Conformation and dynamics of a rhodamine probe attached at two sites on a protein: Implications for molecular structure determination in situ

Journal of the American Chemical Society

Volumn 130, Issue 50, 2008, Pages 17120-17128

  De Simone, Alfonso ^a   Corrie, John E T ^b   Dale, Robert E ^c   Irving, Malcolm ^c   Fraternali, Franca ^c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^c KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIFUNCTIONAL; CARBOXYLATE GROUPS; CYSTEINE RESIDUES; DIASTEREOISOMERS; FLUORESCENCE POLARIZATIONS; HYDRATION EFFECTS; HYDROPHOBIC INTERACTIONS; IN-SITU; MODEL SYSTEMS; NANO-SECONDS; NMR RELAXATIONS; PHENYL RINGS; POLARIZED FLUORESCENCES; POLYALANINE; PROTEIN COMPLEXES; PROTEIN COMPONENTS; PROTEIN SURFACES; REPLICA EXCHANGE MOLECULAR DYNAMICS; ROTATIONAL MOTIONS; STERIC FACTORS; STRUCTURE DETERMINATIONS; TERMINAL REGIONS; TIME SCALES; TROPONIN;

CARBOXYLATION; CONFORMATIONS; FLOW INTERACTIONS; FLUORESCENCE; HYDROGEN; HYDROGEN BONDS; HYDROPHOBICITY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; POLARIZATION; QUANTUM CHEMISTRY;

DYNAMICS;

ANIMALS; CHICKENS; COMPUTER SIMULATION; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR PROBES; PEPTIDES; RHODAMINES; SURFACE PROPERTIES; TIME FACTORS; TROPONIN C;

EID: 58049221123     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja807264v     Document Type: Article

References (36)

1. Hirshberg, M.; Henrick, K.; Lloyd Haire, L.; Vasisht, N.; Brune, M.; Corrie, J. E. T.; Webb, M. R. Biochemistry 1998, 37, 10381-10385.
2. Dutta, S.; Berman, H. M. Structure 2005, 13, 381-388.
3. Veigel, C.; Coluccio, L. M.; Jontes, J. D.; Sparrow, J. C.; Milligan, R. A.; Molloy, J. E. Nature 1999, 398, 530-533.
4. Yildiz, A.; Forkey, J. N.; McKinney, S. A.; Ha, T.; Goldman, Y. E.; Selvin, P. R. Science 2003, 300, 2061-2065.
5. Forkey, J. N.; Quinlan, M. E.; Shaw, M. A.; Corrie, J. E. T.; Goldman, Y. E. Nature 2003, 422, 399-404.
6. Corrie, J. E. T.; Brandmeier, B. D.; Ferguson, R. E.; Trentham, D. R.; Kendrick-Jones, J.; Hopkins, S. C.; van der Heide, U. A.; Goldman, Y. E.; Sabido-David, C.; Dale, R. E.; Criddle, S.; Irving, M. Nature 1999, 400, 425-430.
7. Hopkins, S. C.; Sabido-David, C.; van der Heide, U. A.; Ferguson, R. E.; Brandmeier, B. D.; Dale, R. E.; Kendrick-Jones, J.; Corrie, J. E. T.; Trentham, D. R.; Irving, M.; Goldman, Y. E. J. Mol. Biol. 2002, 318, 1275-1291.
8. Ferguson, R. E.; Sun, Y. B.; Mercier, P.; Brack, A. S.; Sykes, B. D.; Corrie, J. E. T.; Trentham, D. R.; Irving, M. Mol. Cell 2003, 11, 865-874.
9. Sun, Y. B.; Brandmeier, B.; Irving, M. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 17771-17776.
10. Mercier, P.; Ferguson, R. E.; Irving, M.; Corrie, J. E. T.; Trentham, D. R.; Sykes, B. D. Biochemistry 2003, 42, 4333-4348.
11. Julien, O.; Sun, Y. B.; Knowles, A. C.; Brandmeier, B. D.; Dale, R. E.; Trentham, D. R.; Corrie, J. E. T.; Sykes, B. D.; Irving, M. Biophys. J. 2007, 93, 1008-1020.
12. Dale, R. E.; Hopkins, S. C.; van der Heide, U. A.; Marszałek, T.; Irving, M.; Goldman, Y. E. Biophys. J. 1999, 76, 1606-1618.
13. Julien, O.; Mercier, P.; Spyracopoulos, L.; Corrie, J. E. T.; Sykes, B. D. J. Am. Chem. Soc. 2008, 130, 2602-2609.
14. Schröder, G. F.; Alexiev, U.; Grubmüller, H. Biophys. J. 2005, 89, 3757-3770.
15. Ivanova, A.; Jezierski, G.; Vladimirov, E.; Rösch, N. Biomacromolecules 2007, 8, 3429-3438.
16. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151.
17. Periole, X.; Mark, A. E. J. Chem. Phys. 2007, 126, 014903.
18. Baumketner, A.; Shea, J. E. J. Mol. Biol. 2007, 366, 275-285.
19. Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A. J. Chem. Phys. 2004, 121, 10748-10756.
20. Gnanakaran, S.; Garcia, A. E. Proteins 2005, 59, 773-782.
21. Sgourakis, N. G.; Yan, Y. L.; McCallum, S. A.; Wang, C. Y.; Garcia, A. E. J. Mol. Biol. 2007, 368, 1448-1457.
22. Cavallo, L.; Moore, M. H.; Corrie, J. E. T.; Fraternali, F. J. Phys. Chem. A 2004, 108, 7744-7751.
23. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269-6271.
24. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56.
25. Van Gunsteren, W. F.; Billeter, S.; Eising, A.; Hunenberger, P. H.; Kruger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulations: The GROMOS96 Manual and User Guide; Verlag der Fachvereine: Zürich, 1996.
26. Darden, T.; Perera, L.; Li, L.; Pedersen, L. Structure Fold. Des. 1999, 7, R55-R60.
27. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. J. Chem. Phys. 1953, 21, 1087-1092.
28. Okabe, T.; Kawata, M.; Okamoto, Y.; Mikami, M. Chem. Phys. Lett. 2001, 335, 435-439.
29. Seibert, M. M.; Patriksson, A.; Hess, B.; van der Spoel, D. J. Mol. Biol. 2005, 354, 173-183.
30. De Simone, A.; Dodson, G. G.; Verma, C. S.; Zagari, A.; Fraternali, F. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7535-7540.
31. De Simone, A.; Spadaccini, R.; Temussi, P. A.; Fraternali, F. Biophys. J. 2006, 90, 3052-3061.
32. De Simone, A.; Dodson, G. G.; Fraternali, F.; Zagari, A. FEBS Lett. 2006, 580, 2488-2494.
33. Lijnzaad, P.; Berendsen, H. J.; Argos, P. Proteins 1996, 25, 389-397.
34. Penzkofer, A.; Wiedmann, J. Opt. Commun. 1980, 35, 81-86.
35. van der Heide, U. A.; Hopkins, S. C.; Goldman, Y. E. Biophys. J. 2000, 78, 2138-2150.
36. Hopkins, S. C.; Sabido-David, C.; Corrie, J. E. T.; Irving, M.; Goldman, Y. E. Biophys. J. 1998, 74, 3093-3110.