Computational Chemistry Studies of Proteins and Organic Reactions

Computational chemistry has a variety of applications, from understanding a phenomenon of an experiment, to broader applications such as material science, drug discovery, biocatalysis, and many other fields. The following chapters are focused on using computational chemistry tools to understand the mechanisms of enzymes or organic reactions, and to engineer enzymes that produce novel products. Different methods have been applied to achieve these goals, such as molecular mechanics methods, ab initio molecular dynamics, classical molecular dynamics, quantum mechanics (density functional methods), monte carlo methods and machine learning methods. The first chapter is focused on computational modeling of terpene synthase family, to understand the catalysis process of terpene synthase, and further engineer terpene synthase to produce unnatural products. The second chapter is focused on studying organic reaction mechanisms and catalysis using quantum mechanics and molecular dynamics methods. The third chapter is focused on protein structure prediction of terpene synthase.Chapter 1. Mechanistic studies and enzyme engineering of terpene synthase Terpene or terpenoid is the largest class of natural product, with more than 80 000 members. All of which derives from the simple five-carbon isoprene unit. The five-carbon unit can be ligated by prenyltransferases to produce C 10 , C 15 , C 20 … linear structures. These linear structures can then be cyclized by terpene synthase (TPS) to produce multi-ring, multi-stereocenter, cyclic structures. This process usually involves multiple highly reactive carbocation intermediates, brings challenges for modeling and identifying productive binding orientation. Terdockin method is applied to study the catalysis mechanism of the diterpene synthase Rv3377c, as well as ent-kaurene synthase BjKS. Results reveal the mechanism for catalysis, which can be further applied to engineer terpene synthase to produce unnatural products. A few engineer efforts listed in the chapter was made to alter the product outcome for BjKS.Chapter 2. Quantum mechanics studies of organic reactions In the first section of this chapter, the source of the rate acceleration for carbocation cyclization in a biomimetic supramolecular cage is studied using quantum mechanics methods, molecular dynamics, and QM/MM methods. Previous experimental results indicate that the supramolecular cage increases the nazarov reaction rate by roughly 1 000 000 times. The electrocyclization step is slightly enhanced by the catalyst, suggested by computational modeling. The major contribution, indicated by the QM/MM studies, is the activation of the leaving groups, similar as terpene synthase activate the diphosphate leaving group.Chapter 3. Protein structure prediction of terpene synthase Terpene cyclases catalyze one of the most complex chemical reactions in biology, converting simple acyclic oligo-isoprenyl diphosphate substrate to complex polycyclic products via carbocation intermediates. Many computational studies were carried out to illuminate the structural-function relationship of terpene cyclases, which generally rely on a crystal structure. However, among 15,000 terpene cyclases sequences, there are only about 30 types of terpene cyclase crystal structures. To fill in this gap, we proposed a comparative modeling approach to generate high resolution models of class I terpene cyclase, which can be further used as a starting point to predict the productive binding mode of the substrate and potentially set stage for the rational engineering of terpene cyclases