Search results for " Molecular Dynamics Simulation"

DNA minor groove binders: an overview on molecular modeling and QSAR approaches

2007

Molecular recognition of DNA by small molecules and proteins is a fundamental problem in structural biology and drug design. Understanding of recognition in both sequence-selective and sequence neutral ways at the level of successful prediction of binding modes and site selectivity will be instrumental for improvements in the design and synthesis of new molecules as potent and selective gene-regulatory drugs. Minor groove is the target of a large number of non-covalent binding agents. DNA binding with specific sequences, mostly AT, takes place by means of a combination of directed hydrogen bonding to base pair edges, van der Waals interactions with the minor groove walls and generalized ele…

Homology models of melatonin receptors: challenges and recent advances

2013

Melatonin exerts many of its actions through the activation of two G protein-coupled receptors (GPCRs), named MT1 and MT2. So far, a number of different MT1 and MT2 receptor homology models, built either from the prototypic structure of rhodopsin or from recently solved X-ray structures of druggable GPCRs, have been proposed. These receptor models differ in the binding modes hypothesized for melatonin and melatonergic ligands, with distinct patterns of ligand-receptor interactions and putative bioactive conformations of ligands. The receptor models will be described, and they will be discussed in light of the available information from mutagenesis experiments and ligand-based pharmacophore …

Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects.

2022

Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in sol…

Different relaxations in myoglobin after photolysis

2004

To clarify the interplay of kinetic hole-burning (KHB), structural relaxation, and ligand migration in myoglobin (Mb), we measured time-resolved absorption spectra in the Soret region after photolysis of carbon monoxide Mb (MbCO) in the temperature interval 120-260 K and in the time window 350 ns to 200 ms. The spectral contributions of both photolyzed (Mb * ) and liganded Mb (MbCO) have been analyzed by taking into account homogeneous bandwidth, coupling to vibrational modes, and static conformational heterogeneity. We succeeded in separating the “time-dependent” spectral changes, and this work provides possibilities to identify the events in the process of ligand rebinding. KHB is domina…

Spectral broadening of the Soret band in myoglobin: an interpretation by the full spectrum of low-frequency modes from a normal modes analysis.

2005

In this work the temperature dependence of the Soret band line shape in carbon-monoxy myoglobin is re-analyzed by using both the full correlator approach in the time domain and the frequency domain approach. The new analyses exploit the full density of vibrational states of carbon-monoxy myoglobin available from normal modes analysis, and avoid the artificial division of the entire set of vibrational modes coupled to the Soret transition into "high-frequency" and "low-frequency" subsets; the frequency domain analysis, however, makes use of the so-called short-times approximation, while the time domain one avoids it. Time domain and frequency domain analyses give very similar results, thus s…

Large scale motions in models of human nicotinic receptors

2014

Plenty of motion at the bottom: atomically thin liquid gold membrane

2015

The discovery of graphene some ten years ago was the first proof of a free-standing two-dimensional (2D) solid phase. Here, using quantum molecular dynamics simulations of nanoscale gold patches suspended in graphene pores, we predict the existence of an atomically thin, free-standing 2D liquid phase. The liquid phase, enabled by the exceptional planar stability of gold due to relativistic effects, demonstrates extreme fluxionality of metal nanostructures and opens possibilities for a variety of nanoscale phenomena.

Proposal of a Computational Approach for Simulating Thermal Bosonic Fields in Phase Space

2019

When a quantum field is in contact with a thermal bath, the vacuum state of the field may be generalized to a thermal vacuum state, which takes into account the thermal noise. In thermo field dynamics, this is realized by doubling the dimensionality of the Fock space of the system. Interestingly, the representation of thermal noise by means of an augmented space is also found in a distinctly different approach based on the Wigner transform of both the field operators and density matrix, which we pursue here. Specifically, the thermal noise is introduced by augmenting the classical-like Wigner phase space by means of Nos&eacute

Fractional-order theory of heat transport in rigid bodies

2014

Abstract The non-local model of heat transfer, used to describe the deviations of the temperature field from the well-known prediction of Fourier/Cattaneo models experienced in complex media, is framed in the context of fractional-order calculus. It has been assumed (Borino et al., 2011 [53] , Mongiovi and Zingales, 2013 [54] ) that thermal energy transport is due to two phenomena: ( i ) A short-range heat flux ruled by a local transport equation; ( ii ) A long-range thermal energy transfer proportional to a distance-decaying function, to the relative temperature and to the product of the interacting masses. The distance-decaying function is assumed in the functional class of the power-law …

Thioflavin T templates amyloid β(1–40) conformation and aggregation pathway

2015

Aβ(1-40) peptide supramolecular assembly and fibril formation processes are widely recognized to have direct implications in the progression of Alzheimer's disease. The molecular basis of this biological process is still unknown and there is a strong need of developing effective strategies to control the occurring events. To this purpose the exploitation of small molecules interacting with Aβ aggregation represents one of the possible routes. Moreover, the use specific labeling has represented so far one of the most common and effective methods to investigate such a process. This possibility in turn rests on the reliability of the probe/labels involved. Here we present evidences of the effe…