Rational approach to improving reductive catalysis by cytochrome P450cam

Biochimie

Volumn 78, Issue 8-9, 1996, Pages 714-722

  Manchester, Ji ^a,b   Ornstein, Rl ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

Cytochrome P450cam; Molecular dynamics; Pentachloroethane; Redox potential; Reductive dehalogenation

Indexed keywords

CYTOCHROME P450; HALOGENATED HYDROCARBON;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; DEHALOGENATION; DETOXIFICATION; ELECTRON TRANSPORT; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; GENETIC ENGINEERING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTON TRANSPORT; REDUCTION; STRUCTURE ACTIVITY RELATION;

EID: 0030457185     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0300-9084(97)82529-1     Document Type: Article

References (58)

1. 1 Mansuy D, Nastainczyk W, Ullrich V (1974) The mechanism of halothane binding to microsomal P450. Arch Pharmacol 285, 315-324
2. 2 Kubic VL, Anders MW (1981) Mechanism of the microsomal reduction of carbon tetrachloride and halothane. Chem Biol Interactions 34, 201-207
3. 3 Casciola LAF, Ivanetich KM (1984) Metabolism of chloroethanes by rat liver nuclear cytochrome P450, Carcinogenesis 5, 543-548
4. 4 Takano T, Miyazaki Y, Motohashi Y (1985) Interaction of trichloroethane isomers with cytochrome P450 in the perfused rat liver. Fundam Appl Toxicol 5, 353-360
5. 5 Castro CE, Yokoyama WH, Belser NO (1988) Biodehalogenation. Reductive reactivities of microbial and mammalian cytochromes P450 compared with heme and whole-cell models. J Agric Food Chem 36, 915-919
6. 6 Wackett LP, Sadowsky MJ, Newman LM, Hur H-G, Li S (1994) Metabolism of polyhalogenated compounds by a genetically engineered bacterium. Nature 368, 627-629
7. 7 Janssen DB, Pries F, van der Ploeg JR (1994) Genetics and biochemistry of dehalogenating enzymes. Annu Rev Microbiol 48, 163-191
8. 8 Wackett LP, Logan MSP, Blocki FA, Bao-li C (1992) A mechanistic perspective on bacterial metabolism of chlorinated methanes. Biodegradation 3, 19-36
9. 9 Loida PJ (1994) Molecular specificty of substrate recognition and activation in cytochrome P450cam. PhD thesis, University of Illinois at Urbana-Champaign
10. 10 Logan MSP, Newman LM, Schanke CA, Wackett LP (1993) Co-substrate effects in reductive dehalogenation by Pseudomanus putida G786 expressing cytochrome P450cam. Biodegradation 4, 39-50
11. 11 Ornstein RL (1994) On using rational enzyme redesign to improve enzyme-mediated microbial dehalogenation of recalcitrant substances in deep-subsurface environments. In: Structural Biology: State of the Art (Sarma RH, Sarma MH, eds) Adenine Press, Albany, NY, 59-76
12. 12 Ornstein RL (1991) Why timely bioremediation of synthetics may require rational enzyme redesign: Preliminary report on redesigning cytochrome P450cam for trichloroethylene dehalogenation. In: On-Site Bioreclamation: Processes for Xenobiotic and Hydrocarbon Treatment, (Hinchee RE, Olfenbuttel RF, eds) Butterworth-Heinemann, Stoneham MA, Columbus, OH, 509-514
13. 13 Paulsen MD, Ornstein RL (1991) A 175 ps molecular dynamics simulation of camphor-bound cytochrome P450cam. Proteins: Struct Funct Genet 11, 184-204
14. 14 Bass MB, Paulsen MD, Ornstein RL (1992) Substrate mobility in a deeply buried active site: Analysis of norcamphor bound to cytochrome P450cam as determined by a 201 ps molecular dynamics simulation. Proteins: Struct Funct Genet 13, 26-37
15. 15 Paulsen MD, Ornstein RL (1993) Substrate mobility in thiocamphorbound cytochrome P450cam: An explanation of the conflict between the observed product profile and the X-ray structure. Prot Enging 6, 359-365
16. 16 Paulsen MD, Ornstein RL (1992) Predicting the product specificity and coupling of cytochrome P450cam. J Comp Aided Mol Design 6, 449-460
17. 17 Harris D, Loew G (1995) Prediction of regiospecific hydroxylation of camphor analogs by cytochrome P450cam. J Am Chem Soc 117, 2738-2746
18. 18 Paulsen MD, Filipovic D, Sligar SG, Ornstein RL (1993) Controlling the regiospecificity and coupling of cytochrome P450cam: T185F mutant increases coupling and abolishes 3-hydroxynorcamphor product. Protein Sci 2, 357-365
19. 19 Loida PJ, Sligar SG, Paulsen MD, Arnold GE, Ornstein RL (1995) Stereoselective hydroxylation of norcamphor by cytochrome P450cam. Experimental verification of molecular dynamics simulations. J Biol Chem 270, 5326-5330
20. 20 Bass MB, Ornstein RL (1993) Substrate specificty of cytochrome P450cam for 1-and d-norcamphor as studied by molecular dynamics simulations. J Comp Chem 14, 541-548
21. 21 Mueller EJ, Loida PJ, Sligar SG (1995) Twenty-five years of P450cam research: Mechanistic insights into oxygenase catalysis. In: Cytochrome P450cam (Ortiz de Montellano PR, ed) Plenum Press, New York, 83-124
22. 22 Li S, Wackett LP (1993) Reductive dehalogenation by cytochrome P450cam: substrate binding and catalysis. Biochemistry 32, 9355-9361
23. 23 Savéant J-M (1994) Dissociative electron transfer. Adv Electron Transfer Chem 4, 53-116
24. 24 Eberson L (1987) Electron Transfer Reactions in Organic Chemistry. Springer-Verlag, Berlin, vol 25, 234 p
25. 25 Luke BT, Loew GH, McLean AD (1988) Theoretical investigation of the anaerobic reduction of halogenated alkanes by cytochrome P-450. 2. Vertical electron affinities of chlorofluoromethanes as a measure of their activity. J Am Chem Soc 110, 3396-3400
26. 26 Luke BT, Loew GH (1986) A theoretical investigation of the first step in the metabolic reduction of halogenated methanes by cytochrome P450. Int J Quant Chem Quant Biol Symp 12, 99-112
27. 27 Newton MD, Sutin N (1984) Electron transfer reactions in condensed phases. Annu Rev Phys Chem 35, 437-80
28. 28 Paulsen MD, Ornstein RL (1994) Active-site mobility inhibits reductive dehalogenation of 1,1,1-trichloroethane by cytochrome P450cam. J Comput Aided Mol Design 8, 389-404
29. 29 Manchester JI, Ornstein RL (1995) Enzyme-catalyzed dehalogenation of pentachloroethane: Why F87W-cytochrome P450cam is faster than wild-type. Prot Enging 8, 801-807
30. 30 Bass MB, Paulsen MD, Ornstein RL (1991) Molecular dynamics simulations of norcamphor-cytochrome P450cam and mutations of P450cam designed to alter the product specificity. In: Seventh International Conference on Biochemistry and Biophysics of Cytochrome P450: Structure and Function, Biotechnological and Ecological Aspects Moscow, Russia, INCO-TNC, 680-685
31. 31 Marcus RA, Sutin N (1985) Electron transfers in chemistry and biology. Biochem Biophys Acta 811, 265-322
32. 32 Verschueren KHG, Seljée F, Rozeboom HJ, Kalk KH, Dijkstra BW (1993) Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature 363, 693-698
33. 33 Verschueren KHG, Franken SM, Rozeboom HJ, Kalk KH, Dijkstra BW (1993) Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and impliciations for the reaction mechanism. J Mol Biol 232, 856-872
34. 34 Verschueren KHG, Kingma J, Rozeboom HJ, Kalk KH, Janssen DB, Dijkstra BW (1993) Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide ions. Studies with halide compounds reveal a halide binding site in the active site. Biochemistry 32, 9031-9037
35. 35 Paulsen MD, Bass MB, Ornstein RL (1991) Analysis of active site motions from a 175 ps molecular dynamics simulation of cytochrome P-450cam. J Biomol Struct Dynamics 9, 187-203
36. 36 Manchester JI, Paulsen MD, Rein R, Ornstein RL (1996) 1,1,1-trichloroethane-bound cytochrome P450cam dynamics: Does active site water make a difference? Chem Phys 204, 223-231.
37. 37 Poulos TL, Finzel BC, Howard AJ (1987) High-resolution crystal structure of cytochrome P-450cam. J Mol Biol 195, 687-700
38. 38 Bass MB, Hopkins DF, Jaquysh WAN, Ornstein RL (1992) A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding. Proteins Struct Funct Genet 12, 266-277
39. 39 Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81, 3684-3690
40. 40 Hagler AT (1985) Theoretical simulation of conformation, energetics, and dynamics of peptides. In: The Peptides (Hruby VJ, Meienhofer J, eds) Academic Press, New York, 213-299
41. 41 Arnold GE, Ornstein RL (1994) An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme. Proteins: Struct Funct Genet 18, 19-33
42. 42 Paulsen MD, Ornstein RL (1995) Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations. Proteins: Struct Funct Genet 21, 237-243
43. 43 Nicholls A, Sharp KA, Honig B (1991) GRASP: Graphical Representation and Analysis of Surface Properties, v 1.04, Columbia University, New York, NY
44. 44 Guerra M (1990) On the use of diffuse functions for estimating negative electron affinities with LCAO methods. Chem Phys Lett 167, 315-319
45. 45 Eberson L (1982) Electron transfer reactions in organic chemistry, II. An analysis of alkyl halide reduction by electron transfer reagents on the basis of the Marcus theory. Acta Chem Scand B 36, 533-543
46. 46 Andrieux CP, Gallardo I, Savéant J-M, Su K-B (1986) Dissociate electron transfer. Homogeneous and heterogeneous reductive cleavage of the carbon-halogen bond in simple aliphatic halides. J Am Chem Soc 108, 638-647
47. 47 Savéant J-M (1992) Dissociative electron transfer. New tests of the theory in the electrochemical and homogeneous reduction of alkyl halides. J Am Chem Soc 114, 10595-10602
48. 48 Schenkman JB, Sligar SG, Cinti DL (1981) Substrate interaction with cytochrome P-450. Pharm Ther 12, 43-71
49. 49 Sligar SG, Gunsalus IC (1976) A thermodynamic model of regulation: Modulation of redox equilibria in camphor monoxygenase. Proc Natl Acad Sci USA 73, 1078-1082
50. 50 Guengerich FP, Ballou DP, Coon MJ (1975) Purified liver microsomal cytochrome P-450. J Biol Chem 250, 7405-7414
51. 51 Gunsalus IC, Pederson TC, Sligar SG (1975) Oxygenase-catalyzed biological hydroxylations. Annu Rev Biochem 44, 377-407
52. 52 Wilson GS, Tsibris JM, Gunsalus IC (1973) Electrochemical studies of putidaredoxin and its selenium analog. J Biol Chem 248, 6059-6061
53. 53 Creighton, TE (1993) Proteins:Structures and Molecular Properties. WH Freeman, NY, p 13
54. 54 Fersht A (1985) Enzyme Structure and Mechanism. WH Freeman, NY, p 156
55. a values. Biopolymers 32, 897-909
56. a values of two histidine residues in human hemoglobin, the Bohr effect, and the dipole moments of alpha helices. J Mol Biol 183, 491-4-98
57. a for histidine-51 residue in the ternary complex of horse liver alcohol dehydrogenase. Arch Pharmacol Res 15, 229-233
58. 58 Di Primo, C, Hui Bon Hoa, G, Douzou, P., Sligar, S (1990) Mutagenesis of a single hydrogen bond in cytochrome P-450 alters cation binding and heme solvation. J Biol Chem 265, 5361-5363