Cofactor Activation and Substrate Binding in Pyruvate Decarboxylase. Insights into the Reaction Mechanism from Molecular Dynamics Simulations†

Biochemistry ◽  
2005 ◽  
Vol 44 (45) ◽  
pp. 14792-14806 ◽  
Author(s):  
Mette Alstrup Lie ◽  
Leyla Celik ◽  
Karl Anker Jørgensen ◽  
Birgit Schiøtt
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
Pyruvate Decarboxylase ◽  
Dynamics Simulations

Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations

ACS Catalysis ◽  
2021 ◽  
pp. 11626-11638
Author(s):  
Carola Jerves ◽  
Rui P. P. Neves ◽  
Maria J. Ramos ◽  
Saulo da Silva ◽  
Pedro A. Fernandes
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Molecular Dynamics Simulations ◽  
Degrading Enzyme ◽  
Dynamics Simulations

A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1

2018 ◽  
Vol 20 (9) ◽  
pp. 6409-6420 ◽  
Author(s):  
Juan Duan ◽  
Chuncai Hu ◽  
Jiafan Guo ◽  
Lianxian Guo ◽  
Jia Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
New Delhi ◽  
Binding Process ◽  
Dynamics Simulations

We have investigated the substrate-binding pathways of NDM-1 via unbiased molecular dynamics simulations and metadynamics.

scholarly journals Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution fromAb InitioPotential and Molecular Dynamics Simulations

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
S. Tolosa ◽  
A. Hidalgo ◽  
J. A. Sansón
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Free Energy ◽  
Reaction Mechanism ◽  
Molecular Dynamics Simulations ◽  
Infinite Dilution ◽  
Theoretical Study ◽  
Water Model ◽  
Dynamics Simulations ◽  
Hydrolysis Of

A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described usingab initiosolute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3) via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

scholarly journals Substrate Binding at the Qo-Site of the Bacterial Cytochrome bc1 Complex Predicted by Atomistic Molecular Dynamics Simulations

2013 ◽  
Vol 104 (2) ◽  
pp. 490a
Author(s):  
Pekka A. Postila ◽  
Karol Kaszuba ◽  
Marcin Sarewicz ◽  
Artur Osyczka ◽  
Ilpo Vattulainen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
Cytochrome Bc1 ◽  
Bc1 Complex ◽  
Cytochrome Bc1 Complex ◽  
Qo Site ◽  
Dynamics Simulations
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