Du Juan, Liu Lin, Guo Li Zhong, Yao Xiao Jun, Yang Jian Ming
Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China.
J Comput Aided Mol Des. 2017 May;31(5):483-495. doi: 10.1007/s10822-017-0013-x. Epub 2017 Mar 25.
Cytochrome P450 OleT has attracted much attention for its ability to catalyze the decarboxylation of long chain fatty acids to generate alkenes, which are not only biofuel molecule, but also can be used broadly for making lubricants, polymers and detergents. In this study, the molecular basis of the binding mechanism of P450 OleT for arachidic acid, myristic acid, and caprylic acid was investigated by utilizing conventional molecular dynamics simulation and binding free energy calculations. Moreover, random acceleration molecular dynamics (RAMD) simulations were performed to uncover the most probable access/egress channels for different fatty acids. The predicted binding free energy shows an order of arachidic acid < myristic acid < caprylic acid. Key residues interacting with three substrates and residues specifically binding to one of them were identified. The RAMD results suggest the most likely channel for arachidic acid, myristic acid, and caprylic acid are 2e/2b, 2a and 2f/2a, respectively. It is suggested that the reaction is easier to carry out in myristic acid bound system than those in arachidic acid and caprylic acid bound system based on the distance of Hβ atom of substrate relative to P450 OleT Compound I states. This study provided novel insight to understand the substrate preference mechanism of P450 OleT and valuable information for rational enzyme design for short chain fatty acid decarboxylation.
细胞色素P450 OleT因其能够催化长链脂肪酸脱羧生成烯烃而备受关注，这些烯烃不仅是生物燃料分子，还可广泛用于制造润滑剂、聚合物和洗涤剂。在本研究中，利用传统分子动力学模拟和结合自由能计算，研究了P450 OleT与花生酸、肉豆蔻酸和辛酸结合机制的分子基础。此外，进行了随机加速分子动力学（RAMD）模拟，以揭示不同脂肪酸最可能的进出通道。预测的结合自由能显示出花生酸＜肉豆蔻酸＜辛酸的顺序。确定了与三种底物相互作用的关键残基以及特异性结合其中一种底物的残基。RAMD结果表明，花生酸、肉豆蔻酸和辛酸最可能的通道分别是2e/2b、2a和2f/2a。基于底物Hβ原子相对于P450 OleT化合物I状态的距离，表明在肉豆蔻酸结合系统中反应比在花生酸和辛酸结合系统中更容易进行。本研究为理解P450 OleT的底物偏好机制提供了新的见解，并为短链脂肪酸脱羧的合理酶设计提供了有价值的信息。
