Search results for "molecular dynamics simulation"
showing 10 items of 260 documents
N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol
2011
We have prepared palmitoyl sphingomyelin (PSM) analogs in which either the 2-NH was methylated to NMe, the 3-OH was methylated to OMe, or both were methylated simultaneously. The aim of the study was to determine how such modifications in the membrane interfacial region of the molecules affected interlipid interactions in bilayer membranes. Measuring DPH anisotropy in vesicle membranes prepared from the SM analogs, we observed that methylation decreased gel-phase stability and increased fluid phase disorder, when compared to PSM. Methylation of the 2-NH had the largest effect on gel-phase instability (T(m), was lowered by similar to 7 degrees C). Atomistic molecular dynamics simulations sho…
Scalable Constant pH Molecular Dynamics in GROMACS
2022
Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to…
Inhibition of the Cysteine Protease Human Cathepsin L by Triazine Nitriles: Amide⋅⋅⋅Heteroarene π-Stacking Interactions and Chalcogen Bonding in the …
2016
We report an extensive "heteroarene scan" of triazine nitrile ligands of the cysteine protease human cathepsin L (hCatL) to investigate π-stacking on the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket. This heteroarene⋅⋅⋅peptide bond stacking was supported by a co-crystal structure of an imidazopyridine ligand with hCatL. Inhibitory constants (Ki ) are strongly influenced by the diverse nature of the heterocycles and specific interactions with the local environment of the S3 pocket. Binding affinities vary by three orders of magnitude. All heteroaromatic ligands feature enhanced binding by comparison with hydrocarbon analogues. Predicted energetic contributions from the ori…
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges
2020
Flexible spikes The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein enables viral entry into host cells by binding to the angiotensin-converting enzyme 2 (ACE2) receptor and is a major target for neutralizing antibodies. About 20 to 40 spikes decorate the surface of virions. Turoňová et al. now show that the spike is flexibly connected to the viral surface by three hinges that are well protected by glycosylation sites. The flexibility imparted by these hinges may explain how multiple spikes act in concert to engage onto the flat surface of a host cell. Science, this issue p. 203
Molecular modeling approaches in the discovery of new drugs for anti-cancer therapy: the investigation of p53-MDM2 interaction and its inhibition by …
2010
The mdm2 oncogene product, MDM2, is an ubiquitin protein ligase that inhibits the transcriptional activity of the tumor suppressor p53 and promotes its degradation. About 50% of all human cancers present mutations or deletions in the TP53 gene. In the remaining half of all human neoplasias that express the wild-type protein, aberrations of p53 regula- tors, such as MDM2, account for p53 inhibition. For this reason, designing small-molecule inhibitors of the p53-MDM2 protein-protein interaction is a promising strategy for the treatment of cancers retaining wild-type p53. The development of inhibitors has been challenging. Although many small-molecule MDM2 inhibitors have shown potent in vitr…
Vibrational Sum Frequency Generation Spectroscopy of the Water Liquid–Vapor Interface from Density Functional Theory-Based Molecular Dynamics Simulat…
2013
International audience; The vibrational sum frequency generation (VSFG) spectrum of the water liquid-vapor (LV) interface is calculated using density functional theory-based molecular dynamics simulations. The real and imaginary parts of the spectrum are in good agreement with the experimental data, and we provide an assignment of the SFG bands according to the dipole orientation of the interfacial water molecules. We use an instantaneous definition of the surface, which is more adapted to the study of interfacial phenomena than the Gibbs dividing surface. By calculating the vibrational (infrared, Raman) properties for interfaces of varying thickness, we show that the bulk spectra signature…
MMGBSA As a Tool To Understand the Binding Affinities of Filamin–Peptide Interactions
2013
Filamins (FLN) are large dimeric proteins that cross-link actin and work as important scaffolds in human cells. FLNs consist of an N-terminal actin-binding domain followed by 24 immunoglobulin-like domains (FLN1-24). FLN domains are divided into four subgroups based on their amino acid sequences. One of these subgroups, including domains 4, 9, 12, 17, 19, 21, and 23, shares a similar ligand-binding site between the β strands C and D. Several proteins, such as integrins β2 and β7, glycoprotein Ibα (GPIbα), and migfilin, have been shown to bind to this site. Here, we computationally estimated the binding free energies of filamin A (FLNa) subunits with bound peptides using the molecular mechan…
Tracking Ca
2019
We characterize thus-far elusive domain rearrangements of a calcium-transporting ATPase in the native membrane.
Mesoscopic organization in ionic liquids.
2017
We discuss some published results and provide new observations concerning the high level of structural complexity that lies behind the nanoscale correlations in ionic liquids (ILs) and their mixtures with molecular liquids. It turns out that this organization is a consequence of the hierarchical construction on both spatial (from ångström to several nanometer) and temporal (from fraction of picosecond to hundreds of nanosecond) scales, which requires joint use of experimental and computational tools. © 2017, Springer International Publishing Switzerland.
A molecular dynamics study of structure, stability and fragmentation patterns of sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates…
2011
Positively charged supramolecular aggregates formed in vacuo by n AOTNa (sodium bis(2-ethylhexyl)sulfosuccinate) molecules and n(c) additional sodium ions, i.e. [AOT(n)Na(n+n(c))](n(c)), have been investigated by molecular dynamics (MD) simulations for n = 1-20 and n(c) = 0-5. Statistical analysis of physical quantities like gyration radii, atomic B-factors and moment of inertia tensors provides detailed information on their structural and dynamical properties. Even for n(c) = 5, all stable aggregates show a reverse micelle-like structure with an internal solid-like core including sodium counterions and surfactant polar heads surrounded by an external layer consisting of the surfactant alky…