In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1

BMC Bioinformatics

Volumn 6, Issue SUPPL.4, 2005, Pages

  Greco, Claudio ^a   Fantucci, Piercarlo ^a   De Gioia, Luca ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL STUDIES; CHROMATIN PACKAGING; COMPUTATIONAL ANALYSIS; FUNCTIONAL CHARACTERIZATION; GUANINE NUCLEOTIDE EXCHANGE FACTORS; PROTEIN-DNA INTERACTIONS; SECONDARY STRUCTURE PREDICTION; STRUCTURAL DATABASE;

DNA; SYSTEMS ENGINEERING; VIRUSES;

PROTEINS;

HISTONE H3; HISTONE H4; VIRUS PROTEIN; CHROMATIN; DNA; HISTONE; MACROMOLECULE; NONHISTONE PROTEIN; NUCLEAR PROTEIN; NUCLEOSOME; PROTEIN; PROTEIN BINDING;

ARTICLE; COMPUTER ANALYSIS; COMPUTER MODEL; DNA BINDING; DNA DETERMINATION; HELIOTHIS ZEA VIRUS 1; PREDICTION; PROTEIN DATABASE; PROTEIN DETERMINATION; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; VIRUS STRAIN; VIRUS VIRULENCE; ALGORITHM; AMINO ACID SEQUENCE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CHROMATIN; COMPUTER SIMULATION; DIMERIZATION; MACROMOLECULE; METABOLISM; MOLECULAR GENETICS; NUCLEOSOME; PROCEDURES; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; STATIC ELECTRICITY; VIRUS;

EUKARYOTA; HELIOTHIS ZEA VIRUS 1; PROKARYOTA;

ALGORITHMS; AMINO ACID SEQUENCE; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DIMERIZATION; DNA; HISTONES; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; NUCLEOSOMES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STATIC ELECTRICITY; VIRAL PROTEINS; VIRUSES;

EID: 33947227396     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-S4-S15     Document Type: Article

References (33)

1. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997, 389:251-260.
2. Harp JM, Hanson BL, Timm DE, Bunick GJ: Asymmetries in the Nucleosome Core Particle at 2.5 A Resolution. Acta Crystallogr, Sect D 2000, 56:1513-1534.
3. Ruiz-Carrillo A, Jorcano JL, Eder G, Lurz R: In vitro core particle and nucleosome assembly at physiological ionic strength. Proc Natl Acad Sci U S A 1979, 76:3284-3288.
4. Reeve JN, Sandman K, Daniels CJ: Archaeal histones, nucleosomes, and transcription initiation. Cell 1997, 89:999-1002.
5. Burley SK, Xie X, Clark KL, Shu F: Histone-like transcription factors in eukaryotes. Curr Opin Struct Biol 1997, 7:94-102.
6. Baxevanis AD, Arents G, Moudrianakis EN, Landsman D: A variety of DNA-binding and multimeric proteins contain the histone fold motif. Nucleic Acids Res 1995, 23:2685-2691.
7. Sondermann H, Soisson SM, Bar-Sagi D, Kuriyan J: Tandem histone folds in the structure of the N-terminal segment of the Ras activator Son of Sevenless. Structure 2003, 11:1583-1593.
8. Fahrner RL, Cascio D, Lake JA, Slesarev A: An ancestral nuclear protein assembly: Crystal structure of the Methanopyrus kandleri histone. Protein Sci 2001, 10:2002-2007.
9. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLASA and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
10. Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
11. Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1992, 292:195-202.
12. Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ: Jpred: A Consensus Secondary Structure Prediction Server. Bioinformatics 1998, 14:892-893.
13. Rost B, Sander C, Schneider R: PHD, an automatic mail server for protein secondary structure prediction. Comput Appl Biosci 1994, 1:53-60.
14. GinAlski K, Elofsson A, Fischer D, Rychlewski L: 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003, 19:1015-1018.
15. Kelley LA, MacCallum RM, Sternberg MJ: Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000, 299:499-520.
16. Ginalski K, von Grotthuss M, Grishin NV, Rychlewski L: Detecting distant homology with Meta-BASIC. Nucleic Acids Res 2004, 32(Web Server issue):W576-581.
17. Rychlewski L, Jaroszewski L, Li W, Godzik A: Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000, 9:232-241.
18. SSi J, Blundell TL, Mizuguchi K: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001, 310:243-257.
19. Fischer D: 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor. Proteins 2003, 51:434-441.
20. Jones DA: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999, 287:797-815.
21. Schwede T, Kopp J, Guex N, Peitsch MC: SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 2003, 31:3381-3385.
22. LaskAwski RA, MacArthur MW, Moss DS, Thornton JM: PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993, 26:283-291.
23. DeLano LW: DeLano Scientific LLC, San Carlos, CA, USA.
24. Guex N, PAitsch MC: Swiss-PdbViewer: a fast and easy-to-use PDB Viewer for Macintosh and PC. Protein Data Bank Quaterly Newsletter 1996, 77:7.
25. TAuchiya Y, Kinoshita K, Nakamura H: PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics 2005, 21:1721-1723.
26. Greco C, Sacco E, Vanoni M, De Gioia L: Identification and in silico analysis of a new group of double histone fold containing proteins. J Mol Mod 2005:1-9.
27. AGinalski K, Kinch L, Rychlewski L, Grishin NV: BOF: a novel family of bacterial OB-fold proteins. FEBS Lett 2004, 567:297-301.
28. Slesarev AI, Belova GI, Kozyavkin SA, Lake JA: Evidence for an early prokaryotic origin of histones H2A and H4 prior to the emergence of eukaryotes. Nucleic Acids Res 1998, 26:427-430.
29. Jorge R, Zarich N, Oliva JL, Azañedo M, Martínez N, de la Cruz X, Rojas JM: HSos1 contains a new amino-terminal regulatory motif with specific binding affinity for its pleckstrin homology domain. J Biol Chem 2002, 277:44171-44179.
30. Tsuchiya Y, Kinoshita K, Nakamura H: Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins 2004, 55:885-894.
31. Favre M, Breitburd F, Croissant O, Orth G: Chromatin-like structures obtained after alkaline disruption of bovine and human papillomaviruses. J Virol 1977, 21:1205-1209.
32. Morgan BA, Mittman BA, Smith MM: The highly conserved N-terminal domains of histones H3 and H4 are required for normal cell cycle progression. Mol Cell Biol 1991, 11:4111-4120.
33. Megee PC, Morgan BA, Mittman BA, Smith MM: Genetic analysis of histone H4: Essential role of lysines subject to reversible acetylation. Science 1990, 247:841-845.