How Important Is the Synclinal Conformation of Sulfonylureas To Explain the Inhibition of AHAS: A Theoretical Study

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.

Interactions between salicylic acid and antioxidant enzymes tilting the balance of H2O2 from photorespiration in non-target crops under halosulfuron-methyl stress

Halosulfuron-methyl (HSM) is a safe, selective and effective sulfonylurea herbicide (SU) for the control of sedge and broadleaf weeds in sugarcane, corn, tomato, and other crops. The primary site of action is acetolactate synthase (ALS), a key enzyme of branched chain amino acids (BCAAs) synthesis. In addition to ALS inhibition, BCAAs deficiencies and oxidative damage may be involved in toxic effects of SUs. However, secondary targets of HSM relevant to plant physiological responses are unclear. In the present study, comparative growth inhibition and peroxidization injury between sensitive and tolerance crops were observed at biochemical and physiological levels suggesting involvement of H2O2, ethylene, salicylic acid (SA) in the oxidative stress responses to HSM. HSM caused accumulation of H2O2, stimulated photorespiration and consequent accumulation of SA that worsened the peroxidization injury to the sensitive C3 plant soybean (Glycine max). The growth inhibition at low concentrations of HSM could be lessened by supplementary BCAAs, reactive oxygen species scavengers or ethylene inducers, whereas the oxidation damage at high concentrations of HSM could not be reversed and ultimately lead to plant death. H2O2 at a low level stimulated the antioxidase system including glutathione S-transferase activities in the HSM-tolerant C4 maize (Zea mays), which contributes to HSM tolerance. H2O2 plays an important role on HSM stress responses in both HSM-sensitive and HSM-tolerant soybean and maize.