Shape Complementarity, Binding-Site Dynamics, and Transition State Stabilization: A Theoretical Study of Diels–Alder Catalysis by Antibody 1E9
作者： Jiangang Chen , Qiaolin Deng , Renxiao Wang , Kendall N. Houk , Donald Hilvert
DOI: 10.1002/1439-7633(20001117)1:4<255::AID-CBIC255>3.0.CO;2-S
关键词: Quantum 、 Computational chemistry 、 Molecular dynamics 、 Interaction energy 、 Docking (molecular) 、 Catalysis 、 Transition state 、 Chemistry 、 Binding site 、 Cycloaddition 、 Photochemistry
摘要: Antibody 1E9 is a protein catalyst for the Diels–Alder reaction between tetrachlorothiophene dioxide and N-ethylmaleimide. Quantum mechanical calculations have been employed to study 1E9-catalyzed in gas phase. The transition states intermediates were all determined at B3LYP/6-31G*//HF/6-31G* level. cycloaddition step predicted be rate-determining, endo pathway strongly favored. Binding of reactants antibody was investigated by docking molecular dynamics simulations. linear interaction energy (LIE) method adopted estimate free barrier reaction. catalytic efficiency achieved enthalpic stabilization state, near-perfect shape complementarity hydrophobic binding site strategically placed hydrogen-bonding interaction.
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