Ab Initio QM/MM Dynamics Simulation of the Tetrahedral Intermediate of Serine Proteases:  Insights into the Active Site Hydrogen-Bonding Network

2002 ◽  
Vol 124 (49) ◽  
pp. 14780-14788 ◽  
Author(s):  
Maya Topf ◽  
Peter Várnai ◽  
W. Graham Richards
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Active Site ◽  
Serine Proteases ◽  
Dynamics Simulation ◽  
Tetrahedral Intermediate ◽  
Hydrogen Bonding Network

Correlation between mobility and the hydrogen bonding network of water at an electrified-graphite electrode using molecular dynamics simulation

2020 ◽  
Vol 22 (3) ◽  
pp. 1767-1773
Author(s):  
Masaya Imai ◽  
Yasuyuki Yokota ◽  
Ichiro Tanabe ◽  
Kouji Inagaki ◽  
Yoshitada Morikawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Graphite Electrode ◽  
Dynamics Simulation ◽  
Applied Potential ◽  
Dissolved Ions ◽  
Hydrogen Bonding Network

Mobility and hydrogen bonding network of water at a graphite electrode: effects of dissolved ions and applied potential.

scholarly journals Kinetic Study of CO2 Hydration by Small-Molecule Catalysts with A Second Coordination Sphere that Mimic the Effect of the Thr-199 Residue of Carbonic Anhydrase

Biomimetics ◽  
2019 ◽  
Vol 4 (4) ◽  
pp. 66
Author(s):  
Park ◽  
Lee
Keyword(s):  
Hydrogen Bonding ◽  
Carbonic Anhydrase ◽  
Coordination Sphere ◽  
Active Site ◽  
Hydration Reaction ◽  
Ph Titration ◽  
Hydration Rate ◽  
Pka Value ◽  
Secondary Coordination Sphere ◽  
Hydrogen Bonding Network

Zinc complexes were synthesized as catalysts that mimic the ability of carbonic anhydrase (CA) for the CO2 hydration reaction (H2O + CO2 → H+ + HCO3-). For these complexes, a tris(2-pyridylmethyl)amine (TPA) ligand mimicking only the active site, and a 6-((bis(pyridin-2-ylmethyl)amino)methyl)pyridin-2-ol (TPA-OH) ligand mimicking the hydrogen-bonding network of the secondary coordination sphere of CA were used. Potentiometric pH titration was used to determine the deprotonation ability of the Zn complexes, and their pKa values were found to be 8.0 and 6.8, respectively. Stopped-flow spectrophotometry was used to confirm the CO2 hydration rate. The rate constants were measured to be 648.4 and 730.6 M-1s-1, respectively. The low pKa value was attributed to the hydrogen-bonding network of the secondary coordination sphere of the catalyst that mimics the behavior of CA, and this was found to increase the CO2 hydration rate of the catalyst.

scholarly journals Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+Ions and the Hydrogen-Bonding Network in the Active Site

Biochemistry ◽  
2016 ◽  
Vol 55 (27) ◽  
pp. 3834-3846 ◽  
Author(s):  
Melek N. Ucisik ◽  
Philip C. Bevilacqua ◽  
Sharon Hammes-Schiffer
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Active Site ◽  
Hydrogen Bonding Network

Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study

2014 ◽  
Vol 16 (33) ◽  
pp. 17458-17465 ◽  
Author(s):  
Rajdeep Singh Payal ◽  
Sundaram Balasubramanian
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Simulation Study ◽  
Molecular Hydrogen ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Dissolution of cellulose in ionic liquids involves breaking of its inter- and intra-molecular hydrogen bonding network, as seen through ab initio molecular dynamics simulations.

scholarly journals First-principles molecular dynamics simulation of the Ca2UO2(CO3)3 complex in water

2016 ◽  
Vol 45 (24) ◽  
pp. 9812-9819 ◽  
Author(s):  
Chad Priest ◽  
Ziqi Tian ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
First Principles ◽  
Dynamics Simulation ◽  
Ca Ions ◽  
Hydrogen Bonding Network ◽  
First Principles Molecular Dynamics

First principles molecular dynamics simulation reveals the structure and solvation of the Ca2UO2(CO3)3 complex in water and the hydrogen bonding network that differentiates the two Ca ions.

scholarly journals Streptomyces albus G serine β-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes

1992 ◽  
Vol 282 (1) ◽  
pp. 189-195 ◽  
Author(s):  
J Lamotte-Brasseur ◽  
F Jacob-Dubuisson ◽  
G Dive ◽  
J M Frère ◽  
J M Ghuysen
Keyword(s):  
Hydrogen Bonding ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Site Directed Mutagenesis ◽  
Network Configuration ◽  
Beta Lactam ◽  
Beta Lactamases ◽  
Class A ◽  
Streptomyces Albus ◽  
Hydrogen Bonding Network

In previous studies, several amino acids of the active site of class A beta-lactamases have been modified by site-directed mutagenesis. On the basis of the catalytic mechanism proposed for the Streptomyces albus G beta-lactamase [Lamotte-Brasseur, Dive, Dideberg, Charlier, Frère & Ghuysen (1991) Biochem. J. 279, 213-221], the influence that these mutations exert on the hydrogen-bonding network of the active site has been analysed by molecular mechanics. The results satisfactorily explain the effects of the mutations on the kinetic parameters of the enzyme's activity towards a set of substrates. The present study also shows that, upon binding a properly structured beta-lactam compound, the impaired cavity of a mutant enzyme can readopt a functional hydrogen-bonding-network configuration.

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