Stjernschantz Eva, van Vugt-Lussenburg Barbara M A, Bonifacio Alois, de Beer Stephanie B A, van der Zwan Gert, Gooijer Cees, Commandeur Jan N M, Vermeulen Nico P E, Oostenbrink Chris
Leiden/Amsterdam Centre for Drug Research, Division of Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
Proteins. 2008 Apr;71(1):336-52. doi: 10.1002/prot.21697.
Three newly discovered drug metabolizing mutants of cytochrome P450 BM3 (van Vugt-Lussenburg et al., Identification of critical residues in novel drug metabolizing mutants of Cytochrome P450 BM3 using random mutagenesis, J Med Chem 2007;50:455-461) have been studied at an atomistic level to provide structural explanations for a number of their characteristics. In this study, computational methods are combined with experimental techniques. Molecular dynamics simulations, resonance Raman and UV-VIS spectroscopy, as well as coupling efficiency and substrate-binding experiments, have been performed. The computational findings, supported by the experimental results, enable structural rationalizations of the mutants. The substrates used in this study are known to be metabolized by human cytochrome P450 2D6. Interestingly, the major metabolites formed by the P450 BM3 mutants differ from those formed by human cytochrome P450 2D6. The computational findings, supported by resonance Raman data, suggest a conformational change of one of the heme propionate groups. The modeling results furthermore suggest that this conformational change allows for an interaction between the negatively charged carboxylate of the heme substituent and the positively charged nitrogen of the substrates. This allows for an orientation of the substrates favorable for formation of the major metabolite by P450 BM3.
细胞色素P450 BM3的三个新发现的药物代谢突变体（van Vugt-Lussenburg等人，《使用随机诱变鉴定细胞色素P450 BM3新型药物代谢突变体中的关键残基》，《药物化学杂志》2007年；50：455 - 461）已在原子水平上进行了研究，以对其一些特性提供结构解释。在本研究中，计算方法与实验技术相结合。进行了分子动力学模拟、共振拉曼光谱和紫外 - 可见光谱，以及偶联效率和底物结合实验。计算结果得到实验结果的支持，能够对突变体进行结构合理化解释。本研究中使用的底物已知可被人细胞色素P450 2D6代谢。有趣的是，P450 BM3突变体形成的主要代谢产物与人细胞色素P450 2D6形成的代谢产物不同。共振拉曼数据支持的计算结果表明其中一个血红素丙酸酯基团发生了构象变化。建模结果还表明，这种构象变化使得血红素取代基带负电荷的羧酸盐与底物带正电荷的氮之间能够发生相互作用。这使得底物的取向有利于P450 BM3形成主要代谢产物。
