scholarly journals Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

2019 ◽  
Vol 48 (2) ◽  
pp. 561-575 ◽  
Author(s):  
Justin A Lemkul
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dipole Moments ◽  
Sequence Motifs ◽  
Telomeric Dna ◽  
Rna Sequences ◽  
Dna And Rna ◽  
Induced Dipole ◽  
Dynamics Simulations

Abstract DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen-bonded guanine tetrads and diverse loop structures. GQ sequence motifs are overrepresented in promoters, origins of replication, telomeres, and untranslated regions in mRNA, suggesting roles in modulating gene expression and preserving genomic integrity. Given these roles and unique aspects of different structures, GQs are attractive targets for drug design, but greater insight into GQ folding pathways and the interactions stabilizing them is required. Here, we performed molecular dynamics simulations to study two bimolecular GQs, a telomeric DNA GQ and the analogous telomeric repeat-containing RNA (TERRA) GQ. We applied the Drude polarizable force field, which we show outperforms the additive CHARMM36 force field in both ion retention and maintenance of the GQ folds. The polarizable simulations reveal that the GQs bind bulk K+ ions differently, and that the TERRA GQ accumulates more K+ ions, suggesting different ion interactions stabilize these structures. Nucleobase dipole moments vary as a function of position and also contribute to ion binding. Finally, we show that the TERRA GQ is more sensitive than the telomeric DNA GQ to water-mediated modulation of ion-induced dipole-dipole interactions.

scholarly journals New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations

Ab initio based force field and molecular dynamics simulations of crystalline TATB

2004 ◽  
Vol 120 (15) ◽  
pp. 7059-7066 ◽  
Author(s):  
Richard H. Gee ◽  
Szczepan Roszak ◽  
Krishnan Balasubramanian ◽  
Laurence E. Fried
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Dipole Moments ◽  
Hydration Shell ◽  
Minor Groove ◽  
Water Molecules ◽  
Negative Hydration ◽  
Dynamics Simulations ◽  
Dna Double Helix

The DNA double helix is a polyanionic macromolecule that is neutralized in water solutions by metal ions (counterions). The property of counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na+ counterions and negative hydration of K+ and Cs+ counterions incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on the region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions localized in the minor groove of the double helix (about 50 ps for Na+ and lower than 10 ps for K+ and Cs+). The estimated potentials of the mean force for the hydration shells of counterions show that the water molecules are constrained too strongly, and the effect of negative hydration for K+ and Cs+ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

scholarly journals First-Principles-Based Interatomic Potential for SI and Its Thermal Conductivity

2011 ◽  
Author(s):  
Keivan Esfarjani ◽  
Gang Chen ◽  
Asegun Henry
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Properties ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Density Functional ◽  
Interatomic Potential ◽  
Force Constants ◽  
Dynamics Simulations

Based on first-principles density-functional calculations, we have developed and tested a force-field for silicon, which can be used for molecular dynamics simulations and the calculation of its thermal properties. This force field uses the exact Taylor expansion of the total energy about the equilibrium positions up to 4th order. In this sense, it becomes systematically exact for small enough displacements, and can reproduce the thermodynamic properties of Si with high fidelity. Having the harmonic force constants, one can easily calculate the phonon spectrum of this system. The cubic force constants, on the other hand, will allow us to compute phonon lifetimes and scattering rates. Results on equilibrium Green-Kubo molecular dynamics simulations of thermal conductivity as well as an alternative calculation of the latter based on the relaxation-time approximation will be reported. The accuracy and ease of computation of the lattice thermal conductivity using these methods will be compared. This approach paves the way for the construction of accurate bulk interatomic potentials database, from which lattice dynamics and thermal properties can be calculated and used in larger scale simulation methods such as Monte Carlo.

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

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