thoma NH, Zheng N, Chen PL, Lee WH, Pavletich NP. 2002. BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Science 297. 1837-1848.