Computational enzymology: modelling the mechanisms of biological catalysts

2008 ◽  
Vol 36 (1) ◽  
pp. 22-26 ◽  
Author(s):  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Mechanisms ◽  
Quantitative Comparison ◽  
Atomic Level ◽  
Catalysed Reaction ◽  
Biological Catalysis ◽  
Computational Enzymology ◽  
Insight Into ◽  
Comparison With Experiments

Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

Biochemistry ◽  
2013 ◽  
Vol 52 (16) ◽  
pp. 2708-2728 ◽  
Author(s):  
Marc W. van der Kamp ◽  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Computational Enzymology

New insights into the stereospecific reduction by an (S) specific carbonyl reductase from Candida parapsilosis ATCC 7330: experimental and QM/MM studies

2020 ◽  
Vol 10 (17) ◽  
pp. 5925-5934 ◽  
Author(s):  
Sneha Sudhakara ◽  
Chandrasekaran Ramakrishnan ◽  
M. Michael Gromiha ◽  
Anju Chadha
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Mechanisms ◽  
Candida Parapsilosis ◽  
Carbonyl Reductase ◽  
Stereospecific Reduction ◽  
Candida Parapsilosis Atcc 7330 ◽  
Reduction Of Ketones

The quantum mechanics/molecular mechanics study of an (S) specific carbonyl reductase from C. parapsilosis ATCC 7330 showing a dual kinetic response for the reduction of ketones and α-ketoesters suggests different reaction mechanisms for the same.

scholarly journals Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Sérgio Filipe Sousa ◽  
António J. M. Ribeiro ◽  
Rui P. P. Neves ◽  
Natércia F. Brás ◽  
Nuno M. F. S. A. Cerqueira ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Mechanisms ◽  
Enzymatic Reaction

Insight into the catalytic mechanism of meta-cleavage product hydrolase BphD: a quantum mechanics/molecular mechanics study

RSC Advances ◽  
2015 ◽  
Vol 5 (82) ◽  
pp. 66591-66597 ◽  
Author(s):  
Yanwei Li ◽  
Ruiming Zhang ◽  
Likai Du ◽  
Qingzhu Zhang ◽  
Wenxing Wang
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Catalytic Mechanism ◽  
Dienoic Acid ◽  
Cleavage Product ◽  
Natural Substrate ◽  
Catabolic Pathway ◽  
Insight Into

The catalytic mechanism of BphD (the fourth enzyme of the biphenyl catabolic pathway) toward its natural substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) was investigated in atomistic detail by QM/MM approach.

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