Enzymes catalyze biochemical reactions and play a major role in performing and controlling most life processes. Therefore, a detailed understanding of biological systems requires an understanding of the action of the corresponding enzymes. The importance of such an understanding is highlighted by the fact that many diseases can be controlled by developing drugs that block the action of enzymes in the crucial biological pathways of the pathogens that cause these diseases. It is also possible, at least in principle, to develop drugs that restore the activity of defective enzymes that are involved in devastating diseases. Another important development has been the emergence of the field of enzyme design, with promising advances in directed evolution and in computer aided design. However, this progress has not yet led to designer enzymes that can rival native enzymes. Thus, the potential of this important field can be enhanced in a major way by computational approaches that actually determine the activation barriers of the reactions that are being catalyzed. During previous grant periods, we developed refined and applied powerful methods for simulating reactions in enzymes and examined their performance. Using these methods helped us to quantify key catalytic factors and brought us to a stage where we can make significant contributions to the new frontiers of enzyme design and the exploration of catalytic landscapes. Here, we propose the following projects: (i) We will invest major effort into computer-aided enzyme design by: (a) advancing the use of the EVB as a quantitative tool in the final stage of enzyme design;(b) developing coarse grained approaches for the different screening stages, and (c) using our approaches in actual enzyme design projects, including changing the action of promiscuous enzymes, improving available designer enzymes and helping in the design of new enzymes. (ii) We will continue to develop ab initio-free energy perturbation approaches to a level where they can be used effectively in studies of enzymatic reactions. This will include: (a) improving the use of EVB reference potentials for QM(ai)/MM free energy simulations;(b) developing and refining our accelerated QM/MM approach with average potentials and a Langevin dynamics based potential of mean force, and (c) refining the use of the CDFT method in studies of metalloenzymes and in free energy mapping. (iii) We will quantify the relationship between folding and stability by advancing the following projects: (a) exploring the relationship between the pre-organization of the active sites and the local stability of the protein;(b) exploring the relationship between thermostability and catalysis, and (c) using a simplified model to evaluate the total stability and the corresponding chemical activation free energy. (iv) We will conduct studies of several important classes of enzymatic reactions. (v) We will continue with the systematic examination of different non-electrostatic catalytic proposals.
Enzymes catalyze biochemical reactions and play a major role in performing and controlling most life processes. Thus, the detailed understanding of biological systems requires a quantitative description of the factors that determine the action of the corresponding enzymes. This is crucial, since many diseases can be controlled by developing drugs that block the action of enzymes in the key biological pathways of the bacteria or viruses that cause these diseases. It is also possible, at least in principle, to develop drugs that restore the activity of defective enzymes that are involved in devastating diseases. Furthermore, quantifying the contributions of different residues to both the original activity of the enzyme and to the binding of drugs should help in fighting drug resistance. The emergence of directed evolution and enzyme design has opened another exciting front in the field, with great practical (e.g. the novel synthesis of biochemically relevant molecules) and conceptual importance. Nevertheless, despite recent success in computer aided enzyme design, this progress has not led yet to designer enzymes that rival native enzymes. Thus, it is clear that the potential of this important field can be enhanced in a major way by computational approaches that can actually accurately and efficiently evaluate the activation barriers of the reactions that are being catalyzed. During the previous grant periods, we developed powerful computational approaches for the simulation of enzymatic reactions and for the elucidation of the relevant catalytic factors. Now, we are ready to push the frontiers of studies on the structure/function correlation of enzymes, focusing on (i) massive studies of enzyme design where progress in such studies should provide the ultimate proof of the understanding of enzyme catalysis, (ii) gaining a deeper understanding of the relationship between protein folding and catalysis, and (iii) developing and validating powerful strategies for the computation of enzymatic systems. Even moderate successes will help us to refine our methods and, ultimately, to help in the development of effective drugs that will aid in the fight against diseases that are associated with defective enzymes as well as helping in the design of specialized enzymes, and finally, to act as a guide in fighting drug resistance.
|Yoon, Hanwool; Kolev, Vesselin; Warshel, Arieh (2017) Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations. J Phys Chem B 121:9358-9365|
|Jindal, Garima; Warshel, Arieh (2017) Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis. Proteins 85:2157-2161|
|Jindal, Garima; Mondal, Dibyendu; Warshel, Arieh (2017) Exploring the Drug Resistance of HCV Protease. J Phys Chem B 121:6831-6840|
|Yoon, Hanwool; Warshel, Arieh (2017) Simulating the fidelity and the three Mg mechanism of pol ? and clarifying the validity of transition state theory in enzyme catalysis. Proteins 85:1446-1453|
|Jindal, Garima; Ramachandran, Balajee; Bora, Ram Prasad et al. (2017) Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases. ACS Catal 7:3301-3305|
|Astumian, R Dean; Mukherjee, Shayantani; Warshel, Arieh (2016) The Physics and Physical Chemistry of Molecular Machines. Chemphyschem 17:1719-41|
|Matute, Ricardo A; Yoon, Hanwool; Warshel, Arieh (2016) Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase ?. Proteins 84:1644-1657|
|Lameira, Jerônimo; Kupchencko, Ilya; Warshel, Arieh (2016) Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions. J Phys Chem B 120:2155-64|
|Yoon, Hanwool; Warshel, Arieh (2016) The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase. Proteins 84:1616-1624|
|Kim, Ilsoo; Warshel, Arieh (2016) A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD. J Phys Chem B 120:418-32|
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