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J Phys Chem B. 2009 October 1; 113(39): 13018–13025.
Published online 2009 September 3. doi: 10.1021/jp810386z.
PMCID: PMC2750738
Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism
Dan Fishelovitch, Sason Shaik, Haim J. Wolfson,§ and Ruth Nussinov*[perpendicular]
Department of Human Molecular Genetics and Biochemistry, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel, and SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI−Frederick, Building 469, Room 151, Frederick, Maryland 21702
* To whom correspondence should be addressed. Address: CCRNB, SAIC-Frederick, Inc., NCI-Frederick, Bldg. 469, Rm. 149, Frederick, MD 21702. E-mail: ruthn/at/ncifcrf.gov. Phone: 301-846-5579. Fax: 301-846-5598.
Sackler Faculty of Medicine, Tel Aviv University.
The Hebrew University of Jerusalem.
§Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University.
[perpendicular]NCI−Frederick.
Received November 26, 2008; Revised August 5, 2009.
Abstract
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The human cytochrome P450 3A4 mono-oxygenates ~50% of all drugs. Its substrates/products enter/leave the active site by access/exit channels. Here, we perform steered molecular dynamics simulations, pulling the products temazepam and testosterone-6βOH out of the P450 3A4 enzyme in order to identify the preferred substrate/product pathways and their gating mechanism. We locate six different egress pathways of products from the active site with different exit preferences for the two products and find that there is more than just one access/exit channel in CYP3A4. The so-called solvent channel manifests the largest opening for both tested products, thereby identifying this channel as a putative substrate channel. Most channels consist of one or two π-stacked phenylalanine residues that serve as gate keepers. The oxidized drug breaks the hydrophobic interactions of the gating residues and forms mainly hydrophobic contacts with the gate. We argue that product exit preferences in P450s are regulated by protein−substrate specificity.