Search results for "molecular dynamics"

Computing Metal-Binding Proteins for Therapeutic Benefit

2021

Over one third of biomolecules rely on metal ions to exert their cellular functions. Metal ions can play a structural role by stabilizing the structure of biomolecules, a functional role by promoting a wide variety of biochemical reactions, and a regulatory role by acting as messengers upon binding to proteins regulating cellular metal-homeostasis. These diverse roles in biology ascribe critical implications to metal-binding proteins in the onset of many diseases. Hence, it is of utmost importance to exhaustively unlock the different mechanistic facets of metal-binding proteins and to harness this knowledge to rationally devise novel therapeutic strategies to prevent or cure pathological st…

Structural transitions and melting of copper clusters

1993

Molecular dynamics is used to study the melting and structural transitions of small copper clusters. The melting temperature is found to be proportional to the average coordination number. Small icosahedral clusters melt at slightly higher temperatures than the cubic structures. Small cuboctahedral clusters are not stable but transform via a nondiffusive transition to icosahedral structure.

The Interaction of Metal Complexes with G-quadruplex DNA

Un approccio computazionale è stato proposto per lo studio dell’interazione di complessi metallici di basi di Schiff con DNA. Nel capitolo 2, è stato investigato il meccanismo di azione di complessi di Nichel(II), Rame(II) e Zinco(II) con B e G-quadruplex DNA. Il G-quadruplex è una conformazione non canonica adottata da particolari sequenze ricche in guanina. Recentemente, è stata dimostrata la sua esistenza in cellule umane, in regioni telomeriche e non telomeriche, ed è stato proposto come un possibile target per una nuova categoria di agenti antineoplastici. I capitoli successivi sono basati su dati raccolti durante due periodi di ricerca all’estero. Nel capitolo 3, basato sugli studi es…

Simulation of the dynamics of hard ellipsoids

2008

We study a system of uniaxial hard ellipsoids by molecular dynamics simulations, changing both the aspect-ratio X-0 (X-0 = a/b, where a is the length of the revolution axis and b is the length of the two other axes) and the packing fraction phi. We calculate the translational and rotational mean squared displacements, the translational D-trans and the rotational D-rot diffusion coefficients and the associated isodiffusivity lines in the phi - X-0 plane. For the first time, we characterize the cage effect through the logarithmic time derivative of log and log . These quantities exhibit a minimum if the system is supercooled and we show that, consistently with our previous findings, for large…

Geminal ionic liquids: a combined approach to investigate their three-dimensional organisation.

2009

Different investigations, such as 1D and 2D NMR spectroscopy, resonance light scattering spectroscopy and molecular dynamics simulations, have been jointly used to achieve a deeper understanding of the degree of structural order in two geminal ionic liquids. In particular, 3,3'-di-n-butyl-1,1'-(1,3-phenylenedimethylene)diimidazolium and 3,3'-di-n-butyl-1,1'-(1,4-phenylenedimethylene)diimidazolium bis[bis(trifluoromethanesulfonyl)imide] have been studied. These geminal ionic liquids were chosen because of the presence of both a rigid phenylenedimethylene link between two imidazolium rings, which should give a high degree of order to the solvent system, and the different shapes of the two cat…

Trimesic acid on Cu in ethanol: Potential-dependent transition from 2-D adsorbate to 3-D metal-organic framework

2017

We report the potential-dependent interactions of trimesic acid with Cu surfaces in EtOH. CV experiments and electrochemical surface-enhanced Raman spectroscopy show the presence of an adsorbed trimesic acid layer on Cu at potentials lower than 0 V vs Cu. The BTC coverage increases as the potential increases, reaching a maximum at 0 V. Based on molecular dynamics simulations, we report adsorption geometries and possible structures of the organic adlayer. We find that, depending on the crystal facet, trimesic acid adsorbs either flat or with one or two of the carboxyl groups facing the metal surface. At higher coverages, a multi-layer forms that is composed mostly of flat-lying trimesic acid…

How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency.

2022

AbstractThe STimulator of INterferon Genes (STING) protein is a cornerstone of the human immune response. Its activation by cGAMP upon the presence of cytosolic DNA stimulates the production of type I interferons and inflammatory cytokines which are crucial for protecting cells from infections. STING signaling pathway can also influence both tumor-suppressive and tumor-promoting mechanisms, rendering it an appealing target for drug design. In the human population, several STING variants exist and exhibit dramatic differences in their activity, impacting the efficiency of the host defense against infections. Understanding the differential molecular mechanisms exhibited by these variants is o…

Multi-scale theoretical investigation of molecular hydrogen adsorption over graphene: coronene as a case study

2014

The physisorption of molecular hydrogen onto coronene is studied using a multi-scale theoretical approach with Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations. We consider two different kinds of model conformation for the approach of hydrogen towards the coronene i.e., systematic and random. For the systematic attack of hydrogen over coronene, the resulting potential energy profiles from DFT analysis are further found to resemble the Morse potential, and even the highly flexible Murrell–Sorbie (M–S) potential. The resulting M–S fitting also shows a zero-point energy correction of ∼16–17%. On the other hand, the potential energies from the random approach…

Modelling the carbon Snoek peak in ferrite: Coupling molecular dynamics and kinetic Monte-Carlo simulations

2008

Abstract Molecular statics, molecular dynamics and kinetic Monte-Carlo are used to model the carbon Snoek peak in ferrite. Using an interatomic EAM potential for the Fe–C system, saddle point energies for the diffusion of carbon have been evaluated under uniaxial stress by molecular statics. These energies have been reintroduced in a kinetic Monte-Carlo scheme to predict the repartition of carbon atoms in different octahedral sites. This repartition leads to an anelastic deformation calculated by molecular dynamics, which causes internal friction (the Snoek peak) for cyclic stress. This approach leads to quantitative predictions of the internal friction, which are in good agreement with exp…

Histopathology of Skeletal Muscle in a Distal Motor Neuropathy Associated with a Mutant CCT5 Subunit: Clues for Future Developments to Improve Differ…

2023

Genetic chaperonopathies are rare but, because of misdiagnosis, there are probably more cases than those that are recorded in the literature and databases. This occurs because practitioners are generally unaware of the existence and/or the symptoms and signs of chaperonopathies. It is necessary to educate the medical community about these diseases and, with research, to unveil their mechanisms. The structure and functions of various chaperones in vitro have been studied, but information on the impact of mutant chaperones in humans, in vivo, is scarce. Here, we present a succinct review of the most salient abnormalities of skeletal muscle, based on our earlier report of a patient who carried…