Analytical trapping: Extraction of time-independent structures from time-dependent crystallographic data

Journal of Structural Biology

Volumn 147, Issue 3, 2004, Pages 211-222

  Rajagopal, Sudarshan ^a   Kostov, Konstantin S ^a   Moffat, Keith ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

Analytical trapping; Chemical kinetic mechanism; Cluster analysis; Laue diffraction; Photoactive yellow protein; Singular value decomposition; Time resolved crystallography

Indexed keywords

PHOTOACTIVE YELLOW PROTEIN;

ALGORITHM; ANALYTIC METHOD; BLUE LIGHT; CHEMICAL REACTION; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; CRYSTALLOGRAPHY; DENSITY; ELECTRON; EXTRACTION; KINETICS; MACROMOLECULE; MATHEMATICAL ANALYSIS; PHOTORECEPTOR; PRIORITY JOURNAL; REVIEW; SIMULATION;

BACTERIA (MICROORGANISMS);

EID: 4344653824     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2004.04.007     Document Type: Article

References (34)

1. Anderson, S., 2003. Structural changes in the E46Q mutant of PYP. PhD thesis, University of Chicago, USA
2. Anderson, S., Srajer, V., Pahl, R., Rajagopal, S., Schotte, F., Anfinrud, P., Wulff, M., Moffat, K., 2004. Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein, Structure, in press
3. Baxter R.H., Pomarenko N., Srajer V., Pahl R., Moffat K., Norris J.R. Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center. Proc. Natl. Acad. Sci. USA. 101:2004;5982-5987
4. Bourgeois D., Ursby T., Wulff M., Pradervand C., Legrand A., Schildkamp W., Laboure S., Srajer V., Teng T.Y., Roth M., Moffat K. Feasibility and realization of single-pulse laue diffraction on macromolecular crystals at ESRF. J. Synchrotron Radiat. 3:1996;65-74
5. Bourgeois D., Vallone B., Schotte F., Arcovito A., Miele A.E., Sciara G., Wulff M., Anfinrud P., Brunori M. Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography. Proc. Natl. Acad. Sci. USA. 100:2003;8704-8709
6. Cruickshank, D.W.J., Helliwell, J.R., Johnson, L.N., Royal Society (Great Britain), 1992. Time-resolved Macromolecular Crystallography. Oxford University Press, Oxford, 334 p. ([332], leaves of plates)
7. de Groot B.L., Daura X., Mark A.E., Grubmuller H. Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds. J. Mol. Biol. 309:2001;299-313
8. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95:1998;14863-14868
9. Genick U.K., Borgstahl G.E., Ng K., Ren Z., Pradervand C., Burke P.M., Srajer V., Teng T.Y., Schildkamp W., McRee D.E., Moffat K., Getzoff E.D. Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science. 275:1997;1471-1475
10. Goutte C., Toft P., Rostrup E., Nielsen F., Hansen L.K. On clustering fMRI time series. Neuroimage. 9:1999;298-310
11. Helliwell J.R., Nieh Y.P., Raftery J., Cassetta A., Habash J., Carr P.D., Ursby T., Wulff M., Thompson A.W., Niemann A.C., Hadener A. Time-resolved structures of hydroxymethylbilane synthase (Lys59Gln mutant) as it is loaded with substrate in the crystal determined by Laue diffraction. Faraday Trans. 94:1998;2615-2622
12. Henry E., Hofrichter J. Singular value decomposition: application to analysis of experimental data. Methods Enzymol. 210:1992;129-192
13. Heyer L.J., Kruglyak S., Yooseph S. Exploring expression data: identification and analysis of coexpressed genes. Genome Res. 9:1999;1106-1115
14. Jain A.K., Dubes R.C. Algorithms for Clustering Data. 1988;Prentice-Hall, Englewood Cliffs, New Jersey
15. Jain A.K., Murty M.N., Flynn P.J. Data clustering: a review. ACM Comp. Surv. 31:1999;264-323
16. Moffat K. Time-resolved macromolecular crystallography. Annu. Rev. Biophys. Biophys. Chem. 18:1989;309-323
17. Moffat K. Time-resolved biochemical crystallography: a mechanistic perspective. Chem. Rev. 101:2001;1569-1581
18. Moffat K., Henderson R. Freeze trapping of reaction intermediates. Curr. Opin. Struct. Biol. 5:1995;656-663
19. Perman B., Srajer V., Ren Z., Teng T., Pradervand C., Ursby T., Bourgeois D., Schotte F., Wulff M., Kort R., Hellingwerf K., Moffat K. Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle. Science. 279:1998;1946-1950
20. Rajagopal S., Anderson S., Schmidt M., Moffat K. Analysis of experimental time-resolved crystallographic data by singular value decomposition. Acta Cryst. D. 60:2004;860-871
21. Rajagopal, S., Anderson, S., Srajer, V., Schmidt, M., Pahl, R., Moffat, K., in preparation. A Structural Pathway for Signaling in the E46Q mutant of Photoactive Yellow Protein
22. Ren Z., Bourgeois D., Helliwell J., Moffat K., Srajer V., Stoddard B. Laue crystallography: coming of age. J. Synchrotron Radiat. 6:1999;891-917
23. Ren Z., Perman B., Srajer V., Teng T.Y., Pradervand C., Bourgeois D., Schotte F., Ursby T., Kort R., Wulff M., Moffat K. A molecular movie at 1.8. Å resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds Biochemistry. 40:2001;13788-13801
24. Saeed A.I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., Thiagarajan M., Sturn A., Snuffin M., Rezantsev A., Popov D., Ryltsov A., Kostukovich E., Borisovsky I., Liu Z., Vinsavich A., Trush V., Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 34:2003;374-378
25. Schlichting I., Chu K. Trapping intermediates in the crystal: ligand binding to myoglobin. Curr. Opin. Struct. Biol. 10:2000;744-752
26. Schmidt M., Pahl R., Srajer V., Anderson S., Ren Z., Ihee H., Rajagopal S., Moffat K. Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved X-ray data. Proc. Natl. Acad. Sci. USA. 101:2004;4799-4804
27. Schmidt M., Rajagopal S., Ren Z., Moffat K. Application of singular value decomposition to the analysis of time-resolved macromolecular X-ray data. Biophys. J. 84:2003;2112-2129
28. Schotte F., Lim M., Jackson T.A., Smirnov A.V., Soman J., Olson J.S., Phillips G.N. Jr., Wulff M., Anfinrud P.A. Watching a protein as it functions with 150-ps time-resolved X-ray crystallography. Science. 300:2003;1944-1947
29. Sherlock G. Analysis of large-scale gene expression data. Curr. Opin. Immunol. 12:2000;201-205
30. Srajer V., Ren Z., Teng T.Y., Schmidt M., Ursby T., Bourgeois D., Pradervand C., Schildkamp W., Wulff M., Moffat K. Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction. Biochemistry. 40:2001;13802-13815
31. Srajer V., Teng T., Ursby T., Pradervand C., Ren Z., Adachi S., Schildkamp W., Bourgeois D., Wulff M., Moffat K. Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography. Science. 274:1996;1726-1729
32. Stoddard B.L. Caught in a chemical trap. Nat. Struct. Biol. 3:1996;907-909
33. Terwilliger T.C., Berendzen J. Difference refinement - obtaining differences between two related structures. Acta Cryst. D. 51:1995;609-618
34. Ursby T., Bourgeois D. Improved estimation of structure-factor difference amplitudes from poorly accurate data. Acta Cryst. A. 53:1997;564-575