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

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.

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.

Substrate-Assisted Catalytic Mechanism of O-GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation

2012 ◽  
Vol 134 (37) ◽  
pp. 15563-15571 ◽  
Author(s):  
Igor Tvaroška ◽  
Stanislav Kozmon ◽  
Michaela Wimmerová ◽  
Jaroslav Koča
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Catalytic Mechanism ◽  
Glcnac Transferase
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