scholarly journals The rupture mechanism of rubredoxin is more complex than previously thought

2020 ◽  
Vol 11 (23) ◽  
pp. 6036-6044
Author(s):  
Maximilian Scheurer ◽  
Andreas Dreuw ◽  
Martin Head-Gordon ◽  
Tim Stauch
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Strain Analysis ◽  
Rupture Force ◽  
Iron Sulfur ◽  
Hydrogen Bond Networks ◽  
Dynamics Simulations ◽  
Rupture Mechanism ◽  
Sulfur Bond

Using steered molecular dynamics simulations and strain analysis it is shown that, in contrast to previous assumptions, the experimentally found low rupture force of the iron–sulfur-bond in rubredoxin cannot be explained by hydrogen bond networks.

Molecular Dynamics Simulations of Water, Silica, and Aqueous Mixtures in Bulk and Confinement

2018 ◽  
Vol 232 (7-8) ◽  
pp. 1187-1225 ◽  
Author(s):  
Julian Geske ◽  
Michael Harrach ◽  
Lotta Heckmann ◽  
Robin Horstmann ◽  
Felix Klameth ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Aqueous Mixtures ◽  
Simulation Data ◽  
Hydrogen Bond Networks ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Anomalies Of Water

Abstract Aqueous systems are omnipresent in nature and technology. They show complex behaviors, which often originate in the existence of hydrogen-bond networks. Prominent examples are the anomalies of water and the non-ideal behaviors of aqueous solutions. The phenomenology becomes even richer when aqueous liquids are subject to confinement. To this day, many properties of water and its mixtures, in particular, under confinement, are not understood. In recent years, molecular dynamics simulations developed into a powerful tool to improve our knowledge in this field. Here, our simulation results for water and aqueous mixtures in the bulk and in various confinements are reviewed and some new simulation data are added to improve our knowledge about the role of interfaces. Moreover, findings for water are compared with results for silica, exploiting that both systems form tetrahedral networks.

PM-11Lattice Strain Analysis in Gold Nanorods by Means of Atomic Resolution HAADF-STEM Experiments and Molecular Dynamics Simulations

Microscopy ◽  
2017 ◽  
Vol 66 (suppl_1) ◽  
pp. i23-i23
Author(s):  
Kohei Aso ◽  
Jens Maebe ◽  
Tomokazu Yamamoto ◽  
Koji Shigematsu ◽  
Syo Matsumura
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Gold Nanorods ◽  
Strain Analysis ◽  
Atomic Resolution ◽  
Dynamics Simulations

Molecular Dynamics Simulations for Loading-Dependent Diffusion of CO2, SO2, CH4, and Their Binary Mixtures in ZIF-10: The Role of Hydrogen Bond

Langmuir ◽  
2017 ◽  
Vol 33 (42) ◽  
pp. 11543-11553 ◽  
Author(s):  
Li Li ◽  
Deshuai Yang ◽  
Trevor R. Fisher ◽  
Qi Qiao ◽  
Zhen Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Binary Mixtures ◽  
Dynamics Simulations

Rupture Mechanism of Aromatic Systems from Graphite Probed with Molecular Dynamics Simulations

Langmuir ◽  
2010 ◽  
Vol 26 (13) ◽  
pp. 10791-10795 ◽  
Author(s):  
Yumin Leng ◽  
Jian Chen ◽  
Beifei Zhou ◽  
Frauke Gräter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Aromatic Systems ◽  
Dynamics Simulations ◽  
Rupture Mechanism

Reversible Hydrogen Bond Network Dynamics: Molecular Dynamics Simulations of Calix[4]arene-Catenanes

2011 ◽  
Vol 115 (20) ◽  
pp. 6445-6454 ◽  
Author(s):  
Thomas Schlesier ◽  
Thorsten Metzroth ◽  
Andreas Janshoff ◽  
Jürgen Gauss ◽  
Gregor Diezemann
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Network Dynamics ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Dynamics Simulations

Investigations on the mechanisms of interactions between matrix metalloproteinase 9 and its flavonoid inhibitors using a combination of molecular docking, hybrid quantum mechanical/molecular mechanical calculations, and molecular dynamics simulations

2014 ◽  
Vol 92 (9) ◽  
pp. 821-830 ◽  
Author(s):  
Zhi-Guang Zhou ◽  
Qi-Zheng Yao ◽  
Dong Lei ◽  
Qing-Qing Zhang ◽  
Ji Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Biological Activities ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Hydrogen Bond Networks ◽  
Dynamics Simulations ◽  
Binding Free Energies

Many experimental studies have found that flavonoids can inhibit the activities of matrix metalloproteinases (MMPs), but the relevant mechanisms are still unclear. In this paper, the interaction mechanisms of MMP-9 with its five flavonoid inhibitors are investigated using a combination of molecular docking, hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, and molecular dynamics simulations. The molecular dynamics simulation results show a good linear correlation between the calculated binding free energies of QM/MM−Poisson–Boltzmann surface area (PBSA) and the experimental −log(EC50) regarding the studied five flavonoids on MMP-9 inhibition in explicit solvent. It is found that compared with the MM−PBSA method, the QM/MM−PBSA method can obviously improve the accuracy for the calculated binding free energies. The predicted binding modes of the five flavonoid−MMP-9 complexes reveal that the different hydrogen bond networks can form besides producing the Zn−O coordination bonds, which can reasonably explain previous experimental results. The agreement between our calculated results and the previous experimental facts indicates that the force field parameters used here are effective and reliable for investigating the systems of flavonoid−MMP-9 interactions, and thus, these simulations and analyses could be reproduced for the other related systems involving protein−ligand interactions. This paper may be helpful for designing the new MMP-9 inhibitors having higher biological activities by carrying out the structural modifications of flavonoid molecules.

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