scholarly journals Gating Mechanism of Hv1 Studied by Molecular Dynamic Simulations

2020 ◽  
Vol 4 (1) ◽  
pp. 20
Author(s):  
Thi Tuong Vy Phan
Keyword(s):  
Molecular Dynamics ◽  
Cancer Progression ◽  
Md Simulations ◽  
Proton Channel ◽  
Water Molecules ◽  
State Structure ◽  
Ph Homeostasis ◽  
Dynamic Simulations ◽  
Closed State ◽  
Gating Mechanism

The voltage-gated proton channel (Hv1) plays the important role in proton extrusion, pH homeostasis, sperm motility, and cancer progression. The closed-state structure of Hv1 was recently revealed by X-ray crystallography. However, the opened-state structure has not been captured yet. To investigate the mechanism of proton transfer in Hv1, molecular dynamics (MD) simulations were performed with the closed-state structure of Hv1 under electric field and pH conditions. The residues arrangement on the closed-state structure revealed that the selectivity filter (Asp108) which is located in the hydrophobic layer (consists of two Phe residues 146 and 179) might prevent water penetration. In molecular dynamics simulations, we observed that the channel opened by moving 3 Arg up on the S4 helix and a continuous hydrogen-bonded chain of water molecules (a “water wire”) went through the channel when it opened. During simulations, the open channel allowed water molecules to pass through the channel but excluded other ions. This indicates the Hv1 channel is highly selective for protons. Our results clearly showed the Hv1 channel is voltage-and pH-gradient sensing.

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

scholarly journals Solvent-induced depletion interactions in multiparticle collision dynamic simulations

2019 ◽  
Vol 30 (10) ◽  
pp. 1941008 ◽  
Author(s):  
Martin Wagner ◽  
Marisol Ripoll
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Simulation Methods ◽  
Mesoscale Simulation ◽  
Dynamic Simulations ◽  
Collision Dynamic ◽  
Versatile Tool ◽  
Depletion Interactions

Molecular-dynamics-coupled multiparticle collision dynamic (MPC-MD) simulations have emerged to be an efficient and versatile tool in the description of mesoscale colloidal dynamics. However, the compressibility of the coarse-grained fluid leads to this method being prone to spurious depletion interactions that may dominate the colloidal dynamics. In this paper, we review the existing methodology to deal with these interactions, establish and report depletion measurements, and present a method to avoid artificial depletion in mesoscale simulation methods.

scholarly journals Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations

2020 ◽  
Vol 73 (8) ◽  
pp. 734
Author(s):  
W. A. Monika Madhavi ◽  
Samantha Weerasinghe ◽  
Konstantin I. Momot
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Hydrogen Sulfide ◽  
Spin Relaxation ◽  
Rotational Diffusion ◽  
Molecular Geometry ◽  
Md Simulations ◽  
Water Molecules ◽  
Molecular Reorientation ◽  
Nmr Spin Relaxation

Rotational motion of molecules plays an important role in determining NMR spin relaxation properties of liquids. The textbook theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of molecules is described by a continuous time rotational diffusion random walk with a single rotational diffusion coefficient. Previously we and others have shown that reorientation of water molecules on the timescales of picoseconds is not consistent with the Debye rotational-diffusion model. In particular, multiple timescales of molecular reorientation were observed in liquid water. This was attributed to the hydrogen bonding network in water and the consequent presence of collective rearrangements of the molecular network. In order to better understand the origins of the complex reorientational behaviour of water molecules, we carried out molecular dynamics (MD) simulations of a liquid that has a similar molecular geometry to water but does not form hydrogen bonds: hydrogen sulfide. These simulations were carried out at T=208K and p=1 atm (~5K below the boiling point). Ensemble-averaged Legendre polynomial functions of hydrogen sulfide exhibited a Gaussian decay on the sub-picosecond timescale but, unlike water, did not exhibit oscillatory behaviour. We attribute these differences to hydrogen sulfide’s absence of hydrogen bonding.

scholarly journals Investigating the effect of Ser256 phosphorylation on gating of aquaporin-2: Molecular Dynamics study

2021 ◽  
Author(s):  
Pragya Priyadarshini ◽  
Balvinder Singh
Keyword(s):  
Molecular Dynamics ◽  
Water Permeability ◽  
Water Movement ◽  
Hydrophobic Interactions ◽  
Md Simulations ◽  
Post Translational Modification ◽  
Functional Changes ◽  
Gating Mechanism ◽  
Intracellular Storage ◽  
Dynamics Simulations

AbstractRegulation of water transport via aquaporins is crucial for osmoregulation and water homeostasis of an organism. This transport of water is regulated either by gating or trafficking wherein AQPs are transported from intracellular storage sites to plasma membrane. It has been proposed that water movement via AQP2 is regulated by post-translational modification. We aimed to explore the structural and functional changes occurring in AQP2 due to Ser256 phosphorylation. We have carried out molecular dynamics simulations to investigate molecular basis of effect of phosphorylation on water permeability of AQP2. MD simulations show that there are mild variations in the pore sizes of different monomers of the phosphorylated and unphosphorylated AQP2. Analysis of inter and intra-monomeric interactions such as hydrogen bond, electrostatic and hydrophobic interactions has been carried out. Structures of the phosphorylated AQP2 do not show any blocking of mouth of pore of the monomers during the course of MD simulations. Further, water permeability calculations do corroborate the above finding. This molecular dynamics study suggests that phosphorylation of C-terminal Ser-256 residue of AQP2 may not be directly responsible for gating mechanism.

Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields

2020 ◽  
pp. 1-20
Author(s):  
Yingying Zhang ◽  
Kamran Haider ◽  
Divya Kaur ◽  
Van A. Ngo ◽  
Xiuhong Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dipole Moment ◽  
Electrostatic Interactions ◽  
Hybrid Methods ◽  
Force Fields ◽  
Proton Channel ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Continuum Electrostatics ◽  
Hydrogen Bond Networks

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.

Stabilization of DPPC lipid bilayers in the presence of co-solutes: molecular mechanisms and interaction patterns

2021 ◽  
Author(s):  
Fabian Keller ◽  
Andreas Heuer ◽  
Hans-Joachim Galla ◽  
Jens Smiatek
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Lipid Bilayers ◽  
Density Functional ◽  
Molecular Mechanisms ◽  
Md Simulations ◽  
Water Molecules ◽  
Interaction Patterns ◽  
Conceptual Density Functional Theory ◽  
Functional Theory

The interactions between DPPC lipid bilayers in different phases with ectoine, amino ectoine and water molecules are studied by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations.

scholarly journals Polyacrylic Acid to Improve Flotation Tailings Management: Understanding the Chemical Interactions through Molecular Dynamics

Metals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 987
Author(s):  
Gonzalo R. Quezada ◽  
Eder Piceros ◽  
Pedro Robles ◽  
Carlos Moraga ◽  
Edelmira Gálvez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Polyacrylic Acid ◽  
Mining Industry ◽  
Lower Surface ◽  
Water Molecules ◽  
Mineral Surfaces ◽  
Dynamic Simulations ◽  
Amber Force Field ◽  
Lennard Jones ◽  
Saline Medium

Molecular dynamic simulations of polyacrylic acid polyelectrolyte (PAA) analyzed its interaction with the main minerals that make up characteristic tailings of the mining industry, in this case, quartz, kaolinite, and montmorillonite. The simulations were carried out with the package Gromacs 2020.3. The interaction potentials used were General AMBER Force Field (GAFF) for PAA and CLAYFF-MOH for mineral surfaces. The SPC/E model described water molecules and Lennard-Jones 12-6 parameters adjusted for SPC/E model were used for Na+ and Cl− ions. The studied systems were carried out at pH 7, obtaining stable adsorption between the PAA and the studied surfaces. Interestingly, the strongest adsorptions were for montmorillonite at both low and high salt concentrations. The effect of salinity differs according to the system, finding that it impairs the absorption of the polymer on montmorillonite surfaces. However, a saline medium favors the interaction with quartz and kaolinite. This is explained because montmorillonite has a lower surface charge density and a greater capacity to adsorb ions. This facilitated the adsorption of PAA. It was possible to identify that the main interaction by which the polymer is adsorbed is through the hydroxyl of the mineral surface and the COO−Na+ complexes. Molecular dynamics allows us to advance in the understanding of interactions that define the behavior of this promising reagent as an alternative for sustainable treatment of complex tailings in highly saline environments.

scholarly journals Polarizable force field for molecular dynamics simulations of silver nanoparticles

2019 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Polarization Effect ◽  
Md Simulations ◽  
Water Molecules ◽  
Interfacial Water ◽  
Silver Surface ◽  
Polarizable Force Field ◽  
Rod Model ◽  
Adsorption Of Water ◽  
Rigid Rod

Contact of silver metal surfaces with water, ions and organic ligands experiences induced charges, leading to attractive polarization. These forces play an important role at inorganic/organic interfaces and complement other non-bonded surface interactions. Despite the importance of these interactions, it, however, remains difficult to implement polarization effects to classical molecular dynamics (MD) simulations. In this contribution, we first present an overview of two popular polarizable models, such as Drude oscillator and the rigid rod model, which are utilized to mimic the polarizability of bulk metals. Second, we implemented the rigid rod model to the polarizable force field (FF) for a silver atom, which was further adapted for atomistic MD simulations of silver nanoparticles (AgNPs) composed of 1397 atoms. In our model, induced charge polarization is represented by the displacement of a charge-carrying virtual site attached rigidly to an original Ag atom. To explore the role of polarization, we compared the performance of the classical nonpolarizable FF and the new polarizable model in the MD simulations of adsorption of water and ions onto quasi-spherical AgNP and the flat crystalline silver surface. The analysis of the radial distribution function of Ag-Ag atoms demonstrated that the introduction of the polarization effect had minor effects on face-centered cubic (fcc) packing of silver atoms of bare and water-solvated AgNPs. We found that the polarizable FF causes some increase in attractive interactions between the silver surface and water molecules and Na+ ions. As a crucial test of the developed polarizable model, the structure of adsorbed interfacial water molecules was analyzed. Our data suggest that the environment-induced polarization of the silver surface contributes significantly to the structure of adsorbed interfacial water layers and it also plays an important role in the adsorption of positive ions. However, it was also found out that the polarization effect has a rather short-range effect, so that a minor contribution of silver polarization was seen for adsorption of water molecules and ions from distant solvation shells.

Structure of Water Saturated CTMA-Montmorillonite Hybrid: Molecular Dynamics Simulation Investigation

2011 ◽  
Vol 233-235 ◽  
pp. 1872-1877 ◽  
Author(s):  
Run Liang Zhu ◽  
Thomas V. Shapley ◽  
Marco Molinari ◽  
Ge Fei ◽  
Stephen C. Parker
Keyword(s):  
Molecular Dynamics ◽  
Interlayer Space ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Basal Spacing ◽  
Water Molecules ◽  
Surface Oxygen ◽  
Hydrogen Atoms ◽  
Structure Of Water ◽  
Water Saturated

Molecular dynamics (MD) simulations have been used to investigate the interlayer structure of water saturated organoclays. The basal spacing values of cetyltrimethylammonium (CTMA) intercalated montmorillonite (CTMA-Mont) in dry and water saturated states were detected using XRD. Then the results were compared with simulation results of dry CTMA-Mont. The MD simulations show that the CTMA cations form layer structures on siloxane surface and aggregate in the interlayer space. Water molecules can access part of the siloxane surface and form H-bonds with surface oxygen atoms by donating one or two of the hydrogen atoms. Thus, the water molecules close to the surface have a preferred orientation with the dipole pointing towards the surface, while in the interlayer space, the water molecules aggregate to form large clusters. The H-bonds between surface oxygen and water molecules are shown to be slightly weaker than those between water molecules. Although water molecules within interlayer space can form strong H-bonds as in bulk water the number of H-bond for each water molecule is reduced. Our results indicate that MD simulations represent a useful tool for exploring the microstructure of water saturated organoclays.

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