Search results for "molecular dynamics"
showing 10 items of 1075 documents
G-quadruplex recognition by DARPIns through epitope/paratope analogy
2022
AbstractWe investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments invo…
Fluorine Scan of Inhibitors of the Cysteine Protease Human Cathepsin L: Dipolar and Quadrupolar Effects in the π-Stacking of Fluorinated Phenyl Rings…
2016
The π-stacking of fluorinated benzene rings on protein backbone amide groups was investigated, using a dual approach comprising enzyme-ligand binding studies complemented by high-level quantum chemical calculations. In the experimental study, the phenyl substituent of triazine nitrile inhibitors of human cathepsin L (hCatL), which stacks onto the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket, was systematically fluorinated, and differences in inhibitory potency were measured in a fluorimetric assay. Binding affinity is influenced by lipophilicity (clog P), the dipole and quadrupole moments of the fluorinated rings, but also by additional interactions of the introduced fluo…
Experimental investigation and multi-scale modelling of the behavior of mechanically activated metallic powders : from binary systems to High Entropy…
2021
Generally, metal alloys consist of a main element associated with other elements present in smaller quantities such as iron, nickel, aluminum or copper alloys. The precise composition of an alloy is adjusted according to the required performance: high temperature behavior, corrosion resistance, mechanical properties, durability ... In 2004, a Taiwanese scientist, JW Yeh, had the idea of making an alloy base of several elements, at least 5, whose composition in the alloy varies between 5% and 30% at. Yeh invented the high entropy alloy (HEA). Mixed on a microscopic scale, the metals form a remarkably stable solid solution. The explanation is thermodynamic. An alloy is all the more stable as …
Microstructure-process relationship and reactivity at the nanoscale : a molecular dynamics study of Ni, Ni-Al, and Ti-Al metallic systems
2023
The process-microstructure relationship is central in materials science because the microstructure will determine the properties of the materials developed by the processes. In our work, we focused on different metallurgical processes by adopting a description at the atomic scale. This approach allows us to detect the elementary mechanisms that are at the origin of the observed microstructures without having to postulate macroscopic mechanisms or estimate the associated parameters. In this respect, molecular dynamics simulations provide a tool for "in-situ" observation of metallic systems as long as an atomic interaction potential is available. The originality of our approach consists in mo…
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling
2021
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP a…
Light-induced Changes in the Dimerization Interface of Bacteriophytochromes
2015
Phytochromes are dimeric photoreceptor proteins that sense red light levels in plants, fungi, and bacteria. The proteins are structurally divided into a light-sensing photosensory module consisting of PAS, GAF, and PHY domains and a signaling output module, which in bacteriophytochromes typically is a histidine kinase (HK) domain. Existing structural data suggest that two dimerization interfaces exist between the GAF and HK domains, but their functional roles remain unclear. Using mutational, biochemical, and computational analyses of the Deinococcus radiodurans phytochrome, we demonstrate that two dimerization interfaces between sister GAF and HK domains stabilize the dimer with approximat…
Interpretation of EXAFS in ReO3using molecular dynamics simulations
2009
Temperature dependent Re L3-edge EXAFS signals from perovskite-type cubic ReO3 have been successfully interpreted using a combination of classical NVT molecular dynamics (MD) and ab initio multiple-scattering approach. The force field model, required for MD simulations, has been determined by fitting the Re-O and O-O pairwise interatomic potentials to a set of experimental data (lattice parameter, elastic constants and bulk modulus) and phonon frequencies, theoretically calculated from the first principles at high symmetry points of the Brillouin zone. The MD simulations reproduce well the anisotropy of thermal vibration for oxygen atoms and confirm a deviation of the mean Re-O-Re angle fro…
Interpretation of EXAFS in scheelite-type AWO4(A = Ca, Sr, Ba) compounds using molecular dynamics simulations
2013
In this work we successfully interpret the W L3-edge EXAFS spectra in scheelite-type AWO4 (A = Ca, Sr, Ba) compounds using a combination of classical NVT molecular dynamics (MD) and ab initio multiple-scattering (MS) theory. The configuration-averaged EXAFS spectra show good agreement with our room temperature experimental data supporting the reliability of the developed force-field models. The contributions from all coordination shells up to 6 A are elucidated. The contribution of the MS effects into the total EXAFS signal in AWO4 compounds is small, being around 10%.
Interpretation of the U L3-edge EXAFS in uranium dioxide using molecular dynamics and density functional theory simulations
2016
X-ray absorption spectroscopy is employed to study the local structure of pure and Cr-doped UO2 at 300 K. The U L3-edge EXAFS spectrum is interpreted within the multiplescattering (MS) theory using the results of the classical and ab initio molecular dynamics simulations, allowing us to validate the accuracy of theoretical models. The Cr K-edge XANES is simulated within the full-multiple-scattering formalism considering a substitutional model (Cr at U site). It is shown that both unrelaxed and relaxed structures, produced by ab initio density functional theory (DFT) calculations, fail to describe the experiment.
Impulsive solvent heating probed by picosecond x-ray diffraction
2006
The time-resolved diffraction signal from a laser-excited solution has three principal components: the solute-only term, the solute-solvent cross term, and the solvent-only term. The last term is very sensitive to the thermodynamic state of the bulk solvent, which may change during a chemical reaction due to energy transfer from light-absorbing solute molecules to the surrounding solvent molecules and the following relaxation to equilibrium with the environment around the scattering volume. The volume expansion coefficient alpha for a liquid is typically approximately 1 x 10(-3) K(-1), which is about 1000 times greater than for a solid. Hence solvent scattering is a very sensitive on-line t…