Developing advanced X-ray scattering methods combined with crystallography and computation

Methods

Volumn 59, Issue 3, 2013, Pages 363-371

  Perry, J Jefferson P ^a,b   Tainer, John A ^a,c  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b AMRITA UNIVERSITY   (India)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Crystallography; High throughput; In solution; Protein interaction; SAXS; Screening

Indexed keywords

NUCLEOTIDE; PROTEIN;

AB INITIO CALCULATION; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLIZATION; GENOMICS; MACROMOLECULE; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; MOLECULAR SIZE; NUCLEAR MAGNETIC RESONANCE; OLIGOMERIZATION; PARTICLE SIZE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; REVIEW; X RAY CRYSTALLOGRAPHY; CHEMISTRY; CRYSTALLOGRAPHY; METHODOLOGY; PROTEIN DATABASE; PROTEIN FOLDING; SMALL ANGLE SCATTERING; X RAY DIFFRACTION;

CRYSTALLOGRAPHY; DATABASES, PROTEIN; PROTEIN FOLDING; PROTEINS; SCATTERING, SMALL ANGLE; X-RAY DIFFRACTION;

EID: 84884482704     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.01.005     Document Type: Review

References (91)

1. Perry J.J., Fan L., Tainer J.A. Neuroscience 2007, 145:1280-1299.
2. Perry J.J., Cotner-Gohara E., Ellenberger T., Tainer J.A. Current Opinion in Structural Biology 2010, 20:283-294.
3. Tsutakawa S.E., Hura G.L., Frankel K.A., Cooper P.K., Tainer J.A. Journal of Structural Biology 2007, 158:214-223.
4. Vucetic S., Brown C.J., Dunker A.K., Obradovic Z. Proteins 2003, 52:573-584.
5. Dunker A.K., Obradovic Z., Romero P., Garner E.C., Brown C.J. Genome informatics. Workshop on genome informatics 2000, 11:161-171.
6. Dunker A.K., Cortese M.S., Romero P., Iakoucheva L.M., Uversky V.N. The FEBS Journal 2005, 272:5129-5148.
7. Chrencik J.E., Brooun A., Zhang H. Journal of Molecular Biology 2008, 380:828-843.
8. Nishimura N., Hitomi K., Arvai A.S., Rambo R.P., Hitomi C., Cutler S.R., Schroeder J.I., Getzoff E.D. Science 2009, 326:1373-1379.
9. Hura G.L., Menon A.L., Hammel M., Rambo R.P., Poole F.L., Tsutakawa S.E., Jenney F.E., Classen S., Frankel K.A., Hopkins R.C., Yang S.J., Scott J.W., Dillard B.D., Adams M.W., Tainer J.A. Nature methods 2009, 6:606-612.
10. Classen S., Rodic I., Holton J., Hura G.L., Hammel M., Tainer J.A. Journal of synchrotron radiation 2010, 17:774-781.
11. Lipfert J., Doniach S. Annual review of biophysics and biomolecular structure 2007, 36:307-327.
12. Koch M.H., Vachette P., Svergun D.I. Quarterly reviews of biophysics 2003, 36:147-227.
13. Petoukhov M.V., Svergun D.I. Current opinion in structural biology 2007, 17:562-571.
14. Putnam C.D., Hammel M., Hura G.L., Tainer J.A. Quarterly reviews of biophys 2007, 40:191-285.
15. Sokolova A.V., Volkov V.V., Svergun D.I. Journal of applied crystallography 2003, 36:865-868.
16. Sokolova A.V., Volkov V.V., Svergun D.I. Crystallography reports 2003, 48:959-965.
17. Konarev P.V., Petoukhov M.V., Kikney A.G., Svergun D.I. Journal of applied crystallography 2007, 40:s223-s228.
18. Konarev J. Journal of applied crystallography 2004, 36:1277-1282.
19. Akiyama S., Fujisawa T., Ishimori K., Morishima I., Aono S. Journal of molecular biology 2004, 341:651-668.
20. Mylonas E., Svergun D.I. Journal of applied crystallography 2007, 40:s245-s249.
21. Fischer H., de Oliveira Neto M., Napolitano H.B., Polikarpov I., Craievich A.F. Journal of applied crystallography 2010, 41:101-109.
22. Glatter O., Kratky O. Small Angle X-ray Scattering 1982, Academic Press, London, New York.
23. Rambo R.P., Tainer J.A. Biopolymers 2011, 95:559-571.
24. Williams G.J., Williams R.S., Williams J.S., Moncalian G., Arvai A.S., Limbo O., Guenther G., SilDas S., Hammel M., Russell P., Tainer J.A. Nature structural & molecular biology 2011, 18:423-431.
25. Hamada D., Higurashi T., Mayanagi K., Miyata T., Fukui T., Iida T., Honda T., Yanagihara I. Journal of molecular biology 2007, 365:187-195.
26. Grant T.D., Luft J.R., Wolfley J.R., Tsuruta H., Martel A., Montelione G.T., Snell E.H. Biopolymers 2011, 95:517-530.
27. Svergun D.I., Petoukhov M.V., Koch M.H. Biophysical journal 2001, 80:2946-2953.
28. Svergun D.I. Biophysical journal 1999, 76:2879-2886.
29. Svergun D., Franke D. Journal of applied crystallography 2009, 42:342-346.
30. Jacques D.A., Trewhella J. Protein science: a publication of the protein society 2010, 19:642-657.
31. Volkov V.V., Svergun D.I. Journal of applied crystallography 2003, 36:860-864.
32. Wall M.E., Gallagher S.C., Trewhella J. Annual review of physical chemistry 2000, 51:355-380.
33. Schneidman-Duhovny D., Hammel M., Sali A. Nucleic acids research 2010, 38:W540-W544.
34. Davies J.M., Tsuruta H., May A.P., Weis W.I. Structure 2005, 13:183-195.
35. Tubbs J.L., Latypov V., Kanugula S., Butt A., Melikishvili M., Kraehenbuehl R., Fleck O., Marriott A., Watson A.J., Verbeek B., McGown G., Thorncroft M., Santibanez-Koref M.F., Millington C., Arvai A.S., Kroeger M.D., Peterson L.A., Williams D.M., Fried M.G., Margison G.P., Pegg A.E., Tainer J.A. Nature 2009, 459:808-813.
36. Kozin M.B., Svergun D.I. Journal of applied crystallography 2001, 34:33-41.
37. Wriggers W., Milligan R.A., McCammon J.A. Journal of structural biology 1999, 125:185-195.
38. Wriggers W. Biophysical reviews 2010, 2:21-27.
39. Shin D.S., Pellegrini L., Daniels D.S., Yelent B., Craig L., Bates D., Yu D.S., Shivji M.K., Hitomi C., Arvai A.S., Volkmann N., Tsuruta H., Blundell T.L., Venkitaraman A.R., Tainer J.A. EMBO journal 2003, 22:4566-4576.
40. Shin D.S., Didonato M., Barondeau D.P., Hura G.L., Hitomi C., Berglund J.A., Getzoff E.D., Cary S.C., Tainer J.A. Journal of molecular biology 2009, 385:1534-1555.
41. Williams R.S., Moncalian G., Williams J.S., Yamada Y., Limbo O., Shin D.S., Groocock L.M., Cahill D., Hitomi C., Guenther G., Moiani D., Carney J.P., Russell P., Tainer J.A. Cell 2008, 135:97-109.
42. Hopfner K.P., Karcher A., Shin D.S., Craig L., Arthur L.M., Carney J.P., Tainer J.A. Cell 2000, 101:789-800.
43. Svergun D.I., Baberato C., Koch M.H.J. Journal of applied crystallography 1995, 28:768-773.
44. Petoukhov M.V., Svergun D.I. Biophysical journal 2005, 89:1237-1250.
45. Petoukhov M.V., Franke D., Shkumatov A.V., Tria G., Kikhney A.G., Gajda M., Gorba C., Mertens H.D.T., Konarev P.V., Svergun D.I. Journal of applied crystallography 2012, 45:342-350.
46. Sibille N., Bernado P. Biochemical society transactions 2012, 40:955-962.
47. Shi X., Betzi S., Lugari A., Opi S., Restouin A., Parrot I., Martinez J., Zimmermann P., Lecine P., Huang M., Arold S.T., Collette Y., Morelli X. FEBS letters 2012, 586:1759-1764.
48. Ogura K., Kumeta H., Takahasi K., Kobashigawa Y., Yoshida R., Itoh H., Yazawa M., Inagaki F. Genes to cells: devoted to molecular & cellular mechanisms 2012, 17:159-172.
49. Jeffries C.M., Lu Y., Hynson R.M., Taylor J.E., Ballesteros M., Kwan A.H., Trewhella J. Journal of molecular biology 2011, 414:735-748.
50. Ullman O., Fisher C.K., Stultz C.M. Journal of the american chemical society 2011, 133:19536-19546.
51. Wang X., Watson C., Sharp J.S., Handel T.M., Prestegard J.H. Structure 2011, 19:1138-1148.
52. Madl T., Gabel F., Sattler M. Journal of structural biology 2011, 173:472-482.
53. Chacon P., Tama F., Wriggers W. Journal of molecular biology 2003, 326:485-492.
54. Hinsen K., Reuter N., Navaza J., Stokes D.L., Lacapere J.J. Biophysical journal 2005, 88:818-827.
55. Bahar I., Rader A.J. Current opinion in structural biology 2005, 15:586-592.
56. Tama F., Valle M., Frank J., Brooks C.L. Proceedings of the national academy of sciences of the united states of america 2003, 100:9319-9323.
57. Hinsen K., Beaumont E., Fournier B., Lacapere J.J. Methods in molecular biology 2010, 654:237-258.
58. Miyashita O., Gorba C., Tama F. Journal of structural biology 2011, 173:451-460.
59. Gorba C., Tama F. Bioinformatics and biology insights 2010, 4:43-54.
60. Suhre K., Navaza J., Sanejouand Y.H. Acta crystallographica section D: biological crystallography 2006, 62:1098-1100.
61. Forster F., Webb B., Krukenberg K.A., Tsuruta H., Agard D.A., Sali A. Journal of molecular biology 2008, 382:1089-1106.
62. Russel D., Lasker K., Webb B., Velazquez-Muriel J., Tjioe E., Schneidman-Duhovny D., Peterson B., Sali A. PLoS biology 2012, 10:e1001244.
63. Schneidman-Duhovny D., Hammel M., Sali A. Journal of structural biology 2011, 173:461-471.
64. Williams R.S., Dodson G.E., Limbo O., Yamada Y., Williams J.S., Guenther G., Classen S., Glover J.N., Iwasaki H., Russell P., Tainer J.A. Cell 2009, 139:87-99.
65. Tainer J.A., Getzoff E.D., Alexander H., Houghten R.A., Olson A.J., Lerner R.A., Hendrickson W.A. Nature 1984, 312:127-134.
66. Hammel M. European biophysics journal: EBJ 2012, 41:789-799.
67. Rambo R.P., Tainer J.A. Current opinion structural biology 2010, 20:128-137.
68. Receveur-Brechot V., Durand D. Current protein & peptide science 2012, 13:55-75.
69. Bernado P., Svergun D.I. Molecular biosystems 2012, 8:151-167.
70. Bernado P., Mylonas E., Petoukhov M.V., Blackledge M., Svergun D.I. Journal of the american chemical society 2007, 129:5656-5664.
71. Pelikan M., Hura G.L., Hammel M. General physiology and biophysics 2009, 28:174-189.
72. Yang S., Blachowicz L., Makowski L., Roux B. Proceedings of the national academy of sciences of the united states of america 2010, 107:15757-15762.
73. Bernstein N.K., Hammel M., Mani R.S., Weinfeld M., Pelikan M., Tainer J.A., Glover J.N. Nucleic acids research 2009, 37:6161-6173.
74. Hammel M., Yu Y., Fang S., Lees-Miller S.P., Tainer J.A. Structure 2010, 18:1431-1442.
75. Hammel M., Rey M., Yu Y., Mani R.S., Classen S., Liu M., Pique M.E., Fang S., Mahaney B.L., Weinfeld M., Schriemer D.C., Lees-Miller S.P., Tainer J.A. The journal of biological chemistry 2011, 286:32638-32650.
76. Jain R., Hammel M., Johnson R.E., Prakash L., Prakash S., Aggarwal A.K. Journal of molecular biology 2009, 394:377-382.
77. Hammel M., Yu Y., Mahaney B.L., Cai B., Ye R., Phipps B.M., Rambo R.P., Hura G.L., Pelikan M., So S., Abolfath R.M., Chen D.J., Lees-Miller S.P., Tainer J.A. The journal of biological chemistry 2010, 285:1414-1423.
78. Perry J.J., Asaithamby A., Barnebey A., Kiamanesch F., Chen D.J., Han S., Tainer J.A., Yannone S.M. The journal of biological chemistry 2010, 285:25699-25707.
79. Prudden J., Perry J.J., Nie M., Vashisht A.A., Arvai A.S., Hitomi C., Guenther G., Wohlschlegel J.A., Tainer J.A., Boddy M.N. Molecular and cellular biology 2011, 31:2299-2310.
80. Prudden J., Perry J.J., Arvai A.S., Tainer J.A., Boddy M.N. Nature structural & molecular biology 2009, 16:509-516.
81. Yannone S.M., Hartung S., Menon A.L., Adams M.W., Tainer J.A. Current opinion in biotechnology 2012, 23:89-95.
82. Cvetkovic A., Menon A.L., Thorgersen M.P., Scott J.W., Poole F.L., Jenney F.E., Lancaster W.A., Praissman J.L., Shanmukh S., Vaccaro B.J., Trauger S.A., Kalisiak E., Apon J.V., Siuzdak G., Yannone S.M., Tainer J.A., Adams M.W. Nature 2010, 466:779-782.
83. Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., Tainer J.A. Cell 2008, 133:789-800.
84. Hopfner K.P., Craig L., Moncalian G., Zinkel R.A., Usui T., Owen B.A., Karcher A., Henderson B., Bodmer J.L., McMurray C.T., Carney J.P., Petrini J.H., Tainer J.A. Nature 2002, 418:562-566.
85. Svergun D.I. Biological chemistry 2010, 391:737-743.
86. Lunde C.S., Rouhani S., Facciotti M.T., Glaeser R.M. Journal of structural biology 2006, 154:223-231.
87. Siegel D.P., Cherezov V., Greathouse D.V., Koeppe R.E., Killian J.A., Caffrey M. Biophysical journal 2006, 90:200-211.
88. Caffrey M. Current opinion in structural biology 2000, 10:486-497.
89. Grishaev A., Anthis N.J., Clore G.M. Journal of the american chemical society 2012, 134:14686-14689.
90. Perry J.J., Harris R.M., Moiani D., Olson A.J., Tainer J.A. Journal of molecular biology 2009, 391:1-11.
91. Hall J., Aulabaugh A., Rajamohan F., Liu S., Kaila N., Wan Z.K., Ryan M., Magyar R., Qiu X. The journal of biological chemistry 2012, 287:7717-7727.