Modern experimental techniques have reached resolution high enough to measure the structure of entire proteins, carbohydrates, and DNA; however, these experiments are usually restricted to detect only static and symmetric parts of the biomolecular structure, while the dynamics of these structures are important for representing specific interaction between the biomolecules. Thus combining experimental and computational approach will not only help us to save time and resources for experimental research but also suggest ways of developing an effective treatment of various diseases. From decades’ scientists are trying to understand how natural enzymes work and how can we use them in the development of novel, efficient, and cost-effective synthetic enzymes. To accomplish this aim, we have studied the mechanism of action of various enzymes like glycerophosphodiesterase (GpdQ), Streptomyces griseus Aminopeptidase (SgAP), and Neprilysin (NEP) using various computational methods. GpdQ has been proposed as a promising agent for the remediation of pesticides and the deactivation of nerve agents. On the other hand, SgAP has a fairly broad specificity towards both proteins and DNA, a property which is not seen very often. Therefore, it can be used as a reagent for the analysis of protein and DNA structure. Finally, Neprilysin has the potential to slow the progression of neurological diseases. In this work, we have exhausted various computational techniques in understanding the enzyme-substrate interactions, their mechanism of action and use this information to develop metal-containing synthetic analogs of these enzymes. Our molecular dynamics (MD) simulations showed that the chemical nature of the substrate influences its binding mode by changing the coordination flexibility of the enzyme’s active site. Additionally, quantum mechanics (QM) and quantum mechanics/molecular mechanics (QM/MM) approach were used to elaborate the reaction mechanism of these enzymes. Finally, we have also studied the reaction mechanism of Zn(II), Fe(III), and Cu(II) containing metallohydrolases of GpdQ analogs. Our results provided a deeper understanding of the complex mechanism not only of GpdQ, SgAP, and NEP but also of other related binuclear synthetic analogs of metallohydrolases as well and may form the basis for the engineering of optimized enzyme variants (mutants) for applications in bioremediation and other relevant processes in biotechnology.

Authors: Gaurav Sharma, Vindi Mahesha, Qiaoyu Hu, Rajeev Prabhakar