Search results for "molecular dynamics"

The relaxation dynamics of a simple glass former confined in a pore

2000

We use molecular dynamics computer simulations to investigate the relaxation dynamics of a binary Lennard-Jones liquid confined in a narrow pore. We find that the average dynamics is strongly influenced by the confinement in that time correlation functions are much more stretched than in the bulk. By investigating the dynamics of the particles as a function of their distance from the wall, we can show that this stretching is due to a strong dependence of the relaxation time on this distance, i.e. that the dynamics is spatially very heterogeneous. In particular we find that the typical relaxation time of the particles close to the wall is orders of magnitude larger than the one of particles …

Selective Inhibition of STAT3 with Respect to STAT1: Insights from Molecular Dynamics and Ensemble Docking Simulations

2016

STAT3 protein, which is known to be involved in cancer development, is a promising target for anticancer therapy. Successful inhibitors of STAT3 should not affect an activity of closely related protein STAT1, which makes their development challenging. The mechanisms of selectivity of several existing STAT3 inhibitors are not clear. In this work, we studied molecular mechanisms of selectivity of 13 experimentally tested STAT3 inhibitors by means of extensive molecular dynamics and ensemble docking simulations. It is shown that all studied inhibitors bind to the large part of the protein surface in an unspecific statistical manner. The binding to the dimerization interface of the SH2 domain, …

MOLECULAR DYNAMICS - MULTIPLE RECEPTOR CONFORMATIONS APPROACH TO ENHANCE STRUCTURE-BASED VIRTUAL SCREENING ON PPAR-alpha RECEPTOR

2016

Poly-sarcosine and poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulations

2018

Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and their knowledge may help improving nanoparticle design. Here we address, using molecular dynamics simulations, the interactions of human serum albumin, the most abundant serum protein, with two promising hydrophilic polymers used for the coating of therapeutic nanoparticles, poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in a polymer-water mixture, we show that the two polymers have a very similar affinity for the…

Transport of Mobile Particles in an Immobile Environment: Computer Simulations of Sodium Silicates

2007

Molecular dynamics (MD) simulations of various sodium silicate melts, (Na2O)x(SiO2) with x=2, 3, 20, are presented. In these systems, the mobility of sodium ions is much higher, often by orders of magnitude, than that of the silicon and oxygen atoms forming a tetrahedral network structure. We show that the high mobility of sodium is intimately related to the chemical ordering in sodium silicates. A network of percolating sodium-rich channels is formed in the static structure that serve as diffusion channels for the sodium ions. This channel network is revealed in static structure factors by a prepeak at the wavenumber q=0.95 A-1. Inelastic neutron scattering experiments of sodium silicate m…

Heptane adsorption in silicalite-1 : molecular dynamics simulation.

2009

Molecular dynamics (MD) simulations have been used to study the adsorption process of n-heptane molecules in silicalite-1 at 300 K. MD simulated results were compared to experimental neutron diffraction (ND) and experimental self-diffusion coefficients. The analysis of MD data indicated a packing of the adsorbed molecules around 4 mol./u.c., which is not the consequence of an enthalpic effect but of an entropic effect. The role of the n-heptane chain flexibility (cis–trans conformation) in relation with the silicalite-1 channel type (straight versus sinusoidal) was outlined and enabled to understand the mobility change arising at 4 mol./u.c., according to previous experimental results. The …

DNA-Binding and Anticancer Activity of Pyrene-Imidazolium Derivatives

2016

DNA-binding investigations showed that two different derivatives endowed with pyrene and imidazolium moieties, 1 and 2, strongly bind both double-stranded DNA and telomeric sequences in G-quadruplex (G4) conformation. The values of the DNA-binding constants indicate that 1 and 2 show preferential affinity for G4-DNA, of about one and two orders of magnitude, respectively. Moreover, 1 and 2 inhibit short and long-term proliferation of breast cancer cell lines in a time- and dose-dependent fashion. Remarkably, senescence assays indicate that telomeric G4-DNA is a possible biotarget for the cytotoxic activity of 2. Molecular dynamics simulations suggest that the stronger binding of 2 with G4-D…

GENETIC NEUROCHAPERONOPATHIES ASSOCIATED WITH CCT5 AND HSP60 VARIANTS: ANALYSIS OF THEIR MOLECULAR ANATOMY AND POSSIBLE PATHOGENIC IMPLICATIONS

2022

Investigating the inhibition of FTSJ1 a tryptophan tRNA-specific 2’-O-methyltransferase by NV TRIDs, as a mechanism of readthrough in nonsense mutate…

2023

Abstract: Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10% of the CFTR gene mutations are "stop" mutations, which generate a Premature Termination Codon (PTC), thus synthesizing a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, which is the ri-bosome’s capacity to skip a PTC, thus generating a full-length protein. “TRIDs” are molecules exerting ribosome readthrough; for some, the mechanism of action is still under debate. We in-vestigate a possible mechanism of action (MOA) by which our recently synthesized TRIDs, namely NV848, NV914, and NV930, could exert their r…

Dissolution of nitrones in alkylphosphates: A structural study

2022

Nitrones are chemical compounds with well-established anti-oxidant and spin-trapping properties. Their low solubility in water for many of them limits their applications, so opportune solvents must be found. In this study, two recently synthetized oxindole nitrones with proven antiproliferative and antioxidant activity have been dissolved in several liquid amphiphiles, chosen as model solvents. The effect of the polar head nature and the alkyl chain length/type have been investigated by a combined experimental (solubility, UV–vis spectroscopy) / computational (molecular dynamics) approach. The different chemical structures of the various solvents offer different chemical environments to the…