Evaluation of synaptotagmin‐1 action models by all‐atom molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2025 at "FEBS Open Bio"
DOI: 10.1002/2211-5463.13966
Abstract: Neurotransmitter release is triggered in microseconds by the two C2 domains of the Ca2+ sensor synaptotagmin‐1 and by SNARE complexes, which form four‐helix bundles that bridge the vesicle and plasma membranes. The synaptotagmin‐1 C2B domain… read more here.
Keywords: fusion; dynamics simulations; molecular dynamics; synaptotagmin ... See more keywords
Accounting for the Quantum Capacitance of Graphite in Constant Potential Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2024 at "Advanced Materials"
DOI: 10.1002/adma.202405230
Abstract: Molecular dynamics (MD) simulations at a constant electric potential are an essential tool to study electrochemical processes, providing microscopic information on the structural, thermodynamic, and dynamical properties. Despite the numerous advances in the simulation of… read more here.
Keywords: dynamics simulations; capacitance graphite; quantum capacitance; molecular dynamics ... See more keywords
Extensive Molecular Dynamics Simulations Disclosed the Stability of mPGES‐1 Enzyme and the Structural Role of Glutathione (GSH) Cofactor
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Informatics"
DOI: 10.1002/minf.202200140
Abstract: A deep in silico investigation of various microsomal prostaglandin E2 synthase‐1 (mPGES‐1) protein systems is here reported using molecular dynamics (MD) simulations. Firstly, eight different proteins models (Models A−H) were built, starting from the active… read more here.
Keywords: dynamics simulations; gsh; role; molecular dynamics ... See more keywords
Conformer Selection Upon Dilution with Water: The Fascinating Case of Liquid Ethylene Glycol Studied via Molecular Dynamics Simulations
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DOI: 10.1002/open.202200132
Abstract: Abstract The aqueous solution of ethylene glycol (EG) is a binary liquid mixture that displays rich conformational and structural behaviour, which has not yet been adequately explored through atomistic molecular dynamics simulations. Herein, employing an… read more here.
Keywords: dynamics simulations; ethylene glycol; molecular dynamics; solution ... See more keywords
Molecular dynamics simulations of early steps in RNA‐mediated conversion of prions
Sign Up to like & getrecommendations! Published in 2017 at "Protein Science"
DOI: 10.1002/pro.3178
Abstract: The rate‐limiting step in prion diseases is the initial transition of a prion protein from its native form into a mis‐folded state in which the protein not only forms cell‐toxic aggregates but also becomes infectious.… read more here.
Keywords: rna mediated; molecular dynamics; simulations early; polyadenosine rna ... See more keywords
Exploring Graphitic Carbon Nitride as Novel Drug Delivery System for Hesperetin (Anticancer Drug): Insights From DFT Calculations and Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2025 at "International Journal of Quantum Chemistry"
DOI: 10.1002/qua.70018
Abstract: In the present work, density functional theory (DFT) and molecular dynamics (MD) simulations were employed to explore the interaction between Hesperetin (HST), an anticancer drug, and 2D graphitic carbon nitride (GRP) nanocarrier designed for targeted… read more here.
Keywords: drug delivery; dynamics simulations; drug; molecular dynamics ... See more keywords
Large-Scale Molecular Dynamics Simulations of Cellular Compartments.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1394-8_18
Abstract: Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data… read more here.
Keywords: large scale; simulations cellular; molecular dynamics; cellular compartments ... See more keywords
Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7465-8_17
Abstract: An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important-albeit static-pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD)… read more here.
Keywords: protein coupled; ligand binding; dynamics simulations; molecular dynamics ... See more keywords
A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-8582-1_15
Abstract: The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in… read more here.
Keywords: guide molecular; molecular dynamics; origami systems; dna origami ... See more keywords
Molecular Dynamics Simulations with NAMD2.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9752-7_8
Abstract: X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have… read more here.
Keywords: dynamics simulations; biology; simulations namd2; molecular dynamics ... See more keywords
A theoretical study of monomeric polyglutamine chains from molecular dynamics simulations with explicit water
Sign Up to like & getrecommendations! Published in 2017 at "Theoretical Chemistry Accounts"
DOI: 10.1007/s00214-017-2172-1
Abstract: Polyglutamine peptides with an abnormal repeat length are the causative agent of at least nine genetic diseases, known as polyglutamine diseases, which include Huntigton’s disease (HD) and some ataxias, in between the others. In the… read more here.
Keywords: simulations explicit; molecular dynamics; study; polyglutamine ... See more keywords