scholarly journals Reaction mechanism of N-cyclopropylglycine oxidation by monomeric sarcosine oxidase

2020 ◽  
Vol 22 (29) ◽  
pp. 16552-16561
Author(s):  
Mitsuo Shoji ◽  
Yukihiro Abe ◽  
Mauro Boero ◽  
Yasuteru Shigeta ◽  
Yoshiaki Nishiya
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Theoretical Level ◽  
Sarcosine Oxidase

Reaction mechanism of monomeric sarcosine oxidase (MSOX) with N-cyclopropylglycine (CPG) is unravelled at the theoretical level of the hybrid quantum mechanics/molecular mechanical (QM/MM) method.

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

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

2020 ◽  
Vol 168 (3) ◽  
pp. 223-229
Author(s):  
Yoshinori Shibanuma ◽  
Naoki Nemoto ◽  
Norifumi Yamamoto ◽  
Gen-Ichi Sampei ◽  
Gota Kawai
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Adenylate Kinase ◽  
Reaction Coordinate ◽  
Amino Acid Residues ◽  
Aeropyrum Pernix ◽  
Adenylate Kinases

Abstract The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.

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

The reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods

2017 ◽  
Vol 19 (15) ◽  
pp. 9811-9822 ◽  
Author(s):  
Yukihiro Abe ◽  
Mitsuo Shoji ◽  
Yoshiaki Nishiya ◽  
Hiroshi Aiba ◽  
Takahide Kishimoto ◽  
...  
Keyword(s):  
Renal Function ◽  
Reaction Mechanism ◽  
Clinical Diagnostics ◽  
Sarcosine Oxidase

Monomeric sarcosine oxidase (MSOX) is a flavoprotein that oxidizes sarcosine to the corresponding imine product and is widely used in clinical diagnostics to test renal function.

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
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