Modeling structural heterogeneity in proteins from X-ray data

Springer Tracts in Advanced Robotics

Volumn 57, Issue , 2010, Pages 551-566

  Dhanik, Ankur ^a   Van Den Bedem, Henry ^b   Deacon, Ashley ^b   Latombe, Jean Claude ^a  

^a Stanford University   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3-D SPACE; ATOMIC POSITIONS; BEST MATCH; CRYSTALLINE SAMPLES; CUMULATIVE DISTRIBUTION; DIFFRACTION IMAGES; ELECTRON DENSITIES; HARMONIC DISTRIBUTION; MODELING METHOD; PHASE DETERMINATION; PROTEIN CONFORMATION; PROTEIN FRAGMENTS; SIDE CHAINS; STRUCTURAL HETEROGENEITY; X RAY DATA;

ATOMS; CARRIER CONCENTRATION; CRYSTAL ATOMIC STRUCTURE; ELECTRIC DIPOLE MOMENTS; ELECTRIC DISCHARGE MACHINING; ELECTRON DENSITY MEASUREMENT; ELECTRONS; MICROMACHINING; PROTEINS; ROBOTICS; ROBOTS; THREE DIMENSIONAL;

CONFORMATIONS;

EID: 77950011528     PISSN: 16107438     EISSN: 1610742X     Source Type: Book Series    
DOI: 10.1007/978-3-642-00312-7_34     Document Type: Conference Paper

References (29)

1. Afonine, P.V., Kunstleve, R.W.G., Adams, P.D.: The phenix refinement framework. CCP4 newsletter 42 (2005)
2. Berman, H.M., Henrick, K., Nakamura, H., Arnold, E.: Reply to: Is one solution good enough? Nature Structural and Molecular Biology 13, 185 (2006)
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Research, 235-242 (2000)
4. Burling, F.T., Weis, W.I., Flaherty, K.M., Brunger, A.T.: Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 271(5245), 72-77 (1996)
5. Coutsias, E.A., Seok, C., Jacobson, M.P., Dill, K.A.: A kinematic view of loop closure. Journal of Computational Chemistry 25(4), 510-528 (2004)
6. Davis, I.W., Arendall, W.B., Richardson, D.C., Richardson, J.S.: The backrub motion: How protein backbone shrugs when a sidechain dances. Structure 14, 265-274 (2006)
7. DePristo, M.A., de Bakker, P.I., Blundell, T.L.: Heterogeneity and inaccuracy in protein structures solved by x-ray crystallography. Structure 12, 831-838 (2004)
8. Dhanik, A., Yao, P., Marz, N., Propper, R., Kou, C., Liu, G., van den Bedem, H., Latombe, J.C.: Efficient algorithms to explore conformation spaces of flexible protein loops. In: Giancarlo, R., Hannenhalli, S. (eds.) WABI 2007. LNCS (LNBI), vol. 4645, pp. 265-276. Springer, Heidelberg (2007)
9. DiMaio, F., Kondrashov, D.A., Bitto, E., Soni, A., Bingman, C.A., Phillips Jr., G.N., Shavlik, J.W.: Creating protein models from electron-density maps using particle-filtering methods. Bioinformatics 23(21), 2851-2858 (2007)
10. DiMaio, F., Shavlik, J., Phillips, G.N.: A probabilistic approach to protein backbone tracing in electron density maps. Bioinformatics 22(14), e81-e89 (2006)
11. Drenth, J.: Principles of protein X-ray crystallography. Springer, New York (1999)
12. Frauenfelder, H., Sligar, S.G., Wolynes, P.G.: The energy landscapes and motions of proteins. Science 254(5038), 1598-1603 (1991)
13. Furnham, N., Blundell, T.L., DePristo, M.A., Terwilliger, T.C.: Is one solution good enough? Nature Structure Molecular Biology 13(3), 184-185 (2006)
14. Heimer, R.L.: The common optimization interface for operations research: promoting open-source software in the operations research community. IBM Journal of Research and Development 47(1), 57-66 (2003)
15. Ioerger, T., Sacchettini, J.: The textal system: Artificial intelligence techniques for automated protein model building. In: Carter, C.W., Sweet, R.M. (eds.) Methods in Enzymology, pp. 244-270. Springer, Heidelberg (2003)
16. Kuriyan, J., Petsko, G.A., Levy, R.M., Karplus,M.: Effect of anisotropy and anharmonicity on protein crystallographic refinement: An evaluation by molecular dynamics. Proteins: Structure, Function, and Bioinformatics 190, 227-254 (1986)
17. Levin, E.J., Kondrashov, D.A.,Wesenberg, G.E., Phillips Jr., G.N.: Ensemble refinement of protein crystal structures: validation and application. Structure 15, 1040-1052 (2007)
18. Lovell, S.C., Word, J.M., Richardson, J.S., Richardson, D.C.: The penultimate rotamer library. Proteins: Structure, Function, and Bioinformatics 40(3), 389-408 (2000)
19. Okazaki, K.-I., Koga, N., Takada, S., Onuchic, J.N., Wolynes, P.G.: Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. PNAS 103, 11844-11849 (2006)
20. Perrakis, A., Sixma, T.K., Wilson, K.S., Lamzin, V.S.: wARP: Improvement and extension of crystallographic phases by weighted averaging ofmultiple-refined dummy atomic models. Acta Crystallographica D 53, 448-455 (1997)
21. Read, R.J.: Improved fourier coefficients for maps using phases from partial structures with errors. Acta Crystallographica A 42, 140-149 (1986)
22. Schomaker, V., Trueblood, K.N.: On the rigid-body motion of molecules in crystals. Acta Crystallographica B 24, 63 (1968)
23. Terwilliger, T.C.: Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallographica D 59, 38-44 (2003)
24. Terwilliger, T.C.: Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement. Acta Crystallographica D 59, 1174-1182 (2003)
25. Terwilliger, T.C., Grosse-Kunstleve, R.W., Afonine, P.V., Adams, P.D., Moriarty, N.W., Zwart, P., Read, R.J., Turk, D., Hung, L.-W.: Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Crystallographica D 63, 597-610 (2007)
26. Tosatto, S.C.E., Bindewald, E., Hesser, J., Manner, R.: A divide and conquer approach to fast loop modeling. Protein Engineering 15(4), 279-286 (2002)
27. van den Bedem, H., Lotan, I., Latombe, J.C., Deacon, A.M.: Real-space protein-model completion: an inverse-kinematics approach. Acta Crystallographica D 61, 2-13 (2005)
28. Vitkup, D., Ringe, D., Karplus, M., Petsko, G.A.: Why protein R-factors are so large: A self-consistent analysis. Proteins: Structure, Function, and Genetics 46, 345-354 (2002)
29. Wilson, M.A., Brunger, A.T.: The 1.0 Å crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. Journal of Molecular Biology 301(5), 1237-1256 (2000)