Dispelling entropic mystery may rationalize enzyme design: the case of isochorismate-pyruvate lyase from Pseudomonas aeruginosa

Significance 

Enzyme design and protein engineering are among the fields that have recently attracted significant interest from researchers owing to the increasing need to enhance the performance of various biological processes. However, to ensure the effectiveness of various enzymatic catalysis, understanding the entropic effects is equally of great importance. Previous approaches used to describe the entropic effects such as the “Circe effect” are based on assumptions including the loss of the degree of freedoms during binding and the favorable change in activation enthalpy.

The simplified assumption does not provide the magnitude of contribution in each step. Consequently, several design factors are normally considered special when the enzyme in question is to be used for a particular function and stability. Unfortunately, the clarity on the importance and role of the entropic effects in improving the stability and catalytic activities of enzymes is still missing.

Generally, most enzymes exhibit high specificity and efficiency while others exhibit promiscuity and low efficiency, especially towards other substrates. Among the promiscuous enzymes, isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) undergoes a reaction mechanism different from other chorismite mutases like Bacillus subtilis chorismate mutase. For instance, it uses only one active site to either convert chorismate into prephenate or transform isochorismate into pyruvate at low and high efficiencies respectively. However, the reasons for the good mutations in PchB have not been fully explored. This call for precise measurement of the intrinsic entropic effects on reactions especially at atomic levels.

The advancement of computational technologies has been an added advantage in investigating the entropic effects in chorismate mutase reactions. Recent studies have shown that the formation of a near attack conformation, due to the stabilized transition states, have been a great contributor to the catalytic effects of the chorismate mutase. Alternatively, PchB has exhibited the same mechanism even though at lower efficiency. To this end, in order to advance the efficiency of the chorismate mutase reaction, accurate prediction of the entropic effects and their influence on the enzyme-catalyzed mechanism is highly desirable.

To this note, Dr. Liangxu Xie at the Jiangsu University of Technology, Dr. Zhe-Ning Chen at the Chinese Academy of Sciences, Fujian Institute of Research on the Structure of Matter together with Dr. Mingjun Yang at XtalPi Inc. explored the entropic effect in PchB-catalyzed chorismate mutase reaction. Fundamentally, the calculation of the entropic contribution was based on quantum mechanics / molecular mechanics molecular dynamics simulations, and a combination of computational Arrhenius plot approach and quasi-harmonic analysis. Additionally, the entropic contribution to the catalyzed reaction was compared to the measured change in entropy of the uncatalyzed reaction in an aqueous environment. Eventually, the reliability of the reaction path was confirmed based on the more accurate free energy calculations. Their work is published in the journal, Catalysis Science and Technology.

The research team observed a significant change in the entropy in the substrate preorganization process thus resulted in apparent entropic effect in the reaction. From the calculations, the authors confirmed the PchB-catalyzed chorismate mutase reaction was entropy-driven. In summary, the authors were the first to computationally determine the entropic effect in the PchB-catalyzed chorismate mutase reactions, therefore, providing a better explanation regarding the measured entropic effects in different experiments. Altogether, the study provides vital information that will advance the design of enzymes desirable for various application processes.

Dispelling entropic mystery may rationalize enzyme design: the case of isochorismate-pyruvate lyase from Pseudomonas aeruginosa - Advances in Engineering Dispelling entropic mystery may rationalize enzyme design: the case of isochorismate-pyruvate lyase from Pseudomonas aeruginosa - Advances in Engineering

About the author

Liangxu Xie earned B.Sc. degree from National Base of Chemistry, Shandong University in 2011. He received his PhD. degree from the University of Hong Kong under the supervision of Prof. Hao Hu in 2016. From 2016 to 2017, he worked as Research Assistant under the supervision of Prof. Kwong-Yu Chan in the University of Hong Kong. From 2017 to 2018, he joined the group of Prof. Xuhui Huang as Research Associate in Hong Kong University of Science and Technology. He started his independent career in 2019 at Jiangsu University of Technology.

His research interests lie in investigation of enzymatic reaction mechanisms and protein conformational changes using QM/MM molecular dynamics simulations and enhanced sampling methods.

About the author

Mingjun Yang graduated from the University of Science and Technology of China in 2006. He received his Ph.D. in 2011 from Dalian Institute of Chemical Physics, Chinese Academy of Sciences under the supervision of Prof. Keli Han. From 2011 to 2016, he carried out postdoctoral research in the department of chemistry, The University of Hong Kong and the department of pharmaceutical sciences, University of Maryland, Baltimore. In 2016, he joined a startup company XtalPi Inc.

His research interests lie in methodology development for conformation sampling and force field parametrization as well as computational predictions of pharmaceutical properties for drug-like molecules.

About the author

Zhe-Ning Chen received his Ph.D. from Xiamen University (P. R. of China) in 2012 under the supervision of Prof. Xin Xu and Prof. Gang Fu. In 2013, he moved as a postdoctoral fellow to University of Hong Kong (HK) to work in Prof. Hao Hu’s group. In August 2016 he joined Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, as an associate professor. His research interests lie in theoretical catalysis, extended hybrid model and sampling strategy.

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Reference

Xie, L., Yang, M., & Chen, Z.-N. (2019). Understanding the entropic effect in chorismate mutase reaction catalyzed by isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB). Catalysis Science & Technology, 9(4), 957-965.

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