The Role of Tetrel Bonding in the Reaction Mechanism of Methyltransferases

在化学系生命过程化学(CLP)计划的支持下，密歇根大学安娜堡分校的Raymond Trievel博士和德克萨斯大学达拉斯分校的Allison Stling博士正在研究一种重要的酶，称为甲基转移酶。甲基转移酶是一种普遍存在的酶，通过蛋白质、DNA和RNA的甲基化，在众多生物分子的新陈代谢以及细胞信号和基因调控中发挥重要作用。此外，甲基转移酶与许多疾病有关，使其成为设计新的调节物的重要靶点，以研究它们在生物学中的功能意义和信号角色，以及它们在异常生物学或疾病(与癌症、心血管疾病、一些神经疾病和新冠肺炎等微生物病毒感染有关)中的功能障碍。最近的研究表明，这些酶催化的甲基转移反应是通过一种称为Tetrel键的非传统类型的相互作用进行的。生物大分子中Tetrel键的存在只是最近才被发现，这些相互作用对生物过程的贡献，特别是甲基转移，仍然知之甚少。这个项目的目标是用实验和计算的方法来表征甲基转移酶中四元键的功能。从这些研究中获得的知识将潜在地为开发新的甲基转移酶抑制剂提供信息。该项目将吸引本科生和研究生在生物化学、生物物理学、结构生物学和光谱学领域进行研究，提供化学-生物界面的多学科培训。甲基化是生物学中普遍存在的反应，在许多生物分子的新陈代谢中起着核心作用，包括氨基酸、碳水化合物、脂肪、激素和代谢物。此外，甲基化是蛋白质、DNA和RNA中一种显著的共价修饰，与信号转导和基因调控有关。大多数甲基化反应是由S-腺苷甲硫氨酸(ADOMet)依赖的甲基转移酶通过ADOMet甲基团SN2转移到受体底物上来催化的。最近对ADOMet和各种配体结合的甲基转移酶的晶体结构的研究表明，ADOMet的甲基参与了四元键，这是一种类似于卤素键的西格玛反键轨道相互作用。先前利用小分子模型进行的计算研究表明，甲基碳原子和亲核原子之间的Tetrel键代表了SN2反应途径中过渡态之前的中间体。ADOMet甲基碳原子与甲基转移酶活性中心不同配体之间的Tetrel键的发现暗示了这种相互作用是这些酶的催化机制的基础。在这些观察的基础上，这项建议的目的是：1)确定ADOMet甲基四氢呋喃的键在催化中的功能，以及2)表征甲基四氢呋喃键对ADOMet甲基振动模式的影响。将使用甲基转移酶模型和结合生物化学、光谱学、结晶学和计算化学的跨学科方法详细研究这些相互作用的功能重要性。综上所述，这些研究旨在阐明ADOMet甲基和亲核试剂之间的Tetrel键促进甲基转移的机制。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

With the support of the Chemistry of Life Processes (CLP) Program in the Division of Chemistry, Drs. Raymond Trievel of the University of Michigan - Ann Arbor and Allison Stelling of UT-Dallas are studying an important category of enzymes known as methyltransferases. Methyltransferases are ubiquitous enzymes that play fundamental roles in the metabolism of numerous biological molecules, as well as in cell signaling and gene regulation through methylation of proteins, DNA, and RNA. In addition, methyltransferases have been implicated in numerous diseases, rendering them important targets for the design of new modulators to study their functional significance and signaling roles in biology and their dysfunction in abnormal biology or disease (relevant to cancer, cardiovascular disease, some neurological disorders, and microbial viral infections including COVID-19). Recent studies have revealed that the methyl transfer reaction catalyzed by these enzymes occurs through an unconventional type of interaction called a tetrel bond. The existence of tetrel bonds in biological macromolecules has only recently been discovered, and the contributions of these interactions to biological processes, particularly methyl transfer, remain poorly understood. The goal of this project is to characterize the functions of the tetrel bonds in methyltransferases using experimental and computational approaches. The knowledge derived from these studies will potentially inform the development of new methyltransferase linhibitors. This project will engage both undergraduate and graduate students in research in the fields of biochemistry, biophysics, structural biology and spectroscopy, affording multi-disciplinary training at the chemistry-biology interface.Methylation is a ubiquitous reaction in biology that plays a central role in the metabolism of many biological molecules, including amino acids, carbohydrates, lipids, hormones, and metabolites. In addition, methylation represents a prominent covalent modification in proteins, DNA, and RNA, which has been implicated in signal transduction and gene regulation. Most methylation reactions are catalyzed by S-adenosylmethionine (AdoMet)-dependent methyltransferases via an SN2 transfer of the AdoMet methyl group to the acceptor substrate. A recent survey of crystal structures of methyltransferases bound to AdoMet and various ligands has revealed that the AdoMet methyl group engages in tetrel bonding, a type of sigma antibonding orbital interaction similar to halogen bonding. Prior computational studies utilizing small molecule models have demonstrated that tetrel bonding between the methyl carbon atom and the nucleophilic atom represents an intermediate preceding the transition state in the SN2 reaction pathway. The discovery of tetrel bonding between the AdoMet methyl carbon atom and various ligands in methyltransferase active sites implies that this interaction is fundamental to the catalytic mechanism of these enzymes. Building on these observations, the aims of this proposal are to: 1) determine the functions of AdoMet methyl tetrel bonding in catalysis and 2) characterize the effects of methyl tetrel bonding on the AdoMet methyl vibrational modes. The functional importance of these interactions will be investigated in detail using a model methyltransferase and an interdisciplinary approach combining biochemistry, spectroscopy, crystallography, and computational chemistry. Taken together, these studies aim to elucidate the mechanism by which tetrel bonding between the AdoMet methyl group and the nucleophile facilitates methyl transfer.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.