Strategies for crystallizing a chromatin protein in complex with the nucleosome core particle

Analytical Biochemistry

Volumn 442, Issue 2, 2013, Pages 138-145

  Makde, Ravindra D ^a   Tan, Song ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Chromatin; Crystallization strategies; Macromolecular complex crystallization; Nucleosome; Protein DNA interactions

Indexed keywords

CELL PROLIFERATION; CHROMOSOMES; CRYSTALS; DIFFRACTION; DNA SEQUENCES;

CHROMATIN; CHROMATIN PROTEINS; MACROMOLECULAR COMPLEXES; NUCLEOSOME CORE PARTICLES; NUCLEOSOMES; POSTCRYSTALLIZATION; PROTEIN-DNA INTERACTIONS; STRUCTURAL UNDERSTANDING;

PROTEINS;

DNA; HISTONE; PROTEIN; CHROMATIN; FUNGAL PROTEIN; INSECT PROTEIN; NUCLEAR PROTEIN; NUCLEOSOME; PROTEIN BINDING;

ANIMAL CELL; ARTICLE; BINDING AFFINITY; CHROMATIN; CRYSTAL; CRYSTAL STRUCTURE; CRYSTALLIZATION; DIFFRACTION; DNA SEQUENCE; GEL PERMEATION CHROMATOGRAPHY; IONIC STRENGTH; MACROMOLECULE; MOLECULAR WEIGHT; NONHUMAN; NUCLEOSOME; ORTHOLOGY; PH; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PURIFICATION; SYNCHROTRON; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROCEDURES; PROTEIN CONFORMATION; SPECIES DIFFERENCE;

ANIMALS; CHROMATIN; CRYSTALLIZATION; FUNGAL PROTEINS; HISTONES; INSECT PROTEINS; MODELS, MOLECULAR; NUCLEAR PROTEINS; NUCLEOSOMES; PROTEIN BINDING; PROTEIN CONFORMATION; SPECIES SPECIFICITY;

EID: 84884495098     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2013.07.038     Document Type: Article

References (25)

1. K. Luger, A.W. Mäder, R.K. Richmond, D.F. Sargent, and T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 A resolution Nature 389 1997 251 260 (Pubitemid 27406632)
2. T. Kouzarides Chromatin modifications and their function Cell 128 2007 693 705 (Pubitemid 46273577)
3. R.T. Koerber, H.S. Rhee, C. Jiang, and B.F. Pugh Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome Mol. Cell 35 2009 889 902
4. P.R. Clarke, and C. Zhang Spatial and temporal coordination of mitosis by Ran GTPase Nat. Rev. Mol. Cell Biol. 9 2008 464 477 (Pubitemid 351733403)
5. M.E. Nemergut, C.A. Mizzen, T. Stukenberg, C.D. Allis, and I.G. Macara Chromatin docking and exchange activity enhancement of RCC1 by histones H2A and H2B Science 292 2001 1540 1543 (Pubitemid 32493421)
6. R.D. Makde, J.R. England, H.P. Yennawar, and S. Tan Structure of RCC1 chromatin factor bound to the nucleosome core particle Nature 467 2010 562 566
7. S. Tan, R.C. Kern, and W. Selleck The pST44 polycistronic expression system for producing protein complexes in Escherichia coli Protein Expr. Purif. 40 2005 385 395 (Pubitemid 40335922)
8. K. Luger, T.J. Rechsteiner, and T.J. Richmond Expression and purification of recombinant histones and nucleosome reconstitution Methods Mol. Biol. 119 1999 1 16
9. A. D'Arcy, A.M. Sweeney, and A. Haber Practical aspects of using the microbatch method in screening conditions for protein crystallization Methods 34 2004 323 328 (Pubitemid 39119816)
10. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, and N. Echols PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
11. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
12. Schrodinger, LLC., The PyMOL Molecular Graphics System, version 1.4 (2011). URL: www.pymol.org.
13. L. Renault, N. Nassar, I. Vetter, J. Becker, C. Klebe, and M. Roth The 1.7 A crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller Nature 392 1998 97 101 (Pubitemid 28150597)
14. L. Renault, J. Kuhlmann, A. Henkel, and A. Wittinghofer Structural basis for guanine nucleotide exchange on Ran by the regulator of chromosome condensation RCC1 Cell 105 2001 245 255 (Pubitemid 32429514)
15. J.R. England, J. Huang, M.J. Jennings, R.D. Makde, and S. Tan RCC1 uses a conformationally diverse loop region to interact with the nucleosome: a model for the RCC1-nucleosome complex J. Mol. Biol. 398 2010 518 529
16. C.A. Davey, D.F. Sargent, K. Luger, A.W. Maeder, and T.J. Richmond Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A resolution J. Mol. Biol. 319 2002 1097 1113 (Pubitemid 34729421)
17. B. Piña, D. Barettino, M. Truss, and M. Beato Structural features of a regulatory nucleosome J. Mol. Biol. 216 1990 975 990
18. A. Flaus, and T.J. Richmond Positioning and stability of nucleosomes on MMTV 3′LTR sequences J. Mol. Biol. 275 1998 427 441 (Pubitemid 28055063)
19. P.T. Lowary, and J. Widom New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning J. Mol. Biol. 276 1998 19 42 (Pubitemid 28085408)
20. M. Ohtsubo, T. Yoshida, H. Seino, H. Nishitani, K.L. Clark, and G.F. Sprague Mutation of the hamster cell cycle gene RCC1 is complemented by the homologous genes of Drosophila and S. cerevisiae EMBO J. 10 1991 1265 1273 (Pubitemid 21905589)
21. B. Heras, and J.L. Martin Post-crystallization treatments for improving diffraction quality of protein crystals Acta Crystallogr. D Biol. Crystallogr. 61 2005 1173 1180 (Pubitemid 43961288)
22. C. Abergel Spectacular improvement of X-ray diffraction through fast desiccation of protein crystals Acta Crystallogr. D Biol. Crystallogr. 60 2004 1413 1416 (Pubitemid 41079738)
23. T. Ochi, V.M. Bolanos-Garcia, V. Stojanoff, and A. Moreno Perspectives on protein crystallisation Prog. Biophys. Mol. Biol. 101 2009 56 63
24. E.F. Garman, and E.P. Mitchell Glycerol concentrations required for cryoprotection of 50 typical protein crystallization solutions J. Appl. Crystallogr. 29 1996 584 587
25. S.N. Timasheff The control of protein stability and association by weak interactions with water: how do solvents affect these processes? Annu. Rev. Biophys. Biomol. Struct. 22 1993 67 97 (Pubitemid 23180317)