scholarly journals Molecular dynamics simulations of valinomycin interactions with potassium and sodium ions in water solvent

2010 ◽  
Vol 01 (03) ◽  
pp. 216-223 ◽  
Author(s):  
Kholmirzo Kholmurodov ◽  
Maria Abasheva ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sodium Ions ◽  
Water Solvent ◽  
Dynamics Simulations

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

QM/MM molecular dynamics simulations of the hydration of Mg(II) and Zn(II) ions

2013 ◽  
Vol 91 (7) ◽  
pp. 552-558 ◽  
Author(s):  
Saleh Riahi ◽  
Benoît Roux ◽  
Christopher N. Rowley
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Distribution Functions ◽  
Water Model ◽  
Polarizable Force Field ◽  
Water Solvent ◽  
Dynamics Simulations ◽  
Good Agreement

The hydration of Mg2+ and Zn2+ is examined using molecular dynamics simulations using 3 computational approaches of increasing complexity: the CHARMM nonpolarizable force field based on the TIP3P water model, the Drude polarizable force field based on the SWM4-NDP water model, and a combined QM/MM approach in which the inner coordination sphere is represented using a high-quality density functional theory (DFT) model (PBE/def2-TZVPP), and the remainder of the bulk water solvent is represented using the polarizable SWM4-NDP water model. The characteristic structural distribution functions (radial, angular, and tilt) are comparedand show very good agreement between the polarizable force field and QM/MM approaches. They predict an average Mg–O distance of 2.11 Å and an Zn–O distance of 2.13 Å, in good agreement with the available experimental neutron scattering and EXAFS data, while the Mg–O distances calculated using the nonpolarizable force field are 0.1 Å too short. Mg2+ (aq) and Zn2+ (aq) both have a coordination number of 6 and have a remarkably similar octahedral coordination mode, despite the chemical differences between these ions. Thermodynamic integration was used to calculate the relative hydration free energies of these ions (ΔΔGhydr). The nonpolarizable model is in error by 60 kcal mol– 1 and incorrectly predicts that Mg2+ has the more negative hydration energy. The Drude polarizable model predicts a ΔΔGhydr of only –13.2 kcal kcal mol– 1, an improvement over the results of the nonpolarizable force field, but still signficantly different than the experimental value of –30.1 kcal mol–1. The combined QM/MM approach performs much better, predicting a ΔΔGhydr of –34.8 kcal mol–1 in excellent agreement with experiment. These calculations support the experimental observation that Zn2+ has more favourable solvation free energy than Mg2+ despite having a very similar solvation structure.

scholarly journals Investigating the Selectivity of KcsA Channel by an Image Charge Solvation Method (ICSM) in Molecular Dynamics Simulations

2016 ◽  
Vol 19 (4) ◽  
pp. 927-943 ◽  
Author(s):  
Katherine Baker ◽  
Duan Chen ◽  
Wei Cai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Field Effect ◽  
Sodium Ions ◽  
Image Charge ◽  
Solvation Model ◽  
Reaction Field ◽  
Potassium Channel Kcsa ◽  
Charge Solvation ◽  
Dynamics Simulations

AbstractIn this paper, we study the selectivity of the potassium channel KcsA by a recently developed image-charge solvation method (ICSM) combined with molecular dynamics simulations. The hybrid solvation model in the ICSM is able to demonstrate atomistically the function of the selectivity filter of the KcsA channel when potassium and sodium ions are considered and their distributions inside the filter are simulated. Our study also shows that the reaction field effect, explicitly accounted for through image charge approximation in the ICSM model, is necessary in reproducing the correct selectivity property of the potassium channels.

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