Department of Human Molecular Genetics and Biochemistry, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
J Phys Chem B. 2009 Oct 1;113(39):13018-25. doi: 10.1021/jp810386z.
The human cytochrome P450 3A4 mono-oxygenates approximately 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-6betaOH 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 pi-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.
人细胞色素 P450 3A4 单加氧酶大约氧化 50%的所有药物。其底物/产物通过进入/出口通道进入/离开活性部位。在这里，我们进行了导向分子动力学模拟，将产物替马西泮和 testosterone-6betaOH 从 P450 3A4 酶中拉出，以确定首选的底物/产物途径及其门控机制。我们定位了产品从活性部位的六种不同出口途径，两种产物具有不同的出口偏好，并且发现 CYP3A4 中不止一个进入/出口通道。所谓的溶剂通道对两种测试产品都表现出最大的开口，从而将该通道鉴定为潜在的底物通道。大多数通道由一个或两个 pi 堆积的苯丙氨酸残基组成，作为门控物。氧化药物打破了门控残基的疏水性相互作用，并与门形成主要的疏水性接触。我们认为 P450 中产物的出口偏好受蛋白质-底物特异性的调节。
