Structural and Dynamic Implications of an Effector-induced Backbone Amide cis-trans Isomerization in Cytochrome P450cam

Journal of Molecular Biology

Volumn 388, Issue 4, 2009, Pages 801-814

  Asciutto, Eliana K ^a   Madura, Jeffry D ^a   Pochapsky, Susan Sondej ^b   OuYang, Bo ^b   Pochapsky, Thomas C ^b  

^a DUQUESNE UNIVERSITY   (United States)

^b BRANDEIS UNIVERSITY   (United States)

Author keywords

electron transfer; molecular dynamics; NMR

Indexed keywords

CYTOCHROME P450 ISOENZYME; CYTOCHROME P450 ISOENZYME CYP101; ISOLEUCINE; PROLINE; PUTIDAREDOXIN; UNCLASSIFIED DRUG;

ARTICLE; CIS TRANS ISOMERISM; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ISOMERIZATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIMULATION;

EID: 66149170995     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.03.046     Document Type: Article

References (35)

1. Mueller E.J., Loida P.J., and Sligar S.G. Twenty five years of P450cam research. In: Ortiz de Montellano P. (Ed). Cytochrome P450: Structure, Function and Biochemistry. 2nd edit. (1995), Plenum Press, New York 83-124
2. Lipscomb J.D., Sligar S.G., Namtvedt M.J., and Gunsalus I.C. Autooxidation and hydroxylation reactions of oxygenated cytochrome P-450cam. J. Biol. Chem. 251 (1976) 1116-1124
3. Usanov S.A., Graham S.E., Lepesheva G.I., Azeva T.N., Strushkevich N.V., Gilep A.A., et al. Probing the interaction of bovine cytochrome P450scc (CYP11A1) with adrenodoxin: evaluating site-directed mutations by molecular modeling. Biochemistry 41 (2002) 8310-8320
4. Urushino N., Yamamoto K., Kagawa N., Ikushiro S., Kamakura M., Yamada S., et al. Interaction between mitochondrial CYP27B1 and adrenodoxin: role of arginine 458 of mouse CYP27bB1. Biochemistry 45 (2006) 4405-4412
5. Zhang H., Im S.C., and Waskell L. Cytochrome b5 increases the rate of catalysis by cytochrome P4502B4. Acta Pharmacol. Sinica 27 (2006) 213
6. 5 in catalysis by cytochrome P4502B4. Biochem. Biophys. Res. Commun. 338 (2005) 499-506
7. Wei J.Y., Pochapsky T.C., and Pochapsky S.S. Detection of a high-barrier conformational change in the active site of cytochrome P450cam upon binding of putidaredoxin. J. Am. Chem. Soc. 127 (2005) 6974-6976
8. cam-putidaredoxin couple. Biochemistry 42 (2003) 5649-5656
9. 5 and putidaredoxin, two effectors of camphor hydroxylase activity. Biochemistry 45 (2006) 3887-3897
10. Pochapsky T.C., Lyons T.A., Kazanis S., Arakaki T., and Ratnaswamy G. A structure-based model for cytochrome P450cam-putidaredoxin interactions. Biochimie 78 (1996) 723-733
11. cam complex via a combined residual dipolar coupling-spin labeling approach suggests a role for Trp106 of putidaredoxin in complex formation. J. Mol. Biol. 384 (2008) 349-363
12. cam. Structure 16 (2008) 916-923
13. cam. Biochemistry 45 (2006) 14379-14388
14. Poulos T.L. Structural biology of P450-oxy complexes. Drug Metab. Rev. 39 (2007) 557-566
15. Schlichting I., Berendzen J., Chu K., Stock A.M., Maves S.A., Benson D.E., et al. The catalytic pathway of cytochrome P450cam at atomic resolution. Science 287 (2000) 1615-1622
16. Nagano S., Tosha T., Ishimori K., Morishima I., and Poulos T.L. Crystal structure of the cytochrome P450cam mutant that exhibits the same spectral perturbations induced by putidaredoxin binding. J. Biol. Chem. 279 (2004) 42844-42849
17. Stein R.L. Mechanism of enzymatic and nonenzymatic prolyl cis-trans isomerization. Adv. Protein Chem. 44 (1993) 1-24
18. Zhao Y., and Ke H. Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization. Biochemistry 35 (1996) 7356-7361
19. Hur S., and Bruice T.C. The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin. J. Am. Chem. Soc. 124 (2002) 7303-7313
20. Reimer U., ElMokdad N., Schutkowski M., and Fischer G. Intramolecular assistance of cis/trans isomerization of the histidine-proline moiety. Biochemistry 36 (1997) 13802-13808
21. Texter F.L., Spencer D.B., Rosenstein R., and Matthews C.R. Intramolecular catalysis of a proline isomerization reaction in the folding of dihydrofolate-reductase. Biochemistry 31 (1992) 5687-5691
22. cam investigated by molecular dynamics simulations: an interactive look at the underlying mechanisms. Internet J. Chem. 4 (2001) article 6
23. Ludemann S.K., Lounnas V., and Wade R.C. How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. J. Mol. Biol. 303 (2000) 797-811
24. cam 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. J. Mol. Biol. 303 (2000) 813-830
25. Nickerson D.P., and Wong L.L. The dimerization of Pseudomonas putida cytochrome P450cam: practical consequences and engineering of a monomeric enzyme. Protein Eng. 10 (1997) 1357-1361
26. 2O samples of proteins. J. Magn. Reson. B 101 (1993) 333-337
27. Salzmann M., Wider G., Pervushin K., Senn H., and Wuthrich K. TROSY-type triple-resonance experiments for sequential NMR assignments of large proteins. J. Am. Chem. Soc. 121 (1999) 844-848
28. Salzmann M., Pervushin K., Wider G., Senn H., and Wuthrich K. Trosy in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc. Natl Acad. Sci. USA 95 (1998) 13585-13590
29. Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., et al. The AMBER biomolecular simulation programs. J. Comput. Chem. 26 (2005) 1668-1688
30. Bikiel D.E., Boechi L., Capece L., Crespo A., De Biase P.M., Di Lella S., et al. Modeling heme proteins using atomistic simulations. Phys. Chem. Chem. Phys. 8 (2006) 5611-5628
31. Marti M.A., Crespo A., Capece L., Boechi L., Bikiel D.E., Scherlis D.A., and Estrin D.A. Dioxygen affinity in heme proteins investigated by computer simulation. J. Inorg. Biochem. 100 (2006) 761-770
32. cam ternary complex. Biochemistry 28 (1989) 7586-7592
33. Freindorf M., Shao Y., Kong J., and Furlani T.R. Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin. J. Inorg. Biochem. 102 (2008) 427-432
34. Deprez E., Diprimo C., Hoa G.H.B., and Douzou P. Effects of monovalent cations on cytochrome P 450 camphor - evidence for preferential binding of potassium. FEBS Lett. 347 (1994) 207-210
35. Darden T., York D., and Pedersen L. Particle mesh Ewald - an n.Log(n) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092