Search results for "molecular dynamic"

A Perspective : Active Role of Lipids in Neurotransmitter Dynamics

2019

AbstractSynaptic neurotransmission is generally considered as a function of membrane-embedded receptors and ion channels in response to the neurotransmitter (NT) release and binding. This perspective aims to widen the protein-centric view by including another vital component—the synaptic membrane—in the discussion. A vast set of atomistic molecular dynamics simulations and biophysical experiments indicate that NTs are divided into membrane-binding and membrane-nonbinding categories. The binary choice takes place at the water-membrane interface and follows closely the positioning of the receptors’ binding sites in relation to the membrane. Accordingly, when a lipophilic NT is on route to a m…

Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes

2013

Gold nanoparticles (AuNps) are used in nanomedicine in, e.g., drug delivery and bio-imaging. However, it is regrettable that the understanding of nanoparticle properties in cellular surroundings is incompletely understood. Here, we have complemented our previous studies [1] by performing extensive atomistic molecular dynamics simulations of lipid membranes interacting with charged gold nanoparticles. We have elucidated the action of these nanoparticles on membranes characterized by lipid compositional asymmetry in the two leaflets, thereby unraveling the interactions of AuNPs with both the extracellular and the cytosolic sides of plasma membranes of eukaryotic cells. We have found that ther…

A Microscopic Description of SARS-CoV-2 Main Protease Inhibition with Michael Acceptors. Strategies for Improving Inhibitors Design

2020

The irreversible inhibition of the main protease of SARS-CoV-2 by a Michael acceptor known as N3 has been investigated using multiscale methods. The noncovalent enzyme–inhibitor complex was simulated using classical molecular dynamics techniques and the pose of the inhibitor in the active site was compared to that of the natural substrate, a peptide containing the Gln–Ser scissile bond. The formation of the covalent enzyme–inhibitor complex was then simulated using hybrid QM/MM free energy methods. After binding, the reaction mechanism was found to be composed of two steps: (i) the activation of the catalytic dyad (Cys145 and His41) to form an ion pair and (ii) a Michael addition where the …

Influence of the exchange and correlation functional on the structure of amorphous InSb and In3SbTe2 compounds

2016

We have investigated the structural, vibrational, and electronic properties of the amorphous phase of InSb and In3SbTe2 compounds of interest for applications in phase change non-volatile memories. Models of the amorphous phase have been generated by quenching from the melt by molecular dynamics simulations based on density functional theory. In particular, we have studied the dependence of the structural properties on the choice of the exchange-correlation functional. It turns out that the use of the Becke-Lee-Yang-Parr functional provides models with a much larger fraction of In atoms in a tetrahedral bonding geometry with respect to previous results obtained with the most commonly used P…

Surface charges at the CaF2/water interface allow very fast intermolecular vibrational-energy transfer

2020

Abstract We investigate the dynamics of water in contact with solid calcium fluoride, where at low pH, localized charges can develop upon fluorite dissolution. We use 2D surface‐specific vibrational spectroscopy to quantify the heterogeneity of the interfacial water (D2O) molecules and provide information about the sub‐picosecond vibrational‐energy‐relaxation dynamics at the buried solid/liquid interface. We find that strongly H‐bonded OD groups, with a vibrational frequency below 2500 cm−1, display very rapid spectral diffusion and vibrational relaxation; for weakly H‐bonded OD groups, above 2500 cm−1, the dynamics slows down substantially. Atomistic simulations based on electronic‐structu…

Exploration of the Activation Mechanism of the Epigenetic Regulator MLL3: A QM/MM Study

2021

The mixed lineage leukemia 3 or MLL3 is the enzyme in charge of the writing of an epigenetic mark through the methylation of lysine 4 from the N-terminal domain of histone 3 and its deregulation has been related to several cancer lines. An interesting feature of this enzyme comes from its regulation mechanism, which involves its binding to an activating dimer before it can be catalytically functional. Once the trimer is formed, the reaction mechanism proceeds through the deprotonation of the lysine followed by the methyl-transfer reaction. Here we present a detailed exploration of the activation mechanism through a QM/MM approach focusing on both steps of the reaction, aiming to provide new…

In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification

2022

International audience; Although botulinum neurotoxins (BoNTs) are among the most toxic compounds found in nature, their molecular mechanism of action is far from being elucidated. A key event is the conformational transition due to acidification of the interior of synaptic vesicles, leading to translocation of the BoNT catalytic domain into the neuronal cytosol. To investigate these conformational variations, homology modeling and atomistic simulations are combined to explore the internal dynamics of the sub-types BoNT/A1 (the most-used sub-type in medical applications) and BoNT/E1 (the most kinetically efficient sub-type). This first simulation study of di-chain BoNTs in closed and open s…

Reply to Comment on “Mixed Grotthuss and Vehicle Transport Mechanism in Proton Conducting Polymers from Ab initio Molecular Dynamics Simulations”

2011

Magic triangular and tetrahedral clusters

1997

Using the methods of density functional theory and the jellium model we show that clusters with triangular [in two dimensions (2D)] or tetrahedral [in three dimensions (3D)] shapes have a strong shell structure and enhanced stability. Moreover, the shell closings correspond to the lowest magic numbers of a 2D and 3D harmonic oscillator and at the same time to the number of divalent atoms in close-packed triangles and tetrahedrons. Ab initio molecular dynamics simulations for Na and Mg clusters support the results of the jellium model.

Revisiting the Nonadiabatic Process in 1,2-Dioxetane.

2015

Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.; Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111, 8013-8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O-O' and C-C' bond dissociations. New high-level multistate multi configurati…