Search results for "molecular dynamics"
showing 10 items of 1075 documents
Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations
2011
Ionotropic glutamate receptors (iGluRs) are synaptic proteins that facilitate signal transmission in the central nervous system. Extracellular iGluR cleft closure is linked to receptor activation; however, the mechanism underlying partial agonism is not entirely understood. Full agonists close the bilobed ligand-binding domain (LBD), while antagonists prevent closure; the transmembrane ion channel either opens or stays closed, respectively. Although some bulky partial agonists produce intermediate iGluR-LBD closure, the available crystal structures also imply that the cleft can be shut with certain partial agonists. Recently, we have shown that the iGluR-LBD closure stage can be recreated b…
Zinc Binding Sites Conserved in Short Neuropeptides Containing a Diphenylalanine Motif
2019
A diphenylalanine motif in peptides plays a crucial role in supramolecular systems. The current work represents a novel strategy in which a diphenylalanine motif in the central domain of neuropeptides conserves the specific Zn2+ binding site and prevents "hopping" of the Zn2+ ion between alternative metal binding sites. Alternative metal binding sites may also include carboxylic atoms in the terminal domains of a peptide. Therefore, one needs to design a peptide in which the metal will not bind the carboxylic groups in the terminal domains. Herein, we propose that engineering and designing peptides with a diphenylalanine motif in the central domain may yield excellent metal chelators.
Molecular Dynamics simulation of evaporation processes of fluid bridges confined in slit-like pore
2009
A simple fluid, described by point-like particles interacting via the Lennard-Jones potential, is considered under confinement in a slit geometry between two walls at distance Lz apart for densities inside the vapor-liquid coexistence curve. Equilibrium then requires the coexistence of a liquid "bridge" between the two walls, and vapor in the remaining pore volume. We study this equilibrium for several choices of the wall-fluid interaction (corresponding to the full range from complete wetting to complete drying, for a macroscopically thick film), and consider also the kinetics of state changes in such a system. In particular, we study how this equilibrium is established by diffusion proces…
Molecular Dynamics Simulations of the Initial Adsorption Stages of Fibrinogen on Mica and Graphite Surfaces.
2015
Fibrinogen, a blood glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin when activated. Upon adsorption on material surfaces, it also contributes to determine their biocompatibility and has been implicated in the onset of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counterion …
The Internal Dynamics and Early Adsorption Stages of Fibrinogen Investigated by Molecular Dynamics Simulations
2016
Fibrinogen, a plasma glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin upon activation. It also contributes, upon adsorption on material surfaces, to determine their biocompatibility and has been implicated as a cause of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counter io…
Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.
2014
Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it underg…
Resolving Binding Events on the Multifunctional Human Serum Albumin
2020
Abstract Physiological processes rely on initial recognition events between cellular components and other molecules or modalities. Biomolecules can have multiple sites or mode of interaction with other molecular entities, so that a resolution of the individual binding events in terms of spatial localization as well as association and dissociation kinetics is required for a meaningful description. Here we describe a trichromatic fluorescent binding‐ and displacement assay for simultaneous monitoring of three individual binding sites in the important transporter and binding protein human serum albumin. Independent investigations of binding events by X‐ray crystallography and time‐resolved dyn…
Encapsulation capacity and natural payload delivery of an anticancer drug from boron nitride nanotube.
2016
The behavior of confined anticancer carboplatin (CPT) molecules in a single (10, 10) boron nitride nanotube (BNNT) was studied by means of molecular dynamics simulations. Our study revealed a very large storage capacity of BNNT. Analysis of the energy profiles depending on the number of confined molecules, and on their spatial organization allowed us to quantify the ability of BNNT to vectorize CPT. Indeed, BNNT despite its small radius presented a large inner volume that favored stable encapsulation of multiple active anticancer molecules. Moreover, in our molecular dynamics simulations, the empty BNNT and the BNNT filled with CPT diffused spontaneously to the cell membrane and were able t…
The Catalytic Mechanism of Steroidogenic Cytochromes P450 from All-Atom Simulations: Entwinement with Membrane Environment, Redox Partners, and Post-…
2019
Cytochromes P450 (CYP450s) promote the biosynthesis of steroid hormones with major impact on the onset of diseases such as breast and prostate cancers. By merging distinct functions into the same catalytic scaffold, steroidogenic CYP450s enhance complex chemical transformations with extreme efficiency and selectivity. Mammalian CYP450s and their redox partners are membrane-anchored proteins, dynamically associating to form functional machineries. Mounting evidence signifies that environmental factors are strictly intertwined with CYP450s catalysis. Atomic-level simulations have the potential to provide insights into the catalytic mechanism of steroidogenic CYP450s and on its regulation by e…
Emerging dynamics in surfactant-based liquid mixtures: octanoic acid/bis(2-ethylhexyl) amine systems.
2012
This work focuses on the dynamic phenomena emerging in self-assembled transient intermolecular networks formed when two different surfactants are mixed. In particular, the relaxation processes in liquid mixtures composed by bis(2-ethylhexyl)amine (BEEA) and octanoic acid (OA) in the whole composition range has been investigated by dielectric spectroscopy and Brillouin spectroscopy. A thorough analysis of all the experimental data consistently suggests that, mainly driven by acid-base interactions arising when the two surfactants are mixed, supra-molecular aggregates formation causes the slowing down of molecular dynamics. This, in turn, reflects to longer-range relaxations. These changes ha…