Structure and Dynamics of the Reactive State for the Histidine Methylation Process and Catalytic Mechanism of SETD3: Insights from Quantum Mechanics/Molecular Mechanics Investigation

ACS Catalysis ◽  
2020 ◽  
Vol 10 (22) ◽  
pp. 13314-13322
Author(s):  
Hao Deng ◽  
Yue Ma ◽  
Wan-Sheng Ren ◽  
Van Quan Vuong ◽  
Ping Qian ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Catalytic Mechanism ◽  
Structure And Dynamics

A QM/MM study of the catalytic mechanism of succinic semialdehyde dehydrogenase from Synechococcus sp. PCC 7002 and Salmonella typhimurium

RSC Advances ◽  
2015 ◽  
Vol 5 (123) ◽  
pp. 101672-101682 ◽  
Author(s):  
Jing Zhang ◽  
Yongjun Liu
Keyword(s):  
Quantum Mechanics ◽  
Salmonella Typhimurium ◽  
Molecular Mechanics ◽  
Catalytic Mechanism ◽  
Succinic Semialdehyde ◽  
Succinic Semialdehyde Dehydrogenase ◽  
Semialdehyde Dehydrogenase ◽  
Synechococcus Sp

The catalytic mechanism of succinic semialdehyde dehydrogenase (SSADH) has been studied using a combined quantum mechanics and molecular mechanics (QM/MM) approach.

Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method

2017 ◽  
Vol 19 (27) ◽  
pp. 17985-17997 ◽  
Author(s):  
Hiroshi C. Watanabe ◽  
Maximilian Kubillus ◽  
Tomáš Kubař ◽  
Robert Stach ◽  
Boris Mizaikoff ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Condensed Phase ◽  
Quantum Chemical ◽  
Chemical Properties ◽  
Many Body ◽  
Charge Fluctuations ◽  
Structure And Dynamics ◽  
Chemical Effects ◽  
Solvation Structure

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics.

A Quantum Mechanics/Molecular Mechanics Study of the Catalytic Mechanism of the Thymidylate Synthase†

Biochemistry ◽  
2007 ◽  
Vol 46 (12) ◽  
pp. 3704-3713 ◽  
Author(s):  
Natalia Kanaan ◽  
Sergio Martí ◽  
Vicent Moliner ◽  
Amnon Kohen
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Thymidylate Synthase ◽  
Catalytic Mechanism

The reaction mechanism of retaining glycosyltransferases

2016 ◽  
Vol 44 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Albert Ardèvol ◽  
Javier Iglesias-Fernández ◽  
Víctor Rojas-Cervellera ◽  
Carme Rovira
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Active Site ◽  
Molecular Mechanisms ◽  
Catalytic Mechanism ◽  
Strong Support ◽  
Front Face ◽  
Displacement Reaction ◽  
Displacement Mechanism

The catalytic mechanism of retaining glycosyltransferases (ret-GTs) remains a controversial issue in glycobiology. By analogy to the well-established mechanism of retaining glycosidases, it was first suggested that ret-GTs follow a double-displacement mechanism. However, only family 6 GTs exhibit a putative nucleophile protein residue properly located in the active site to participate in catalysis, prompting some authors to suggest an unusual single-displacement mechanism [named as front-face or SNi (substitution nucleophilic internal)-like]. This mechanism has now received strong support, from both experiment and theory, for several GT families except family 6, for which a double-displacement reaction is predicted. In the last few years, we have uncovered the molecular mechanisms of several retaining GTs by means of quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, which we overview in the present work.

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