scholarly journals Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2

2016 ◽  
Vol 18 (44) ◽  
pp. 30344-30356 ◽  
Author(s):  
Petr Jeřábek ◽  
Jan Florián ◽  
Václav Martínek
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Cytochrome P450 ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Cytochrome P450 1A2 ◽  
Structure And Dynamics ◽  
Human Cytochrome ◽  
Membrane Bound ◽  
Dynamics Simulations

The structure and dynamics of the membrane-bound full-length human cytochrome P450 1A2 (CYP1A2) in aqueous solution determined by coarse-grained and all-atom molecular dynamics simulations.

scholarly journals Structure and dynamics of liposomes designed for drug delivery: coarse-grained molecular dynamics simulations to reveal the role of lipopolymer incorporation

RSC Advances ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 3745-3755 ◽  
Author(s):  
Mohammed Lemaalem ◽  
Nourddine Hadrioui ◽  
Abdelali Derouiche ◽  
Hamid Ridouane
Keyword(s):  
Drug Delivery ◽  
Molecular Dynamics ◽  
Polyethylene Glycol ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Structure And Dynamics ◽  
Statistical Ensembles ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

In this work, coarse-grained molecular dynamics simulations are carried out in NPTH and NVTE statistical ensembles in order to study the structure and dynamics properties of liposomes coated with polyethylene glycol (PEG).

scholarly journals Surface Interaction of Ionic Liquids: Stabilization of Polyethylene Terephthalate-Degrading Enzymes in Solution

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 119
Author(s):  
Zeenat Zara ◽  
Deepti Mishra ◽  
Saurabh Kumar Pandey ◽  
Eva Csefalvay ◽  
Fatemeh Fadaei ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Ionic Liquid ◽  
Ionic Liquids ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Polyethylene Terephthalate ◽  
Pure Water ◽  
Structure And Dynamics ◽  
Dynamics Simulations

The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET.

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>

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