Search results for " MOLECULAR DYNAMICS"
showing 10 items of 126 documents
Molecular Basis for Endocrine Disruption by Pesticides Targeting Aromatase and Estrogen Receptor
2020
The intensive use of pesticides has led to their increasing presence in water, soil, and agricultural products. Mounting evidence indicates that some pesticides may be endocrine disrupting chemicals (EDCs), being therefore harmful for the human health and the environment. In this study, three pesticides, glyphosate, thiacloprid, and imidacloprid, were tested for their ability to interfere with estrogen biosynthesis and/or signaling, to evaluate their potential action as EDCs. Among the tested compounds, only glyphosate inhibited aromatase activity (up to 30%) via a non-competitive inhibition or a mixed inhibition mechanism depending on the concentration applied. Then, the ability of the thr…
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…
All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome
2018
The spliceosome (SPL) is a majestic macromolecular machinery composed of five small nuclear RNAs and hundreds of proteins. SPL removes noncoding introns from precursor messenger RNAs (pre-mRNAs) and ligates coding exons, giving rise to functional mRNAs. Building on the first SPL structure solved at near–atomic-level resolution, here we elucidate the functional dynamics of the intron lariat spliceosome (ILS) complex through multi-microsecond-long molecular-dynamics simulations of ∼1,000,000 atoms models. The ILS essential dynamics unveils (i) the leading role of the Spp42 protein, which heads the gene maturation by tuning the motions of distinct SPL components, and (ii) the critical particip…
Density functional study of Cu2+-phenylalanine complex under micro-solvation environment
2013
Abstract We present an atomistic study carried out using density functional calculations including structural relaxations and Car–Parrinello Molecular Dynamics (CPMD) simulations, aiming to investigate the structures of phenylalanine-copper (II) ([Phe-Cu] 2+ ) complexes and their micro-solvation processes. The structures of the [Phe-Cu] 2+ complex with up to four water molecules are optimized using the B3LYP/6-311++G** model in gas phase to identify the lowest energy structures at each degree of solvation ( n = 0–4). It is found that the phenylalanine appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n …
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State
2012
ABSTRACT: The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to non-equilibrium molecular dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment …
A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model
2014
Chaperonins mediate protein folding in a cavity formed by multisubunit rings. The human CCT has eight non-identical subunits and the His147Arg mutation in one subunit, CCT5, causes neuropathy. Knowledge is scarce on the impact of this and other mutations upon the chaperone's structure and functions. To make progress, experimental models must be developed. We used an archaeal mutant homolog and demonstrated that the His147Arg mutant has impaired oligomeric assembly, ATPase activity, and defective protein homeostasis functions. These results establish for the first time that a human chaperonin gene defect can be reproduced and studied at the molecular level with an archaeal homolog. The major…
Visualizing Solubilization by a Realistic Particle Model in Chemistry Education
2019
An application for the visualization of the mixing process of two different types of structureless interacting particles is presented. The application allows to demonstrate on a qualitative basis, as well as by quantitatively monitoring the time evolution of the fractions of aggregates of different sizes, that the formation of a homogeneous mixture is the result of favorable solute-solvent interactions as well as by temperature. It is suggested that, along with the use of suitable macroscopic examples, visualizations by the present application are useful in elucidating concepts related to miscibility/solubility. The application is based on a two-dimensional realistic dynamic model where ato…
The Interaction of Small Molecules with Biomolecules
2014
The binding of small molecules with biological targets is associated to interesting chemical and biological properties of the resulting supramolecular systems. We have recently reported on the synthesis and characterization of cationic first row transition metal complexes and the study of their DNA binding properties, in aqueous solutions at neutral pH, essentially investigated by viscosimetry and spectroscopic techniques such as circular dichroism, absorption and fluorescence in the UV-visible wavelength range. Of course, such procedure cannot furnish atomic level details of the molecule-DNA interaction. Computational Chemistry may provide support for the interpretation of experimental dat…
A step forward in disclosing the secret of stradivari's varnish by NMR spectroscopy
2017
It is commonly thought that the varnishes used by the great violin-maker Antonio Stradivari may have a role in determining not only the esthetical features but also the acoustic properties of his instruments, and the idea of a “lost secret” is still widespread among musicians and violin-makers. Previous scientific researches on varnish samples of Stradivari's instruments revealed that they were generally made by a mix of linseed oil with and colophony or metal rosinates in different ratios ranging between 75/25 (oil/resin) and 60/40 (oil/rosinate). However, it is still not clear whether the mixture composition can be related to any structural and/or functional feature of the resulting varni…
Simulations of Glassforming Network Fluids: Classical Molecular Dynamics versus Car-Parrinello Molecular Dynamics
2010
Abstract Static and dynamic Properties of molten germanium dioxide are studied by two simulation methods, classical Molecular Dynamics (MD) using the Oeffner-Elliott (OE) potential, and “ab initio” Car-Parrinello Molecular Dynamics (CPMD). While CPMD provides a (presumably) more accurate description of the local structure and the forces, it severely suffers from finite size effects when the structure beyond the first neighbor shells is considered. For glassforming fluids, the demanding equilibrium needs are a further reason, why simply MD is still preferable, when a “good” effective potential is available.