Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores

2020 ◽  
Vol 22 (34) ◽  
pp. 19188-19194
Author(s):  
Gang Hu ◽  
Jiye Fu ◽  
Yi Qiao ◽  
Hao Meng ◽  
Zunliang Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Biological Macromolecule ◽  
Conformational States

As a type of biological macromolecule, the conformation of proteins dynamically changes in a solution, which often results in a change in their function.

scholarly journals Molecular Dynamics Study of Ion Transport in Polymer Electrolytes of All-Solid-State Li-Ion Batteries

Micromachines ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1012
Author(s):  
Takuya Mabuchi ◽  
Koki Nakajima ◽  
Takashi Tokumasu
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Ion Transport ◽  
Polyethylene Oxide ◽  
Polymer Electrolytes ◽  
Li Ion Batteries ◽  
Transport Mechanisms ◽  
Li Ion ◽  
Dynamics Simulations ◽  
The Relationship

Atomistic analysis of the ion transport in polymer electrolytes for all-solid-state Li-ion batteries was performed using molecular dynamics simulations to investigate the relationship between Li-ion transport and polymer morphology. Polyethylene oxide (PEO) and poly(diethylene oxide-alt-oxymethylene), P(2EO-MO), were used as the electrolyte materials, and the effects of salt concentrations and polymer types on the ion transport properties were explored. The size and number of LiTFSI clusters were found to increase with increasing salt concentrations, leading to a decrease in ion diffusivity at high salt concentrations. The Li-ion transport mechanisms were further analyzed by calculating the inter/intra-hopping rate and distance at various ion concentrations in PEO and P(2EO-MO) polymers. While the balance between the rate and distance of inter-hopping was comparable for both PEO and P(2EO-MO), the intra-hopping rate and distance were found to be higher in PEO than in P(2EO-MO), leading to a higher diffusivity in PEO. The results of this study provide insights into the correlation between the nanoscopic structures of ion solvation and the dynamics of Li-ion transport in polymer electrolytes.

Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations

2014 ◽  
Vol 118 (19) ◽  
pp. 5119-5129 ◽  
Author(s):  
Sara K. Hansen ◽  
Mikkel Vestergaard ◽  
Lea Thøgersen ◽  
Birgit Schiøtt ◽  
Niels Chr. Nielsen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Molecular Dynamics Simulations ◽  
Solid State Nmr ◽  
Nmr Spectra ◽  
Lipid Dynamics ◽  
Dynamics Simulations

Theoretical study of Na+ transport in the solid-state electrolyte Na3OBr based on deep potential molecular dynamics

2021 ◽  
Author(s):  
Han-Xiao Li ◽  
Xu-Yuan Zhou ◽  
Yue-Chao Wang ◽  
Hong Jiang
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Theoretical Study ◽  
Na Transport ◽  
Solid State Electrolyte

Deep potential molecular dynamics is used to study Na+ transport in Na3OBr.

scholarly journals Analysis of an all-solid state nanobattery using molecular dynamics simulations under an external electric field

2021 ◽  
Vol 23 (1) ◽  
pp. 597-606
Author(s):  
Victor Ponce ◽  
Diego E. Galvez-Aranda ◽  
Jorge M. Seminario
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
External Electric Field ◽  
Dynamics Simulations

Speciation at the SEI and SSE of a solid-state nanobattery.

scholarly journals The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5489
Author(s):  
Alexander Vogel ◽  
Mathias Bosse ◽  
Marcel Gauglitz ◽  
Sarah Wistuba ◽  
Peter Schmidt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Neuropeptide Y ◽  
Solid State Nmr ◽  
Bound State ◽  
Receptor Activation ◽  
Order Parameters ◽  
Dynamics Simulation ◽  
15N Nmr

We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.

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