scholarly journals Trehalose Stabilizing Protein in a Water Replacement Scenario: Insights from Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Qiang Shao ◽  
Jinan Wang ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Pure Water ◽  
Dynamics Simulation ◽  
Mixed Solution ◽  
Water Replacement ◽  
Model Protein ◽  
Active Research ◽  
Dynamics Simulations ◽  
Water Hydrogen

AbstractHow trehalose has exceptional property in helping biomolecules preserve their native structures remains a subject of active research. Running molecular dynamics simulations on a model protein in low-concentrated trehalose solution and pure water, respectively, the present study verifies the ability of trehalose in stabilizing protein native structure and provides a comprehensive atomic-level picture of the molecular interactions among protein, trehalose, and water in their mixed solution. Trehalose directly interacts to and meanwhile affects the interactions between the other species via hydrogen bonding: 1) trehalose molecules are clustered through inter-molecular hydrogen bonding interaction; 2) trehalose forms hydrogen bond with water which influences the strength of water-water hydrogen bonding network but does not impair protein-water hydrogen bonding; 3) trehalose is accessible to form hydrogen bonds towards protein and simultaneously replace water molecules around protein which reduces the hydrogen bonding possibility from water to protein, in accordance with “water replacement” scenario.

Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study

2014 ◽  
Vol 16 (33) ◽  
pp. 17458-17465 ◽  
Author(s):  
Rajdeep Singh Payal ◽  
Sundaram Balasubramanian
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Simulation Study ◽  
Molecular Hydrogen ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Dissolution of cellulose in ionic liquids involves breaking of its inter- and intra-molecular hydrogen bonding network, as seen through ab initio molecular dynamics simulations.

scholarly journals Collaborative Behavior of Urea and KI in Denaturing Protein Native Structure

2019 ◽  
Author(s):  
Qiang Shao ◽  
Jinan Wang ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Structural Dynamics ◽  
Electrostatic Interactions ◽  
Side Chain ◽  
Mixed Solution ◽  
Native Structure ◽  
Indirect Influence ◽  
Collaborative Behavior ◽  
Dynamics Simulations

AbstractIn this work, the combined influence of urea and KI on protein native structure is quantitatively investigated through the comparative molecular dynamics simulations on the structural dynamics of a polypeptide of TRPZIP4 in a series of urea/KI mixed solutions (urea concentration: 4M, KI salt concentration: 0M-6M). The observed enhanced denaturing ability of urea/KI mixture can be explained by direct interactions of urea/K+/water towards protein (electrostatic and vdW interactions from urea and electrostatic interactions from K+ and water) and indirect influence of KI on the strengthened interaction of urea towards protein backbone and side-chain. The latter indirect influence is fulfilled through the weakening of hydrogen bonding network among urea and water by the appearance of K+–water and I—urea interactions. As a result, the denaturing ability enhancement of urea and KI mixed solution is induced by the collaborative behavior of urea and KI salt.

scholarly journals Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

2021 ◽  
Vol 140 (2) ◽  
Author(s):  
Iogann Tolbatov ◽  
Alessandro Marrone
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Pure Water ◽  
Dynamics Simulation ◽  
Ligand Interaction ◽  
Amber Force Field ◽  
Dummy Atom ◽  
Dynamics Simulations ◽  
Potential Use

AbstractThe coordination of Pb(II) in aqueous solutions containing thiols is a pivotal topic to the understanding of the pollutant potential of this cation. Based on its hard/soft borderline nature, Pb(II) forms stable hydrated ions as well as stable complexes with the thiol groups of proteins. In this paper, the modeling of Pb(II) coordination via classical molecular dynamics simulations was investigated to assess the possible use of non-bonded potentials for the description of the metal–ligand interaction. In particular, this study aimed at testing the capability of cationic dummy atom schemes—in which part of the mass and charge of the Pb(II) is fractioned in three or four sites anchored to the metal center—in reproducing the correct coordination geometry and, also, in describing the hard/soft borderline character of this cation. Preliminary DFT calculations were used to design two topological schemes, PB3 and PB4, that were subsequently implemented in the Amber force field and employed in molecular dynamics simulation of either pure water or thiol/thiolate-containing aqueous solutions. The PB3 scheme was then tested to model the binding of Pb(II) to the lead-sensing protein pbrR. The potential use of CDA topological schemes in the modeling of Pb(II) coordination was here critically discussed.

FMM/GPU Accelerated Molecular Dynamics Simulation of Phase Transitions in Water-Nitrogen-Metal Systems

2012 ◽  
Author(s):  
Elena Moiseeva ◽  
Constantin Mikhaylenko ◽  
Victor Malyshev ◽  
Dmitry Maryin ◽  
Nail Gumerov
Keyword(s):  
Molecular Dynamics ◽  
Graphics Processing Units ◽  
High Performance ◽  
Fast Multipole Method ◽  
Pure Water ◽  
Water Dynamics ◽  
Dynamics Simulation ◽  
Problem Size ◽  
Central Processing ◽  
Dynamics Simulations

To characterize the behavior of water with dissolved gas (nitrogen) near a solid metallic substrate, which is important for realistic modeling of flows in nanochannels, the method of molecular dynamics is used. High performance computing is achieved via the Fast Multipole Method (FMM) for the force evaluation and via utilization of heterogeneous architectures which consists of central processing units (CPUs) and graphics processing units (GPUs). The FMM allows one to speed up computations of the long-range interactions (Coulomb potential) due to the linear scaling of the algorithm with the problem size. Utilization of the GPU provides significant acceleration of computations. Realization of the FMM on GPUs allows one to perform computational experiments for very large systems. The paper shows that the described technique can be used for water dynamics simulations in a region of size up to 100 nanometers, or of the order 100 millions molecules on personal supercomputers equipped with several GPUs. Results of numerical experiments on structure formation on the contact interface of a water droplet and metal surface both for pure water and for water with dissolved air are reported.

scholarly journals Molecular dynamics simulation of ice growth from supercooled pure water and from salt solution

2006 ◽  
Vol 44 ◽  
pp. 113-117 ◽  
Author(s):  
M.A. Carignano ◽  
E. Baskaran ◽  
P.B. Shepson ◽  
I. Szleifer
Keyword(s):  
Molecular Dynamics ◽  
Metastable State ◽  
Salt Solution ◽  
Pure Water ◽  
Cluster Formation ◽  
Dynamics Simulation ◽  
Final State ◽  
Ice Growth ◽  
Dynamics Simulations ◽  
Salt Systems

AbstractThe kinetics of ice growth on the prismatic and basal planes is studied by molecular dynamics simulations. The time evolution of two systems has been investigated. In one a slab of ice is initially in contact with supercooled water, while in the second the ice is in contact with a supercooled salt solution. The simulations were done at a temperature below the eutectic temperature, and complete solidification is observed. The total freezing time is longer in the systems with ions than in the systems with pure water. The final state for the salt systems always shows the formation of ion clusters. For the ionic system growing on the prismatic plane, an intermediate metastable state is observed before total solidification. The duration of this metastable state depends on the ability of the system to get all the ions participating in cluster formation. The simulations enable understanding of the mechanisms for ice formation under different solution conditions.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

Molecular Dynamics Simulation Study of Lecithin Inhibiting Hydrate-Dissociation

2017 ◽  
Vol 890 ◽  
pp. 252-259
Author(s):  
Le Wang ◽  
Guan Cheng Jiang ◽  
Xin Lin ◽  
Xian Min Zhang ◽  
Qi Hui Jiang
Keyword(s):  
Molecular Dynamics ◽  
Water Movement ◽  
Simulation Analysis ◽  
Mass Density ◽  
Dynamics Simulation ◽  
Dissociation Process ◽  
Hydrate Dissociation ◽  
Hydrocarbon Chains ◽  
Dynamics Simulations ◽  
Mass Density Profile

Molecular dynamics simulations are used to study the dissociation inhibiting mechanism of lecithin for structure I hydrates. Adsorption characteristics of lecithin and PVP (poly (N-vinylpyrrolidine)) on the hydrate surfaces were performed in the NVT ensemble at temperatures of 277K and the hydrate dissociation process were simulated in the NPT ensemble at same temperature. The results show that hydrate surfaces with lecithin is more stable than the ones with PVP for the lower potential energy. The conformation of lecithin changes constantly after the balanced state is reached while the PVP molecular dose not. Lecithin molecule has interaction with lecithin nearby and hydrocarbon-chains of lecithin molecules will form a network to prevent the diffusion of water and methane molecules, which will narrow the available space for hydrate methane and water movement. Compared with PVP-hydrate simulation, analysis results (snapshots and mass density profile) of the dissociation simulations show that lecithin-hydrate dissociates more slowly.

Sign in / Sign up

Export Citation Format

Share Document