Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law

Biopolymers

Volumn 95, Issue 8, 2011, Pages 559-571

  Rambo, Robert P ^a   Tainer, John A ^a,b  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

flexibility; SAXS; unstructured

Indexed keywords

BIOLOGICAL MACROMOLECULE; CELL BIOLOGY; CONFORMATIONAL CHANGE; CRITICAL TECHNOLOGIES; FLEXIBILITY; INTERACTION NETWORKS; PARTICLE DENSITIES; SAXS; SAXS MODELING; SCATTERING INTENSITY; SMALL ANGLE SCATTERING; SMALL ANGLE X-RAY SCATTERING; UNSTRUCTURED;

CYTOLOGY; EXPERIMENTS; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; QUALITY ASSURANCE; RNA; SCATTERING;

MACROMOLECULES;

ABSCISIC ACID; ABSCISIC ACID BINDING PROTEIN; BIOPOLYMER; GLUCOSE ISOMERASE; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ARTICLE; CRYSTAL STRUCTURE; DNA REPAIR; ELECTRON; MACROMOLECULE; MATHEMATICAL ANALYSIS; MOLECULAR RECOGNITION; NONHUMAN; POROD DEBYE LAW; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN STRUCTURE; QUALITY CONTROL; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DNA; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; PROTEIN FOLDING; PROTEINS; RNA; SCATTERING, SMALL ANGLE; SOLUTIONS; X-RAY DIFFRACTION;

EID: 79958045453     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21638     Document Type: Article

References (60)

1. Rambo, R. P.,; Tainer, J. A., Curr Opin Struct Biol 2010, 20, 128-137.
2. Dyson, H. J.,; Wright, P. E., Nat Rev Mol Cell Biol 2005, 6, 197-208.
3. Dunker, A. K.,; Silman, I.,; Uversky, V. N.,; Sussman, J. L., Curr Opin Struct Biol 2008, 18, 756-764.
4. Wells, M.,; Tidow, H.,; Rutherford, T. J.,; Markwick, P.,; Jensen, M. R.,; Mylonas, E.,; Svergun, D. I.,; Blackledge, M.,; Fersht, A. R., Proc Natl Acad Sci USA 2008, 105, 5762-5767.
5. Receveur, V.,; Czjzek, M.,; Schulein, M.,; Panine, P.,; Henrissat, B., J Biol Chem 2002, 277, 40887-40892.
6. 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.
7. Pretto, D. I.,; Tsutakawa, S.,; Brosey, C. A.,; Castillo, A.,; Chagot, M. E.,; Smith, J. A.,; Tainer, J. A.,; Chazin, W. J., Biochemistry 2010, 49, 2880-2889.
8. 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.
9. Cotner-Gohara, E.,; Kim, I. K.,; Hammel, M.,; Tainer, J. A.,; Tomkinson, A. E.,; Ellenberger, T., Biochemistry 2010, 49, 6165-6176.
10. 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., J Biol Chem 2009, 285, 1414-1423.
11. Yamagata, A.,; Tainer, J. A., EMBO J 2007, 26, 878-890.
12. 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.
13. 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 J 2003, 22, 4566-4576.
14. Hopfner, K. P.,; Karcher, A.,; Shin, D. S.,; Craig, L.,; Arthur, L. M.,; Carney, J. P.,; Tainer, J. A., Cell 2000, 101, 789-800.
15. Cvetkovic, A.,; Menon, A. L.,; Thorgersen, M. P.,; Scott, J. W.,; Poole, F. L., II,; Jenney, F. E., Jr.,; 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.
16. Takamoto, K.,; Das, R.,; He, Q.,; Doniach, S.,; Brenowitz, M.,; Herschlag, D.,; Chance, M. R., J Mol Biol 2004, 343, 1195-1206.
17. DiDonato, M.,; Craig, L.,; Huff, M. E.,; Thayer, M. M.,; Cardoso, R. M.,; Kassmann, C. J.,; Lo, T. P.,; Bruns, C. K.,; Powers, E. T.,; Kelly, J. W.,; Getzoff, E. D.,; Tainer, J. A., J Mol Biol 2003, 332, 601-615.
18. 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., J Mol Biol 2009, 385, 1534-1555.
19. Karunatilaka, K. S.,; Solem, A.,; Pyle, A. M.,; Rueda, D., Nature 2010, 467, 935-939.
20. Prudden, J.,; Perry, J. J.,; Arvai, A. S.,; Tainer, J. A.,; Boddy, M. N., Nat Struct Mol Biol 2009, 16, 509-516.
21. Selmer, M.,; Al-Karadaghi, S.,; Hirokawa, G.,; Kaji, A.,; Liljas, A., Science 1999, 286, 2349-2352.
22. Putnam, C. D.,; Tainer, J. A., DNA Repair (Amst) 2005, 4, 1410-1420.
23. Petoukhov, M. V.,; Svergun, D. I., Curr Opin Struct Biol 2007, 17, 562-571.
24. Hura, G. L.,; Menon, A. L.,; Hammel, M.,; Rambo, R. P.,; Poole, F. L., II,; Tsutakawa, S. E.,; Jenney, F. E., Jr,; Classen, S.,; Frankel, K. A.,; Hopkins, R. C.,; Yang, S. J.,; Scott, J. W.,; Dillard, B. D.,; Adams, M. W.,; Tainer, J. A., Nat Methods 2009, 6, 606-612.
25. Putnam, C. D.,; Hammel, M.,; Hura, G. L.,; Tainer, J. A., Q Rev Biophys 2007, 40, 191-285.
26. Glatter, O.,; Kratky, O., Small Angle X-ray Scattering; Academic Press: London, 1982.
27. Guinier, A., Ann Phys 1939, 12, 76.
28. Mylonas, E.,; Svergun, D. I., J Appl Crystallogr 2007, 40, s245-s249.
29. Fischer, H.,; de Oliveira Neto, M.,; Napolitano, H. B.,; Polikarpov, I.,; Craievich, A. F., J Appl Crystallogr 2009, 43, 101-109.
30. Koch, M. H.,; Vachette, P.,; Svergun, D. I., Q Rev Biophys 2003, 36, 147-227.
31. Durand, D.,; Vives, C.,; Cannella, D.,; Perez, J.,; Pebay-Peyroula, E.,; Vachette, P.,; Fieschi, F., J Struct Biol 2010, 169, 45-53.
32. Porod, G., Kolloid Zeitschrift 1951, 124, 31.
33. Debye, P.,; Anderson, J. H. R.,; Brumberger, H., J Appl Phys 1957, 28, 679-683.
34. Ruland, W., J Appl Crystallogr 1971, 4, 70-73.
35. Konarev, P. V.,; Volkov, V. V.,; Sokolova, A. V.,; Koch, M. H. J.,; Svergun, D. I., J Appl Crystallogr 2003, 36, 1277-1282.
36. Quillin, M. L.,; Wingfield, P. T.,; Matthews, B. W., Proc Natl Acad Sci USA 2006, 103, 19749-19753.
37. Squire, P. G.,; Himmel, M. E., Arch Biochem Biophys 1979, 196, 165-177.
38. Kozak, M., J Appl Crystallogr 2005, 38, 4.
39. 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.
40. Stoddard, C. D.,; Montange, R. K.,; Hennelly, S. P.,; Rambo, R. P.,; Sanbonmatsu, K. Y.,; Batey, R. T., Structure 2010, 18, 787-797.
41. Rambo, R. P.,; Tainer, J. A., RNA 2010, 16, 638-646.
42. Williams G. J.,; Williams, R. S.,; Williams, J. S.,; Moncalian, G.,; Arvai, A.,; Limbo, O.,; Guenther, G.,; SilDas, S.,; Hammel, M.,; Russel, P.,;<, Tainer, J.A., Nat Struct Biol 2011, 18, 423-431.
43. Franke, D.,; Svergun, D., J Appl Crystallogr 2009, 42, 342-346.
44. Svergun, D. I.,; Petoukhov, M. V.,; Koch, M. H., Biophys J 2001, 80, 2946-2953.
45. Matthews, B. W., J Mol Biol 1968, 33, 491-497.
46. Mareuil, F.,; Sizun, C.,; Perez, J.,; Schoenauer, M.,; Lallemand, J. Y.,; Bontems, F., Eur Biophys J 2007, 37, 95-104.
47. Parikh, S. S.,; Walcher, G.,; Jones, G. D.,; Slupphaug, G.,; Krokan, H. E.,; Blackburn, G. M.,; Tainer, J. A., Proc Natl Acad Sci USA 2000, 97, 5083-5088.
48. Huffman, J. L.,; Sundheim, O.,; Tainer, J. A., Mutat Res 2005, 577, 55-76.
49. Tsutakawa, S. E.,; Classen, S.,; Chapados, B. R.,; Arvai, A.,; Finger, L. D.,; Guenther, G.,; Tomlinson, C. G.,; Thompson, P.,; Sarker, A. H.,; Shen, B.,; Cooper, P. K.,; Grasby, J. A.,; Tainer, J. A., Cell 2011,accepted.
50. Sarker, A. H.,; Tsutakawa, S. E.,; Kostek, S.,; Ng, C.,; Shin, D. S.,; Peris, M.,; Campeau, E.,; Tainer, J. A.,; Nogales, E.,; Cooper, P. K., Mol Cell 2005, 20, 187-198.
51. Tainer, J. A.,; McCammon, J. A.,; Ivanov, I., J Am Chem Soc, 132, 7372-7378.
52. 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.
53. Perry, J. J.,; Cotner-Gohara, E.,; Ellenberger, T.,; Tainer, J. A., Curr Opin Struct Biol 2010, 20, 283-294.
54. 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.
55. Fieser, T. M.,; Tainer, J. A.,; Geysen, H. M.,; Houghten, R. A.,; Lerner, R. A., Proc Natl Acad Sci USA 1987, 84, 8568-8572.
56. Hallewell, R. A.,; Laria, I.,; Tabrizi, A.,; Carlin, G.,; Getzoff, E. D.,; Tainer, J. A.,; Cousens, L. S.,; Mullenbach, G. T., J Biol Chem 1989, 264, 5260-5268.
57. Schnecke, V.,; Swanson, C. A.,; Getzoff, E. D.,; Tainer, J. A.,; Kuhn, L. A., Proteins 1998, 33, 74-87.
58. Garcin, E. D.,; Arvai, A. S.,; Rosenfeld, R. J.,; Kroeger, M. D.,; Crane, B. R.,; Andersson, G.,; Andrews, G.,; Hamley, P. J.,; Mallinder, P. R.,; Nicholls, D. J.,; St-Gallay, S. A.,; Tinker, A. C.,; Gensmantel, N. P.,; Mete, A.,; Cheshire, D. R.,; Connolly, S.,; Stuehr, D. J.,; Aberg, A.,; Wallace, A. V.,; Tainer, J. A.,; Getzoff, E. D., Nat Chem Biol 2008, 4, 700-707.
59. Das, R.,; Baker, D., Annu Rev Biochem 2008, 77, 363-382.
60. Svergun, D. I.,; Feigin, L. A.,; Taylor, G. W., Structure Analysis by Small-Angle X-ray and Neutron Scattering; Plenum Press: New York, 1987.