Extracting free energies of counterion binding to polyelectrolytes by molecular dynamics simulations

2021 ◽  
Vol 155 (11) ◽  
pp. 114902
Author(s):  
Wen-de Tian ◽  
Mohsen Ghasemi ◽  
Ronald G. Larson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
Counterion Binding ◽  
Dynamics Simulations

scholarly journals Evaluating Free Energies of Dimerization of Short Polyglutamine Peptides with Molecular Dynamics Simulations

2016 ◽  
Vol 110 (3) ◽  
pp. 400a
Author(s):  
Riley J. Workman ◽  
Jeffry D. Madura
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
Dynamics Simulations

scholarly journals Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations

2012 ◽  
Vol 102 (4) ◽  
pp. 795-801 ◽  
Author(s):  
James Gumbart ◽  
Benoît Roux
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Membrane Insertion ◽  
Free Energies ◽  
Dynamics Simulations

Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations

2020 ◽  
Vol 22 (15) ◽  
pp. 8021-8034
Author(s):  
Daniel Sadowsky ◽  
J. Samuel Arey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Ionic Solutes

A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water.

Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

2014 ◽  
Vol 141 (4) ◽  
pp. 045102 ◽  
Author(s):  
S. Jakobtorweihen ◽  
A. Chaides Zuniga ◽  
T. Ingram ◽  
T. Gerlach ◽  
F. J. Keil ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Partition Coefficients ◽  
Free Energies ◽  
Solute Partitioning ◽  
Dynamics Simulations

Precision of free energies calculated by molecular dynamics simulations of peptides in solution

1992 ◽  
Vol 13 (4) ◽  
pp. 429-442 ◽  
Author(s):  
Jan Hermans ◽  
R.H. Yun ◽  
Amil G. Anderson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
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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