The Locally Optimal Method of Cyclic Alignment to Reveal Latent Periodicities in Genetic Texts: The NAD-binding Protein Sites

Molecular Biology

Volumn 37, Issue 4, 2003, Pages 561-570

  Laskin, A A ^a,b   Korotkov, E V ^a,b   Chaley, M B ^a,b   Kudryashov, N A ^b  

^a INSTITUTE OF BIOENGINEERING   (Russian Federation)

^b NATIONAL RESEARCH NUCLEAR UNIVERSITY MEPHI   (Russian Federation)

Author keywords

Alignment; Dynamic programming; Information decomposition; NAD binding domain; Periodicity; Profile analysis; Repeats; Rossman fold; Structural functional correlation

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; DATA BASE; GENE DELETION; GENE INSERTION; GENETICS; LATENT PERIOD; PERIODICITY; PROTEIN BINDING; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL SIGNIFICANCE; SWISS-PROT; TANDEM REPEAT;

INSERTION SEQUENCES;

EID: 0042524430     PISSN: 00268933     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1025139427862     Document Type: Article

References (39)

1. Korotkov E.V., Korotkova M.A. 1996. Enlarged similarity of nucleic acid sequences. DNA Res. 3, 157-164.
2. Korotkov E.V., Korotkova M.A. 1995. DNA regions with latent periodicity in some human clones. DNA Seq. 5, 353-358.
3. Chaley M.B., Korotkov E.V., Skryabin K.G. 1999. Method revealing latent periodicity of the nucleotide sequences for a case of small samples. DNA Res. 6, 153-163.
4. Korotkov E.V., Korotkova M.A., Rudenko V.M., Skryabin K.G. 1999. The latent periodicity in amino acid sequences. Mol. Biol. 33, 611-617.
5. Korotkova M.A., Korotkov E.V., Rudenko V.M. 1999. Latent periodicity of protein sequences. J. Mol. Model. 5, 103-115.
6. Heger A., Holm L. 2000. Rapid automatic detection and alignment of repeats in protein sequences. Proteins. 41, 224-237.
7. Landau G.M., Schmidt J.P., Sokol D. 2001. An Algorithm for approximate tandem repeats. J. Comp. Biol. 8, 1-18.
8. Neuwald A.F., Poleksic A. 2000. PSI-BLAST searches using hidden Markov models of structural repeats: prediction of unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. Nucleic. Acids Res. 28, 3570-3580.
9. Coward E., Drablos F. 1998. Detecting periodic patterns in biological sequences. Bioinformatics. 14, 498-507.
10. Katti M.V., Sami-Subbu R., Ranjekar P.K., Gupta V.S. 2000. Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications. Protein Sci. 9, 1203-1209.
11. Andrade M.A., Ponting C.P., Gibson T.J., Bork P. 2000. Homology-based method for identification of protein repeats using statistical significance estimates. J. Mol. Biol. 298, 521-537.
12. Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580.
13. Marcotte E.M., Pellegrini M., Yeates T.O., Eisenberg D. 1999. A census of protein repeats. J. Mol. Biol. 293, 151-160.
14. Landschulz W.H., Johnson P.F., McKnight S.L. 1988. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science. 240, 1759-1764.
15. Gribskov M., McLachlan A.D., Eisenberg D. 1987. Profile analysis: Detection of distantly related proteins. Proc. Natl. Acad. Sci. USA. 84, 4355-4358.
16. Fischetti V., Landau G., Schmidt J., Sellers P. 1992. In Proceedings of the 3rd Annual Symposium on Combinatorial Pattern Matching. Eds. Apostolico A., Crochemore M., Galil Z., Manber U., Lecture Notes in Computer Science. N.Y.-London-Berlin: Springer-Verlag, 644, 111-120.
17. Benson G., Waterman M.S. 1994. A method for fast database search for all k-nucleotide repeats. Nucleic Acids Res. 22, 4828-4836.
18. Benson G. 2001. In: Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching. Eds. Amir A., Landau G.M., Lecture Notes in Computer Science. N.Y.-London-Berlin: Springer-Verlag, 2089, 118-130.
19. Webber C., Barton G.J. 2001. Estimation of P-values for global alignment of protein sequences. Bioinformatics. 17, 1158-1167.
20. Comet J.P., Aude J.C., Glemet E., Risler J.L., Henaut A., Slonimski P.P., Codani J.J. 1999. Significance of Z-value statistics of Smith-Waterman scores for protein alignments. Comp. Chem. 23, 317-331.
21. Aravind L., Koonin E.V. 1999. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol. 287, 1023-1040.
22. Altschul S.F., Koonin E.V. 1998. Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem. Sci. 23, 444-447.
23. Karlin S., Dembo A., Kawabata T. 1990. Statistical composition of high-scoring segments from molecular sequences. Ann. Stat. 18, 571-581.
24. Mott R., Tribe R. 1999. Approximate statistics of gapped alignments. J. Comp. Biol. 6, 91-112.
25. Bairoch A., Apweiler R. 2000. The Swiss-Prot protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 25, 45-48.
26. Junker V.L., Apweiler R., Bairoch A. 1999. Representation of functional information in the SWISS-PROT data bank. Bioinformatics. 15, 1066-1067.
27. Sussman J.L., Abola E.E., Lin D., Jiang J., Manning N.O., Prilusky J. 1999. The protein data bank. Genetica. 106, 149-158.
28. Laskin A., Korotkov E., Kudryashov N. 2002. In: Proceedings of the 3rd International Conference on Bioinformatics of Genome Regulation and Structure. Novosibirsk. 3, 97-99.
29. Rao S.T., Rossman M.G. 1973. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76, 241-256.
30. Rossman M.G., Moras D., Olsen K.W. 1974. Chemical and biological evolution of a nucleotide-binding protein. Nature. 250, 194-199.
31. Sander C., Schneider R. 1991. Database of homology-derived protein structures. Proteins. 9, 56-68.
32. Brenner S.E., Chothia C., Hubbard T.I.P., Murzin A.G. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
33. Lesk A.M. 1995. NAD-binding domains of dehydrogenases. Curr. Opin. Struct. Biol. 5, 775-783.
34. Bellamacina C.R. 1996. The nicotinamide inucleotide binding motif: a comparison of nucleotide binding proteins. FASEB J. 10, 1257-1269.
35. Baker P.J., Britton K.L., Rice D.W., Rob A., Stillman T.J. 1992. Structural consequences of sequence paterns in the fingerprint region of the nucleotide binding fold. J. Mol. Biol. 228, 662-671.
36. Kutzenko A.S., Lamzin V.S., Popov V.O. 1998. Conserved supersecondary structural motif in NAD-binding dehydrogenases. FEBS Lett. 423, 105-109.
37. Fjellstorm O., Olausson T., Hu X., Kallebring B., Ahmad S., Bragg P.D., Rydstrom J. 1995. Three-dimensional structure prediction of the NAD-binding site of proton-pumping transhydrogenase from Escherichia coli. Proteins. 2, 91-104.
38. Wierenga R.K., Terpstra P., Hol W.G.J. 1986. Prediction of the occurence of ADP-binding βαβ-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol. 187, 101-107.
39. McKie J.H., Douglas K.T. 1991. Evidence for gene duplication forming similar binding folds for NAD(P)H and FAD in pyridine nucleotide-dependent flavoenzymes. FEBS Lett. 279, 5-8.