scholarly journals Molecular Dynamics Simulations of Mite Aquaporin DerfAQP1 from the Dust Mite Dermatophagoides farinae (Acariformes: Pyroglyphidae)

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Li-lei Wang ◽  
Li-li Yu ◽  
Ying Zhou ◽  
Mei-li Wu ◽  
Fei-xiang Teng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Tertiary Structure ◽  
Large Family ◽  
Data Bank ◽  
Mite Species ◽  
Dynamics Simulation ◽  
Protein Data Bank Code ◽  
Dermatophagoides Farinae ◽  
Dust Mite ◽  
Dynamics Simulations

Aquaporins are a large family of transmembrane channel proteins that facilitate the passive but highly selective transport of water and other small solutes across biological membranes. House dust mite (Dermatophagoides farinae) is the major source of household immunogens, and we have recently reported six cDNA sequence encoding aquaporins from this mite species. To better understand the structure and role of mite aquaporin, we constructed a tertiary structure for DerfAQP1 by homology modeling from the X-ray structure of malaria aquaporin PfAQP (Protein Data Bank code No. 3C02) and conducted molecular dynamics simulation. The simulation arranged seven water molecules in a single file through the pores of the DerfAQP1. Further, two conserved Asn-Pro-Ala motifs were located on Asn203 and Asn77; residues Arg206, Trp57, Met190, Gly200, and Asp207 constituted an extracellular vestibule of the pore; and residues His75, Val80, Ile65, and Ile182 constituted the cytoplasmic portions. The overall free energy profile for water transport through DerfAQP1 revealed an energy barrier of ~2.5 kcal/mol. These results contribute to the understanding of mite physiology and pathology.

scholarly journals Molecular Dynamics Simulations for Biological Systems

2017 ◽  
pp. 1044-1071 ◽  
Author(s):  
Prerna Priya ◽  
Minu Kesheri ◽  
Rajeshwar P. Sinha ◽  
Swarna Kanchan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

Molecular Dynamics Simulations for Biological Systems

2016 ◽  
pp. 286-313 ◽  
Author(s):  
Prerna Priya ◽  
Minu Kesheri ◽  
Rajeshwar P. Sinha ◽  
Swarna Kanchan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

scholarly journals Homology Modeling and Molecular Dynamics Simulation Studies of a Marine Alkaline Protease

2012 ◽  
Vol 6 ◽  
pp. BBI.S10663 ◽  
Author(s):  
Xiaofeng Ji ◽  
Wei Wang ◽  
Yuan Zheng ◽  
Jianhua Hao ◽  
Mi Sun
Keyword(s):  
Molecular Dynamics ◽  
Alkaline Protease ◽  
Tertiary Structure ◽  
Dynamical Behavior ◽  
Homology Model ◽  
Dynamics Simulation ◽  
Water Solvent ◽  
Explicit Solvent ◽  
Bacterium Strain ◽  
Dynamics Simulations

A cold-adapted marine alkaline protease (MP, accession no. ACY25898) was produced by a marine bacterium strain, which was isolated from Yellow Sea sediment in China. Many previous researches showed that this protease had potential application as a detergent additive. It was therefore crucial to determine the tertiary structure of MP. In this study, a homology model of MP was constructed using the multiple templates alignment method. The tools PROCHECK, ERRAT, and Verify_3D were used to check the effectiveness of the model. The result showed that 94% of residues were found in the most favored allowed regions, 6% were in the additional allowed region, and 96.50% of the residues had average 3D-1D scores of no less than 0.2. Meanwhile, the overall quality factor (ERRAT) of our model was 80.657. In this study, we also focused on elucidating the molecular mechanism of the two “flap” motions. Based on the optimized model, molecular-dynamics simulations in explicit solvent environments were carried out by using the AMBER11 package, for the entire protein, in order to characterize the dynamical behavior of the two flaps. Our results showed an open motion of the two flaps in the water solvent. This research may facilitate inhibitor virtual screening for MP and may also lay the foundationknowledge of mechanism of the inhibitors.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

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.

scholarly journals Folding and Intrinsic Disorder of the Receptor Tyrosine Kinase KIT Insert Domain Seen by Conventional Molecular Dynamics Simulations

2021 ◽  
Vol 22 (14) ◽  
pp. 7375
Author(s):  
Julie Ledoux ◽  
Alain Trouvé ◽  
Luba Tchertanov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Tertiary Structure ◽  
Average Distance ◽  
Intrinsic Disorder ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Hydrophobic Core ◽  
Direct Evaluation ◽  
Dynamics Simulations

The kinase insert domain (KID) of RTK KIT is the key recruitment region for downstream signalling proteins. KID, studied by molecular dynamics simulations as a cleaved polypeptide and as a native domain fused to KIT, showed intrinsic disorder represented by a set of heterogeneous conformations. The accurate atomistic models showed that the helical fold of KID is mainly sequence dependent. However, the reduced fold of the native KID suggests that its folding is allosterically controlled by the kinase domain. The tertiary structure of KID represents a compact array of highly variable α- and 310-helices linked by flexible loops playing a principal role in the conformational diversity. The helically folded KID retains a collapsed globule-like shape due to non-covalent interactions associated in a ternary hydrophobic core. The free energy landscapes constructed from first principles—the size, the measure of the average distance between the conformations, the amount of helices and the solvent-accessible surface area—describe the KID disorder through a collection of minima (wells), providing a direct evaluation of conformational ensembles. We found that the cleaved KID simulated with restricted N- and C-ends better reproduces the native KID than the isolated polypeptide. We suggest that a cyclic, generic KID would be best suited for future studies of KID f post-transduction effects.

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.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

Molecular Dynamics Simulation of Sputtering with Mmany-Body Interactions

1988 ◽  
Vol 100 ◽  
Author(s):  
Davy Y. Lo ◽  
Tom A. Tombrello ◽  
Mark H. Shapiro ◽  
Don E. Harrison
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Single Crystal ◽  
Low Energy ◽  
Dynamics Simulation ◽  
Embedded Atom Method ◽  
Many Body ◽  
Embedded Atom ◽  
Dynamics Simulations ◽  
Small Single Crystal

ABSTRACTMany-body forces obtained by the Embedded-Atom Method (EAM) [41 are incorporated into the description of low energy collisions and surface ejection processes in molecular dynamics simulations of sputtering from metal targets. Bombardments of small, single crystal Cu targets (400–500 atoms) in three different orientations ({100}, {110}, {111}) by 5 keV Ar+ ions have been simulated. The results are compared to simulations using purely pair-wise additive interactions. Significant differences in the spectra of ejected atoms are found.

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