Characterization of sequence variability in nucleosome core histone folds

Proteins: Structure, Function and Genetics

Volumn 52, Issue 3, 2003, Pages 454-465

  Sullivan, Steven A ^a   Landsman, David ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Sequence conservation

Indexed keywords

DNA; HISTONE; HISTONE H2B; HISTONE H3; HISTONE H4; MYOGLOBIN; PROTEIN SUBUNIT;

AMINO ACID SEQUENCE; ARTICLE; CONSERVATION BIOLOGY; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; GENETIC VARIABILITY; INTERNET; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NUCLEOSOME; PHYSICOCHEMICAL MODEL; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS;

BINDING SITES; DATABASES, PROTEIN; DNA; HISTONES; HYDROPHOBICITY; MODELS, MOLECULAR; MUTATION; NUCLEOSOMES; PROTEIN BINDING; PROTEIN FOLDING; SEQUENCE ALIGNMENT; VARIATION (GENETICS);

EID: 0042171802     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10441     Document Type: Article

References (36)

1. Thomas JO, Kornberg RD. Cleavable cross-links in the analysis of histone-histone associations. FEBS Lett 1975;58:353-358.
2. Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN. The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci USA 1991;88:10148-10152.
3. 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.
4. Sullivan S, Sink DW, Trout KL, Makalowska I, Taylor PM, Baxevanis AD, Landsman, D. The histone database. Nucleic Acids Res 2002;30:341-342.
5. Pereira SL, Reeve JN. Histones and nucleosomes in Archaea and Eukarya: a comparative analysis. Extremophiles 1998;2:141-148.
6. Brown DT. Histone variants: are they functionally heterogeneous? Genome Biol 2001;2.
7. Ausio J, Abbott DW, Wang X, Moore SC. Histone variants and histone modifications: a structural perspective. Biochem Cell Biol 2001;79:693-708.
8. Von Holt C, Strickland WN, Brandt WF, Strickland MS. More histone structures. FEBS Lett 1979;100:201-218.
9. Jenuwein T, Allis CD. Translating the histone code. Science 2001;293:1074-1080.
10. Harp JM, Hanson BL, Timm DE, Bunick GJ. Asymmetries in the nucleosome core particle at 2.5 A resolution. Acta Crystallogr D Biol Crystallogr 2000;56 Pt 12:1513-1534.
11. White CL, Suto RK, Luger K. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. Embo J 2001;20:5207-5218.
12. Walker DR, Koonin EV. SEALS: a system for easy analysis of lots of sequences. Proc Int Conf Intell Syst Mol Biol 1997;5:333-339.
13. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876-4882.
14. Hawksworth DL, Kalin-Arroyo MT. Magnitude and distribution of biodiversity. In: Heywood VH, editor. Global biodiversity assessment. Cambridge: Cambridge University Press; 1995. p 107-191.
15. Raghava GPS. A graphical Web server for the analysis of protein sequences and alignment. Biotech Softw Int Rpt 2001;2:254-257.
16. Taylor WR. The classification of amino acid conservation. J Theor Biol 1986;119:205-218.
17. Livingstone CD, Barton GJ. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci 1993;9:745-756.
18. Goodstadt L, Ponting CP. CHROMA: consensus-based colouring of multiple alignments for publication. Bioinformatics 2001;17:845-846.
19. Andersen CA, Palmer AG, Brunak S, Rost B. Continuum secondary structure captures protein flexibility. Structure (Camb) 2002;10:175-184.
20. Rost B, Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins 1994;20:216-226.
21. Valdar WS, Thornton JM. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001;42:108-124.
22. Valdar, WS. Scoring residue conservation. Proteins 2002;48:227-241.
23. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992;8:275-282.
24. Karlin S, Brocchieri L. Evolutionary conservation of RecA genes in relation to protein structure and function. J Bacteriol 1996;178:1881-1894.
25. Shindyalov IN, Bourne PE. WPDB: a PC-based tool for analyzing protein structure. J. App. Cryst. 1995;28:847-852.
26. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
27. Dayhoff MO, Schwartz RM, Orcutt BC. A model of evolutionary change in proteins: matrices for detecting distant relationships. In: Dayhoff, MO, editor. Atlas of protein sequence and structure. Washington: National Biomedical Research Foundation; 1978. Vol. 5, p 345-358.
28. Patthy L. 1999. Protein evolution. Oxford: Blackwell Science; 1999. 228 p.
29. Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJ. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol 1987;195:957-961.
30. Livingstone CD, Barton GJ. Identification of functional residues and secondary structure from protein multiple sequence alignment. Methods Enzymol 1996;266:497-512.
31. Suzuki T, Imai K. Evolution of myoglobin. Cell Mol Life Sci 1998;54:979-1004.
32. Klyszejko-Stafanowicz L, Krajewska WM, Lipinska A. Histone occurrence, isolation, characterization, and biosynthesis. In: Hnilica LS, Stein GS, Stein JL, editors. Histones and other basic nuclear proteins. Boca Raton: CRC Press; 1989. p 17-72.
33. Eickbush TH, Moudrianakis EN. The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry 1978;17:4955-4964.
34. Worcel A, Han S, Wong ML. Assembly of newly replicated chromatin. Cell 1978;15:969-977.
35. Ng HH, Feng Q, Wang H, Erdjument-Bromage H, Tempst P, Zhang Y, Struhl K. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev 2002;16:1518-1527.
36. Ahmad K, Henikoff S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 2002;9:1191-1200.