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Substrate mobility in a deeply buried active site: Analysis of norcamphor bound to cytochrome P‐450 cam as determined by a 201‐psec molecular dynamics simulation
Author(s) -
Bass Michael B.,
Paulsen Mark D.,
Ornstein Rick L.
Publication year - 1992
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340130103
Subject(s) - substrate (aquarium) , chemistry , cytochrome , molecular dynamics , stereochemistry , active site , cytochrome p450 , hydroxylation , enzyme , biophysics , biochemistry , biology , computational chemistry , ecology
Abstract While cytochrome P‐450 cam , catalyzes the hydroxylation of camphor to 5‐ exo ‐hydroxycamphor with 100% stereospecificity, norcamphor is hydroxylated by this enzyme yielding 45% 5‐ exo ‐, 47% 6‐ exo ‐, and 8% 3‐ exo ‐hydroxynorcamphor (Atkins, W.M., Sligar, S.G., J. Am. Chem. Soc. 109:3754–3760, 1987). The present study describes a 201‐psec molecular dynamics (MD) simulation of norcamphorbound cytochrome P‐450 cam to elucidate the relationship between substrate conformational mobility and formation of alternative products. First, these data suggest that the product specificity is, at least partially, due to the mobility of the substrate within the active site. Second, the high mobility of norcamphor in the active site leads to an average increase in separation between the home iron and the substrate of about 1.0 Å; this increase in separation may be the cause of the uncoupling of electron transfer when norcamphor is the substrate. Third, the active site water located in the norcamphor‐bound crystal structure possesses mobility that correlates well with the spin‐state equilibrium of this enzyme–substrate complex. © 1992 Wiley‐Liss, Inc.