Yildiz Ibrahim, Yildiz Banu Sizirici, Kirmizialtin Serdal
Chemistry Department and CIVE Department, Khalifa University, P.O. Box 127788, Abu Dhabi, UAE.
Chemistry Program, New York University at Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE.
ACS Omega. 2018 Nov 2;3(11):14689-14703. doi: 10.1021/acsomega.8b02638. eCollection 2018 Nov 30.
Choline oxidase catalyzes oxidation of choline into glycine betaine through a two-step reaction pathway employing flavin as the cofactor. On the light of kinetic studies, it is proposed that a hydride ion is transferred from α-carbon of choline/hydrated-betaine aldehyde to the N5 position of flavin in the rate-determining step, which is preceded by deprotonation of hydroxyl group of choline/hydrated-betaine aldehyde to one of the possible basic side chains. Using the crystal structure of glycine betaine-choline oxidase complex, we formulated two computational systems to study the hydride-transfer mechanism including main active-site amino acid side chains, flavin cofactor, and choline as a model system. The first system used pure density functional theory calculations, whereas the second approach used a hybrid ONIOM approach consisting of density functional and molecular mechanics calculations. We were able to formulate in silico model active sites to study the hydride-transfer steps by utilizing noncovalent chemical interactions between choline/betaine aldehyde and active-site amino acid chains using an atomistic approach. We evaluated and compared the geometries and energetics of hydride-transfer process using two different systems. We highlighted chemical interactions and studied the effect of protonation state of an active-site histidine base on the energetics of transfer. Furthermore, we evaluated energetics of the second hydride-transfer process as well as hydration of betaine aldehyde.
胆碱氧化酶通过以黄素为辅因子的两步反应途径催化胆碱氧化为甘氨酸甜菜碱。根据动力学研究，有人提出在速率决定步骤中，氢离子从胆碱/水合甜菜碱醛的α-碳转移到黄素的N5位，在此之前，胆碱/水合甜菜碱醛的羟基去质子化到一个可能的碱性侧链。利用甘氨酸甜菜碱-胆碱氧化酶复合物的晶体结构，我们构建了两个计算系统来研究氢化物转移机制，包括主要活性位点氨基酸侧链、黄素辅因子和胆碱作为模型系统。第一个系统使用纯密度泛函理论计算，而第二种方法使用由密度泛函和分子力学计算组成的混合ONIOM方法。我们能够通过使用原子方法利用胆碱/甜菜碱醛与活性位点氨基酸链之间的非共价化学相互作用，在计算机上构建模型活性位点来研究氢化物转移步骤。我们使用两个不同的系统评估并比较了氢化物转移过程的几何结构和能量学。我们突出了化学相互作用，并研究了活性位点组氨酸碱的质子化状态对转移能量学的影响。此外，我们评估了第二个氢化物转移过程的能量学以及甜菜碱醛的水合作用。
