Structure of the enzyme-substrate complex for guanosine triphosphate hydrolysis by elongation factor EF-Tu: Comparison of quantum mechanics/molecular mechanics and molecular dynamics results

2008 ◽  
Vol 63 (6) ◽  
pp. 321-323 ◽  
Author(s):  
M. S. Shadrina ◽  
B. L. Grigorenko ◽  
A. V. Nemukhin
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Elongation Factor ◽  
Guanosine Triphosphate ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Molecular Dynamics Results

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics†

2012 ◽  
Vol 34 (9) ◽  
pp. 750-756 ◽  
Author(s):  
Marcin Nowosielski ◽  
Marcin Hoffmann ◽  
Aneta Kuron ◽  
Malgorzata Korycka-Machala ◽  
Jaroslaw Dziadek
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics

On the Nature of the Enzyme–Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study

ACS Catalysis ◽  
2020 ◽  
Vol 10 (15) ◽  
pp. 8321-8333 ◽  
Author(s):  
José L. Velázquez-Libera ◽  
Julio Caballero ◽  
Iñaki Tuñón ◽  
Erix W. Hernández-Rodríguez ◽  
J. Javier Ruiz-Pernía
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Arginase I
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