Simulation-based fitting of protein-protein interaction potentials to SAXS experiments

Biophysical Journal

Volumn 94, Issue 12, 2008, Pages 4924-4931

  Seung, Joong Kim ^a   Dumont, Charles ^a   Gruebele, Martin ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CHEMICAL MODEL; COMPUTER SIMULATION; CRYSTALLOGRAPHY; ELECTROMAGNETIC FIELD; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN BINDING; RADIATION SCATTERING; SMALL ANGLE SCATTERING;

ALGORITHMS; COMPUTER SIMULATION; CRYSTALLOGRAPHY; ELECTROMAGNETIC FIELDS; MODELS, CHEMICAL; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SCATTERING, RADIATION; SCATTERING, SMALL ANGLE;

EID: 45849120983     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.123240     Document Type: Article

References (29)

1. Tardieu, A., A. Le Verge, M. Malfois, F. Bonneté, S. Finet, M. Riés-Kautt, and L. Belloni. 1999. Proteins in solution: from x-ray scattering intensities to interaction potentials. J. Cryst. Growth. 196:193-203.
2. Javid, N., K. Vogtt, C. Krywka, M. Tolan, and R. Winter. 2007. Protein-protein interactions in complex cosolvent solutions. Phys. Chem. Chem. Phys. 8:679-689.
3. Otting, G., and K. Wüthrich. 1989. Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules. Biochemistry. 111:1871-1875.
4. Zanotti, J. M., M. C. Bellissent-Funel, and J. Parello. 1999. Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin. Biophys. J. 76:2390-2411.
5. Rösgen, J., B. M. Pettitt, and D. W. Bolen. 2005. Protein folding, stability, and solvation structure in osmolyte solutions. Biophys. J. 89:2988-2997.
6. Leitner, D. M., M. Havenith, and M. Gruebele. 2006. Biomolecule large-amplitude motion and solvation dynamics: modeling and probes from THz to X-rays. Int. Rev. Phys. Chem. 25:553-582.
7. Ebbinghaus, S., S. J. Kim, M. Heyden, X. Yu, U. Heugen, M. Gruebele, D. Leitner, and M. Havenith. 2007. An extended dynamical solvation shell around proteins. Proc. Natl. Acad. Sci. USA. In press.
8. Yang, W. Y., and M. Gruebele. 2003. Folding at the speed limit. Nature. 423:193-197.
9. Silow, M., Y. Tan, A. R. Fersht, and M. Oliveberg. 1999. Formation of short-lived protein aggregates directly from the coil in two-state folding. Biochemistry. 38:13006-13012.
10. Yang, W., and M. Gruebele. 2006. Binary and ternary aggregation with tethered protein constructs. Biophys. J. 90:2930-2937.
11. Otzen, D. E., S. Miron, M. Akke, and M. Oliveberg. 2004. Transient aggregation and stable dimerization induced by introducing an Alzheimer sequence into a water-soluble protein. Biochemistry. 43:12964-12978.
12. Niehbur, M., and M. H. J. Koch. 2005. Effects of urea and trimethylamine-N-oxide (TMAO) on the interactions of lysozyme in solution. Biophys. J. 89:1978-1983.
13. 6-85. Protein Sci. 15:2596-2604.
14. Ghaemmaghami, S., J. M. Word, R. E. Burton, J. S. Richardson, and T. G. Oas. 1998. Folding kinetics of a fluorescent variant of monomeric lambda repressor. Biochemistry. 37:9179-9185.
15. Larson, S. M., A. A. D. Nardo, and A. R. Davidson. 2000. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol. 303:433-446.
16. Edelhoch, H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry. 6:1948-1954.
17. Fischetti, R., S. Stepanov, G. Rosenbaum, R. Barrea, E. Black, D. Gore, R. Heurich, E. Kondrashkina, A. J. Kropf, S. Wang, K. Zhang, T. C. Irving, and G. B. Bunke. 2004. The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source. J. Synchrotron Radiat. 11:399-405.
18. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
19. Chandler, D. 1989. Modern Statistical Mechanics. Oxford University Press, Oxford, UK.
20. Rayleigh, L. 1914. On the diffraction of light by spheres of small relative index. Proc. Roy. Soc. Lond. A-90:219-225.
21. Rayleigh, L. 1910. The incidence of light upon a transparent sphere of dimension comparable to the wavelength. Proc. Roy. Soc. Lond. A-84:25-46.
22. Suhonen, H. 2005. Simulation of Small-Angle X-Ray Scattering from Collagen Fibrils. Master's thesis. University of Helsinki, Helsinki, Finland.
23. Moré, J. J., B. S. Garbow, and K. E. Hillstrom. 1980. User Guide for MINPACK-1. In Argonne National Laboratory Report ANL-80-74. Argonne National Laboratory, Argonne, IL. 1-48.
24. Moré, J. J., D. C. Sorensen, and K. E. Hillstrom. 1984. The MINPACK Project. In Sources and Development of Mathematical Software. W. J. Cowell, editor. Prentice-Hall, New York. 88-111.
25. Svergun, D., C. Barberato, and M. H. J. Koch. 1995. CRYSOL: a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Cryst. 28:768-773.
26. Svergun, D., S. Richard, M. H. J. Koch, Z. Sayers, S. Kuprin, and G. Zaccai. 1998. Hydration shell in solution: validation by x-ray and neutron scattering. Proc. Natl. Acad. Sci. USA. 95:2267-2272.
27. Narayanan, J., and X. Y. Liu. 2003. Protein interactions in undersaturated and supersaturated solutions: a study using light and x-ray scattering. Biophys. J. 84:523-532.
28. Bosdevant, N., D. Borgis, and T. Ha-Duong. 2007. A coarse-grained protein-protein potential derived from an all-atom force field. J. Phys. Chem. B. 111:9390-9399.
29. Humphrey, W. F., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14:33-38.