Search results for " molecular dynamics simulations"

showing 4 items of 14 documents

Structure, stability, and fragmentation of sodium bis(2-ethylhexyl)sulfosuccinate negatively charged aggregates in vacuo by MD simulations.

2014

Negatively charged supramolecular aggregates formed in vacuo by n bis(2-ethylhexyl)sulfosuccinate (AOT(-)) anions and n + n(c) sodium counterions (i.e., [AOT(n) Na(n+nc)](nc)) have been investigated by molecular dynamics (MD) simulations for n = 1 to 20 and n(c) = -1 to -5. By comparing the maximum excess charge values of negatively and positively charged AOTNa aggregates, it is found that the charge storage capability is higher for the latter systems, the difference decreasing as the aggregation number increases. Statistical analysis of physical properties like gyration radii and moment of inertia tensors of aggregates provides detailed information on their structural properties. Even for …

SodiumSupramolecular chemistryMolecular Conformationchemistry.chemical_elementFragmentation patternsMolecular Dynamics SimulationAOTNa Self-assembling Charged reverse micelles Molecular dynamics simulation (MD) Supramolecular aggregates in vacuo Fragmentation patternsMicelleMolecular dynamicsSurface-Active AgentsPulmonary surfactantStructural BiologyAotNa; self-assembling; charged revrse micelle; Molecular Dynamics simulations; Supramolecular aggregates in vacuo; Fragmentation patternsSpectroscopyAlkylMicellesSettore CHIM/02 - Chimica Fisicachemistry.chemical_classificationIonsDioctyl Sulfosuccinic AcidAggregation numberAotNacharged revrse micelleself-assemblingSupramolecular aggregates in vacuoCrystallographychemistryThermodynamicsMolecular Dynamics simulationsCounterionJournal of the American Society for Mass Spectrometry
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HSV-1 Glycoprotein D and Its Surface Receptors: Evaluation of Protein–Protein Interaction and Targeting by Triazole-Based Compounds through In Silico…

2023

Protein–protein interactions (PPI) represent attractive targets for drug design. Thus, aiming at a deeper insight into the HSV-1 envelope glycoprotein D (gD), protein–protein docking and dynamic simulations of gD-HVEM and gD-Nectin-1 complexes were performed. The most stable complexes and the pivotal key residues useful for gD to anchor human receptors were identified and used as starting points for a structure-based virtual screening on a library of both synthetic and designed 1,2,3-triazole-based compounds. Their binding properties versus gD interface with HVEM and Nectin-1 along with their structure-activity relationships (SARs) were evaluated. Four [1,2,3]triazolo[4,5-b]pyridines were i…

glycoprotein DOrganic Chemistrymolecular dynamics simulationsGeneral MedicineHSV-1Settore CHIM/08 - Chimica FarmaceuticaCatalysisComputer Science ApplicationsInorganic Chemistryprotein–protein interactionprotein–protein interaction; HSV-1; 123-triazoles; docking; molecular dynamics simulations; glycoprotein Ddocking123-triazolesPhysical and Theoretical ChemistryMolecular BiologySpectroscopyInternational Journal of Molecular Sciences
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Molecular dynamics simulations of a new model of human a7 nicotinic receptor

2014

human receptors epibatidine molecular dynamics simulations
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Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State

2012

ABSTRACT: The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to non-equilibrium molecular dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment …

myoglobin molecular dynamics simulations non equilibriumThermal fluctuationsMolecular Dynamics SimulationNitric OxideArticleAbsorptionchemistry.chemical_compoundMolecular dynamicsComputational chemistryMaterials ChemistryPhysical and Theoretical ChemistryHemePhotonsSteady stateChemistryMyoglobinPhotodissociationTemperatureSettore FIS/07 - Fisica Applicata(Beni Culturali Ambientali Biol.e Medicin)Recombinant ProteinsSurfaces Coatings and FilmsProtein Structure TertiaryMyoglobinChemical physicsMutationRelaxation (physics)Stationary stateProtein Binding
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