Molecular Dynamics Simulations of Matrix Metalloproteinase 2:  Role of the Structural Metal Ions†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (31) ◽  
pp. 8943-8952 ◽  
Author(s):  
Natalia Díaz ◽  
Dimas Suárez
Keyword(s):  
Molecular Dynamics ◽  
Matrix Metalloproteinase ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Matrix Metalloproteinase 2 ◽  
Structural Metal ◽  
Dynamics Simulations

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

Exploring secondary interactions and the role of temperature in moisture-contaminated polymer networks through molecular simulations

Soft Matter ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. 2942-2956
Author(s):  
Rishabh D. Guha ◽  
Ogheneovo Idolor ◽  
Katherine Berkowitz ◽  
Melissa Pasquinelli ◽  
Landon R. Grace
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Temperature Variation ◽  
Polymer Networks ◽  
Molecular Simulations ◽  
Effect Of Temperature ◽  
Secondary Interactions ◽  
Dynamics Simulations ◽  
Secondary Bonding

We investigated the effect of temperature variation on the secondary bonding interactions between absorbed moisture and epoxies with different morphologies using molecular dynamics simulations.

scholarly journals Molecular insights on poly(N-isopropylacrylamide) coil-to-globule transition induced by pressure

2021 ◽  
Vol 23 (10) ◽  
pp. 5984-5991
Author(s):  
Letizia Tavagnacco ◽  
Ester Chiessi ◽  
Emanuela Zaccarelli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Chain ◽  
Linear Polymer ◽  
Dynamics Simulations ◽  
Linear Polymer Chain

By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we unveil the role of pressure in the coil-to-globule transition of poly(N-isopropylacrylamide) (PNIPAM).

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

Kinetic Insights into the Role of the Solvent in the Polymorphism of 5-Fluorouracil from Molecular Dynamics Simulations

2006 ◽  
Vol 110 (7) ◽  
pp. 3323-3329 ◽  
Author(s):  
Said Hamad ◽  
Changman Moon ◽  
C. Richard A. Catlow ◽  
Ashley T. Hulme ◽  
Sarah L. Price
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations
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