Stability and Migration of Metal Ions in G4-Wires by Molecular Dynamics Simulations

2006 ◽  
Vol 110 (51) ◽  
pp. 26337-26348 ◽  
Author(s):  
Manuela Cavallari ◽  
Arrigo Calzolari ◽  
Anna Garbesi ◽  
Rosa Di Felice
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
And Migration ◽  
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>

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>

Metal ions affect the formation and stability of amyloid β aggregates at multiple length scales

2018 ◽  
Vol 20 (13) ◽  
pp. 8951-8961 ◽  
Author(s):  
Myeongsang Lee ◽  
Jae In Kim ◽  
Sungsoo Na ◽  
Kilho Eom
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Neurodegenerative Disease ◽  
Molecular Dynamics Simulations ◽  
Metal Ion ◽  
Amyloid Β ◽  
Length Scales ◽  
Multiple Length Scales ◽  
Dynamics Simulations

The effect of metal ion on the formation of amyloid β (Aβ) aggregates, which are a hallmark for neurodegenerative disease, was studied based on full atomistic molecular dynamics simulations.

Simulation of metal–organic framework self-assembly

2015 ◽  
Vol 17 (14) ◽  
pp. 8649-8652 ◽  
Author(s):  
Makoto Yoneya ◽  
Seiji Tsuzuki ◽  
Masaru Aoyagi
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Metal Organic Framework ◽  
Metal Organic Frameworks ◽  
Spontaneous Growth ◽  
Metal Organic ◽  
Initial Placement ◽  
Dynamics Simulations

Spontaneous growth of metal–organic frameworks (MOFs) composed of metal ions and 4,4′-bipyridine ligands was successfully demonstrated by molecular dynamics simulations, starting from a random initial placement of the metals and the ligands.

Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution

2021 ◽  
Author(s):  
Jingjing Xue ◽  
Xinpeng Li ◽  
Rongri Tan ◽  
Wenjun Zong
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Salt Solution ◽  
Dna Structure ◽  
High Concentration ◽  
Bivalent Metal ◽  
Bivalent Metal Ions ◽  
The Stability ◽  
Dynamics Simulations

Abstract A-DNA is one of the biologically active double helical structure. The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology. In aqueous solution, the A-DNA structure will have a free transformation, the A-DNA structure will be translated into B-form structure with the evolution of time, and eventually stabilized in the the B-DNA structure. To explore the stability function of the bivalent metal ions on the A-DNA structure, a series of molecular dynamics simulations have been performed on the A-DNA of sequence (CCCGGCCGGG). The results show that bivalent metal ions (Mg2+, Zn2+, Ca2+) generate a great effect on the structural stability of A-DNA in the environment of high concentration. As the interaction between metal ions and electronegative DNA chains, the stability of A-DNA in solution is gradually improved with the increasing of the solution concentration of ions. In metal salt solution with high concentration, metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure. Also, in the condition of the same concentration and valency of the metal ions, the stability of A-DNA structure is different. The calculations indicate that the structure of A-DNA in CaCl2 solution is less stable than in MgCl2 and ZnCl2 solution.

Sign in / Sign up

Export Citation Format

Share Document