Structural dynamics of nucleosome core particle: Comparison with nucleosomes containing histone variants

Proteins: Structure, Function and Genetics

Volumn 58, Issue 3, 2005, Pages 683-696

  Ramaswamy, Amutha ^a   Bahar, Ivet ^b   Ioshikhes, Ilya ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

DNA protein interactions; Equilibrium fluctuations; Normal mode analysis; Nucleosome dynamics

Indexed keywords

DNA; HISTONE;

AMINO TERMINAL SEQUENCE; ARTICLE; COMPRESSION; CORRELATION ANALYSIS; DYNAMICS; MOTION; NUCLEOSOME; PREDICTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; CHROMATIN; DIMERIZATION; DNA; DROSOPHILA; HEAT; HISTONES; HUMANS; MICROSCOPY, ATOMIC FORCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; NUCLEOTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 12944254396     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20357     Document Type: Article

References (52)

1. van Holde KE. Chromatin. New York: Springer; 1989. 497 p.
2. Wolffe A. Chromatin: structure and function. San Diego: Academic Press; 1998. 447 p.
3. Ramakrishnan V. Histone structure and the organization of nucleosome. Ann Rev Biophys Biomol Struct 1997;26:83-112.
4. Workman JL, Kingston RE. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Ann Rev Biophys Biomol Struct 1998;67:545-579.
5. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997;389:251-260.
6. Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A. Structure of the nucleosome core particle at 7Å resolution. Nature 1984;311: 532-537.
7. Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN. The nucleosomal core histone octamer at 3.1 Å resolution: a tripartite protein assembly and a left-handed super helix. Proc Natl Acad Sci USA 1991;88:10148-10152.
8. Suto RK, Clarkson MJ, Tremethick DJ, Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol 2000;7:1121-1124.
9. Eickbush TH, Moudrianakis EN. The histone core complex: An octamer assembled by two sets of protein-protein interactions. Biochem 1978;17:4955-4964.
10. Hayes JJ, Clark DJ, Wolffe AP. Histone contributions to the structure of DNA in the nucleosome. Proc Natl Acad Sci USA 1991;88:6829-6833.
11. Hayes JJ, Tullius TD, Wolffe AP. The structure of DNA in a nucleosome. Proc Natl Acad Sci USA 1990;87:7405-7409.
12. Davie JR. Covalent modifications of histones: expression from chromatin templates. Curr Opin Genet Dev 1998;8:173-178.
13. Brown DT. Histone variants: are they functionally heterogeneous? Genome Biol 2001;2: reviews 0006.1-reviews 0006.6.
14. Adam M, Robert F, Larochelle M, Gaudreau L. H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol Cell Biol 2001;21:6270-6279.
15. Abbott DW, Ivanova VS, Wang X, Bonner WM, Ausio J. Characterization of the stability and folding of H2A.Z chromatin particles: implications for transcriptional activation. J Biol Chem 2001;276: 41945-41949.
16. Fan JY, Gordon F, Luger K, Hansen JC, Tremethick DJ. The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nat Struct Biol 2002;9:172-176.
17. Jackson JD, Gorovsky MA. Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants. Nucleic Acid Res 2000;28:3811-3816.
18. Clarkson MJ, Wells JRE, Gibson F, Saint R, Tremethick DJ. Regions of variant histone His2AvD required for Drosophila development. Nature 1999;399:694-697.
19. Santisteban MS, Kalashnikova T, Smith MM. Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell 2000;103:411-422.
20. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr., Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J Am Chem Soc 1995;117:5179-5197.
21. Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT. Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins 1988;4:31-47.
22. Levitt M, Sander C, Stern PS. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 1985;181:423-447.
23. Gibrat JF, Go N. Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 1990;8:258-279.
24. Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996;77:1905-1908.
25. Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.
26. Haliloglu T, Bahar I, Erman B. Gaussian dynamics of folded proteins. Phys Rev Lett 1997;79:3090-3093.
27. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429.
28. Tama F, Sanejouand Y.-H. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001;14:1-6.
29. Atilgan AR, Durrell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001;80:505-515.
30. Bahar I, Wallqvist A, Covell DG, Jernigan RL. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry 1998;37:1067-1075.
31. Haliloglu T, Bahar I. Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins 1999;37:654-667.
32. Kundu S, Melton JS, Sorensen DC, Phillips GN Jr. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J 2002;83:723-732.
33. Ming D, Kong Y, Lambert MA, Huang Z, Ma J. How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci USA 2002;99:8620-8625.
34. Tama F, Wriggers W, Brooks CL III. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and continuum elastic network theory. J Mol Biol 2002;321:297-305.
35. Tama F, Valle M, Frank J, Brooks CL III. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci USA 2003;100:9319-9323.
36. Bahar I, Jernigan RL. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. J Mol Biol 1998;281:871-884.
37. Bahar I, Erman B, Jernigan RL, Atilgan AR, Covell DG. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J Mol Biol 1999;285:1023-1037.
38. Temiz AN, Bahar I. Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase. Proteins 2002;49: 61-70.
39. Bahar I, Atilgan AR, Demirel MC, Erman B. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys Rev Lett 1998;80:2733-2736.
40. Bahar I, Jernigan RL. Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry 1999;38: 3478-3490.
41. Demirel MC, Atilgan AR, Jernigan RL, Erman B, Bahar I. Identification of kinetically hot residues in proteins. Protein Sci 1998;7:2522-2532.
42. Keskin O, Jernigan RL, Bahar I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J 2000;78:2093-2106.
43. Tama F, Wriggers W, Brooks III CL. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J Mol Biol 2002;321:297-305.
44. Harp JM, Hanson BL, Timm DE, Bunick GJ. Asymmetries in the nucleosome core particle at 2.5Å resolution. Acta Crystallogr D Biol Crystallogr 2000;56:1513-1534.
45. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J Mol Biol 2002;319:1097-1113.
46. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acid Res 2000;28:235-242.
47. Huang CC, Couch GS, Petterse EF, Ferrin TE. Chimera: An extensible molecular modeling application constructed using standard components. Pacific Symposium on Biocomputing 1996;1: 724. http://www.cgl.ucsf.edu/chimera
48. Johnson LM, Fisher Adams G, Grunstein M. Identification of a non-basic domain in the histone N-terminus required for repression of the yeast silent mating loci. EMBO J 1992;11:2201-2209.
49. Ebralidse KK, Grachev SA, Mirzabekov AD. A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA. Nature 1988;331:365-367.
50. Smith RM, Rill RL. Mobile histone tails in nucleosomes: assignments of mobile segments and investigations of their role in chromatin folding. J Biol Chem 1989;264:10574-10581.
51. Muthurajan UM, Park YJ, Edayathumangalam RS, Suto RK, Chakravarthy S, Dyer PN, Luger K. Structure and dynamics of nucleosomal DNA. Biopolymers 2003;68:547-556.
52. Park YJ, Dyer PN, Tremethick DJ, Luger K. A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome. J Biol Chem 2004;279:24274-24282.