Solution structural ensembles of substrate-free cytochrome P450 cam

Biochemistry

Volumn 51, Issue 16, 2012, Pages 3383-3393

  Asciutto, Eliana K ^a   Young, Matthew J ^b   Madura, Jeffry ^a   Pochapsky, Susan Sondej ^b   Pochapsky, Thomas C ^b  

^a DUQUESNE UNIVERSITY   (United States)

^b BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESSIBLE VOLUME; ACTIVE SITE; ASYMMETRIC BROADENING; CHEMICAL SHIFT PERTURBATIONS; CYTOCHROME P450; ELECTRONIC ENVIRONMENTS; ENZYME CONFORMATIONS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MULTIPLE REGIONS; MULTIPLE RESONANCES; RELATIVE ORIENTATION; RESIDUAL DIPOLAR COUPLINGS; RING CURRENTS; SECONDARY STRUCTURES; SOLUTION STRUCTURES; STRUCTURAL FEATURE; SUBSTRATE REMOVAL; SUBSTRATE-BOUND; SUBSTRATE-FREE;

AMIDES; CAMS; ENZYMES; HYDROGEN BONDS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE;

SUBSTRATES;

CYP101A1; CYTOCHROME P450; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SIMULATION;

CAMPHOR 5-MONOOXYGENASE; CATALYTIC DOMAIN; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, SECONDARY; SOLUTIONS; SUBSTRATE SPECIFICITY;

EID: 84860132456     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi300007r     Document Type: Article

References (35)

1. Fischer, E. (1894) Einfluss der Configuration auf die Wirkung der Enzyme Ber. Dtsch. Chem. Ges. 27, 2985-2993
2. Koshland, D. E. (1958) Application of a theory of enzyme specificity to protein synthesis Proc. Natl. Acad. Sci. U.S.A. 44, 98-104
3. Niesen, M. J. M., Bhattacharya, S., and Vaidehi, N. (2011) The role of conformational ensembles in ligand recognition in G-protein coupled receptors J. Am. Chem. Soc. 133, 13197-13204
4. Fraser, J. S., van den Bedem, H., Samelson, A. J., Lang, P. T., Holton, J. M., Echols, N., and Alber, T. (2011) Accessing protein conformational ensembles using room-temperature X-ray crystallography Proc. Natl. Acad. Sci. U.S.A. 108, 16247-16252
5. Frauenfelder, H., Petsko, G. A., and Tsernoglou, D. (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics Nature 280, 558-563
6. 2 ferredoxin Biochemistry 40, 5602-5614
7. Labeikovsky, W., Eisenmesser, E. Z., Bosco, D. A., and Kern, D. (2007) Structure and dynamics of Pin1 during catalysis by NMR J. Mol. Biol. 367, 1370-1381
8. Fetler, L., Kantrowitz, E. R., and Vachette, P. (2007) Direct observation in solution of a preexisting structural equilibrium for a mutant of the allosteric aspartate transcarbamoylase Proc. Natl. Acad. Sci. U.S.A. 104, 495-500
9. cam upon binding of putidaredoxin J. Am. Chem. Soc. 127, 6974-6976
10. cam J. Biol. Chem. 251, 1116-1124
11. cam: Probing the effector role of putidaredoxin in catalysis J. Biol. Chem. 280, 42134-42141
12. cam Structure 16, 916-923
13. cam J. Mol. Biol. 388, 801-814
14. cam Biochemistry 50, 1664-1671
15. cam: Practical consequences and engineering of a monomeric enzyme Protein Eng. 10, 1357-1361
16. 5 and putidaredoxin, two effectors of camphor hydroxylase activity Biochemistry 45, 3887-3897
17. Ruckert, M. and Otting, G. (2000) Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments J. Am. Chem. Soc. 122, 7793-7797
18. Weigelt, J. (1998) Single scan, sensitivity- and gradient-enhanced TROSY for multidimensional NMR experiments J. Am. Chem. Soc. 120, 12706-12706
19. Goddard, T. D. and Kneller, D. G. (2008) SPARKY 3, University of California, San Francisco.
20. Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Crowley, M., Walker, R. C., Zhang, W., Merz, K. M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K. F., Paesani, F. V., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., and Kollman, P. A. (2008) AMBER 10, University of California, San Francisco.
21. cam J. Mol. Biol. 195, 687-700
22. Lee, Y. T., Wilson, R. F., Rupniewski, I., and Goodin, D. B. (2010) P450cam visits an open conformation in the absence of substrate Biochemistry 49, 3412-3419
23. Pochapsky, T. C., Kazanis, S., and Dang, M. (2010) Conformational plasticity and structure/function relationships in cytochromes P450 Antioxid. Redox Signaling 13, 1273-1296
24. Dang, M., Pochapsky, S. S., and Pochapsky, T. C. (2011) Spring-loading the active site of cytochrome P450cam Metallomics 3, 339-343
25. Raag, R. and Poulos, T. L. (1989) The structural basis for substrate-induced changes in redox potential and spin equilibrium in cytochrome P450cam Biochemistry 28, 917-922
26. cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms J. Mol. Biol. 303, 797-811
27. Sligar, S. G. (1976) Coupling of spin, substrate and redox equilibria in cytochrome P450 Biochemistry 15, 5399-5406
28. cam J. Phys. Chem. Lett. 2, 158-164
29. cam Biochemistry 48, 4254-4261
30. Poulos, T. L., Finzel, B. C., and Howard, A. J. (1986) Crystal structure of substrate-free Pseudomonas putida cytochrome P450 Biochemistry 25, 5314-5322
31. cam Biochemistry 45, 14379-14388
32. Ma, M., Bell, S. G., Yang, W., Hao, Y. M., Rees, N. H., Bartlam, M., Zhou, W. H., Wong, L. L., and Rao, Z. H. (2011) Structural analysis of CYP101C1 from Novosphingobium aromaticivorans DSM12444 ChemBioChem 12, 88-99
33. Poulos, T. L. (2007) Structural biology of P450-oxy complexes Drug Metab. Rev. 39, 557-566
34. Miao, Y. L. and Baudry, J. (2011) Active site hydration and water diffusion in cytochrome P450cam: A highly dynamic process Biophys. J. 101, 1493-1503
35. DeLano, W. L. (2008) The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA.