Search results for "molecular dynamics simulation"
showing 10 items of 260 documents
Protein corona composition of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles correlates strongly with the amino acid composition …
2017
Extensive molecular dynamics simulations reveal that the interactions between proteins and poly(ethylene glycol) (PEG) can be described in terms of the surface composition of the proteins. PEG molecules accumulate around non-polar residues while avoiding the polar ones. A solvent-accessible-surface-area model of protein adsorption accurately fits a large set of data on the composition of the protein corona of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles recently obtained by label-free proteomic mass spectrometry.
Monitoring molecular dynamics of bacterial cellulose composites reinforced with graphene oxide by carboxymethyl cellulose addition
2017
[EN] Broadband Dielectric Relaxation Spectroscopy was performed to study the molecular dynamics of dried Bacterial Cellulose/Carboxymethyl Cellulose-Graphene Oxide (BC/CMC-GO) composites as a function of the concentration of CMC in the culture media. At low temperature the dielectric spectra are dominated by a dipolar process labelled as a beta -relaxation, whereas electrode polarization and the contribution of dc-conductivity dominate the spectra at high temperatures and low frequency. The CMC concentration affects the morphological structure of cellulose and subsequently alters its physical properties. X-ray diffractometry measurements show that increasing the concentration of CMC promote…
A first peek into sub-picosecond dynamics of spin energy levels in magnetic biomolecules
2019
We estimate the time- and temperature-evolution of spin energy levels in a metallopeptide by combining molecular dynamics with crystal field analysis. Fluctuations of tens of cm-1 for spin energy levels at fs times gradually average out at longer times. We confirm that local vibrations are key in spin dynamics.
Advanced approach to the local structure reconstruction and theory validation on the example of the W L 3 -edge extended x-ray absorption fine struct…
2018
The authors gratefully acknowledge the assistance of the ELETTRA XAFS beamline staff members during the EXAFS experiment No 20150303. This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014-2018 under grant agreement No 633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission.
Limits of stability in supported graphene nanoribbons subject to bending
2016
Graphene nanoribbons are prone to in-plane bending even when supported on flat substrates. However, the amount of bending that ribbons can stably withstand remains poorly known. Here, by using molecular dynamics simulations, we study the stability limits of 0.5-1.9 nm wide armchair and zigzag graphene nanoribbons subject to bending. We observe that the limits for maximum stable curvatures are below ~10 deg/nm, in case the bending is externally forced and the limit is caused by buckling instability. Furthermore, it turns out that the limits for maximum stable curvatures are also below ~10 deg/nm, in case the bending is not forced and the limit arises only from the corrugated potential energy…
Lipid carbonyl groups terminate the hydrogen bond network of membrane-bound water.
2015
We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the …
Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight
2012
M.PvuII is a DNA methyltransferase from the bacterium Proteus vulgaris that catalyzes methylation of cytosine at the N4 position. This enzyme also displays promiscuous activity catalyzing methylation of adenine at the N6 position. In this work we use QM/MM methods to investigate the reaction mechanism of this promiscuous activity. We found that N6 methylation in M.PvuII takes place by means of a stepwise mechanism in which deprotonation of the exocyclic amino group is followed by the methyl transfer. Deprotonation involves two residues of the active site, Ser53 and Asp96, while methylation takes place directly from the AdoMet cofactor to the target nitrogen atom. The same reaction mechanism…
Pharmacophore Models Derived from Molecular Dynamics Simulations of Protein-Ligand Complexes: A Case Study
2018
A single, merged pharmacophore hypothesis is derived combining 2000 pharmacophore models obtained during a 20 ns molecular dynamics simulation of a protein-ligand complex with one pharmacophore model derived from the initial PDB structure. This merged pharmacophore model contains all features that are present during the simulation and statistical information about the dynamics of the pharmacophore features. Based on the dynamics of the pharmacophore features we derive two distinctive feature patterns resulting in two different pharmacophore models for the analyzed system – the first model consists of features that are obtained from the PDB structure and the second uses two features that ca…
Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7
2018
AbstractNitrophorins (NP) 1–7 are NO-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. The isoform NP7 displays peculiar properties, such as an abnormally high isoelectric point, the ability to bind negatively charged membranes, and a strong pH sensitivity of NO affinity. A unique trait of NP7 is the presence of Glu in position 27, which is occupied by Val in other NPs. Glu27 appears to be important for tuning the heme properties, but its influence on the pH-dependent NO release mechanism, which is assisted by a conformational change in the AB loop, remains unexplored. Here, in order to gain insight into the functional role of Glu27, we examine the ef…
Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses
2020
ABSTRACTCoronaviruses may produce severe acute respiratory syndrome (SARS). As a matter of fact, a new SARS-type virus, SARS-CoV-2, is responsible of a global pandemic in 2020 with unprecedented sanitary and economic consequences for most countries. In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. Our results evidence two stable binding modes involving an interaction site spanning either the protein dimer interface or only one monomer. The …