scholarly journals Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate

2019 ◽  
Vol 123 (13) ◽  
pp. 2889-2903 ◽  
Author(s):  
Bodee Nutho ◽  
Adrian J. Mulholland ◽  
Thanyada Rungrotmongkol
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Serine Protease ◽  
Zika Virus ◽  
Concerted Reaction

Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations

ACS Catalysis ◽  
2014 ◽  
Vol 4 (11) ◽  
pp. 3869-3876 ◽  
Author(s):  
Ana R. Calixto ◽  
Natércia F. Brás ◽  
Pedro A. Fernandes ◽  
Maria J. Ramos
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Human Renin

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism

Biochemistry ◽  
2016 ◽  
Vol 55 (40) ◽  
pp. 5764-5771 ◽  
Author(s):  
Yojiro Hamada ◽  
Yusuke Kanematsu ◽  
Masanori Tachikawa
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics

Quantum mechanics and molecular mechanics study of the reaction mechanism of quorum quenching enzyme: N-acyl homoserine lactonase with C6-HSL

RSC Advances ◽  
2016 ◽  
Vol 6 (28) ◽  
pp. 23396-23402 ◽  
Author(s):  
Shujun Zhang ◽  
Hao Su ◽  
Guangcai Ma ◽  
Yongjun Liu
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Lactone Ring ◽  
Quorum Quenching ◽  
Homoserine Lactone ◽  
Ester Bond ◽  
Acyl Homoserine Lactone

N-Acyl-homoserine lactonase fromOchrobactrumsp. strain (AidH) is a novel AHL (N-acyl-homoserine lactone)-lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs.

Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics

2002 ◽  
Vol 106 (46) ◽  
pp. 12059-12065 ◽  
Author(s):  
Yong S. Lee ◽  
Sharon E. Worthington ◽  
Morris Krauss ◽  
Bernard R. Brooks
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Chorismate Mutase

scholarly journals Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I

2020 ◽  
Vol 59 (4) ◽  
pp. 2594-2603 ◽  
Author(s):  
Sonia Jafari ◽  
Ulf Ryde ◽  
Adam Emad Ahmed Fouda ◽  
Fatemeh Sadat Alavi ◽  
Geng Dong ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Glyoxalase I

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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