Search results for "molecular dynamics"

Average Structure vs. Real Structure: Molecular Dynamics Studies of Silica

2003

The microscopic structure of a crystal and thermal fluctuations of the atoms constituting the crystal are intimately connected with the macroscopic elastic properties including mechanical stability. In some cases, however, the picture is more complex than that which is drawn in text books on solid state physics. (i) The instantaneous microscopic structure can deviate in a non-Gaussian way from the average structure even when domain disorder and/or crystal defects are absent. Quasi harmonic approximations may then turn out to be meaningless. (ii) The crystal is subject to external pressures that are sufficiently large in order to render the definition of elastic constants non unique. These t…

2015

In many technical applications, but also in natural processes like ice nucleation in clouds, crystallization proceeds in the presence of stresses and flows, hence the importance to understand the crystallization mechanism in simple situations. We employ molecular dynamics simulations to study the crystallization kinetics of a nearly hard sphere liquid that is weakly sheared. We demonstrate that shear flow both enhances and suppresses the crystallization kinetics of hard spheres. The effect of shear depends on the quiescent mechanism: suppression in the activated regime and enhancement in the diffusion-limited regime for small strain rates. At higher strain rates crystallization again become…

Phase Behavior of Active Swimmers in Depletants: Molecular Dynamics and Integral Equation Theory

2013

We study the structure and phase behavior of a binary mixture where one of the components is self-propelling in nature. The inter-particle interactions in the system were taken from the Asakura-Oosawa model, for colloid-polymer mixtures, for which the phase diagram is known. In the current model version the colloid particles were made active using the Vicsek model for self-propelling particles. The resultant active system was studied by molecular dynamics methods and integral equation theory. Both methods produce results consistent with each other and demonstrate that the Vicsek model based activity facilitates phase separation, thus broadening the coexistence region.

Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors.

2011

Reliable and effective virtual high-throughput screening (vHTS) methods are desperately needed to minimize the expenses involved in drug discovery projects. Here, we present an improvement to the negative image-based (NIB) screening: the shape, the electrostatics, and the solvation state of the target protein’s ligand-binding site are included into the vHTS. Additionally, the initial vHTS results are postprocessed with molecular mechanics/generalized Born surface area (MMGBSA) calculations to estimate the favorability of ligand-protein interactions. The results show that docking produces very good early enrichment for phosphodiesterase-5 (PDE-5); however, in general, the NIB and the ligand-…

Solubility and solvation features of native cyclodextrins in 1-ethyl-3-methylimidazolium acetate

2022

The comprehension of the mechanism entailing efficient solvation of cyclodextrins (CD) by green solvents is of great relevance to boost environmentally sustainable usages of smart supramolecular systems. Here, 1-ethyl-3- methylimidazolium acetate, an ecofriendly ionic liquid (IL), is considered as an excellent solvent for native CDs. This IL efficiently dissolves up to 40 wt.% β- and γ-CD already at ambient temperature and X-ray scattering indicates that CDs do not tend to detrimental flocculation under these drastic concentration conditions. Simu- lation techniques reveal the intimate mechanism of CD solvation by the ionic species: while the strong hydrogen bonding acceptor acetate anion i…

Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives.

2015

Abstract Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importanc…

Post-Translational Regulation of CYP450s Metabolism As Revealed by All-Atoms Simulations of the Aromatase Enzyme.

2019

Phosphorylation by kinases enzymes is a widespread regulatory mechanism able of rapidly altering the function of target proteins. Among these are cytochrome P450s (CYP450), a superfamily of enzymes performing the oxidation of endogenous and exogenous substrates thanks to the electron supply of a redox partner. In spite of its pivotal role, the molecular mechanism by which phosphorylation modulates CYP450s metabolism remains elusive. Here by performing microsecond-long all-atom molecular dynamics simulations, we disclose how phosphorylation regulates estrogen biosynthesis, catalyzed by the Human Aromatase (HA) enzyme. Namely, we unprecedentedly propose that HA phosphorylation at Y361 markedl…

All-Atom simulations disclose how cytochrome reductase reshapes the substrate access/egress routes of its partner cyp450s

2020

Cytochromes P450 enzymes (CYP450s) promote the oxidative metabolism of a variety of substrates via the electrons supplied by the cytochrome P450 reductase (CPR) and upon formation of a CPR/CYP450 adduct. In spite of the pivotal regulatory importance of this process, the impact of CPR binding on the functional properties of its partner CYP450 remains elusive. By performing multiple microsecond-long all-Atom molecular dynamics simulations of a 520â »000-Atom model of a CPR/CYP450 adduct embedded in a membrane mimic, we disclose the molecular terms for their interactions, considering the aromatase (HA) enzyme as a proxy of the CYP450 family. Our study strikingly unveils that CPR binding alters…

The chemistry of acetone at extreme conditions by density functional molecular dynamics simulations

2011

Density functional molecular dynamics simulations have been performed in the NVT ensemble (moles (N), volume (V) and temperature (T)) on a system formed by ten acetone molecules at a temperature of 2000 K and density ρ = 1.322 g cm(-3). These conditions resemble closely those realized at the interface of an acetone vapor bubble in the early stages of supercompression experiments and result in an average pressure of 5 GPa. Two relevant reactive events occur during the simulation: the condensation of two acetone molecules to give hexane-2,5-dione and dihydrogen and the isomerization to the enolic propen-2-ol form. The mechanisms of these events are discussed in detail.

Novel σ1 antagonists designed for tumor therapy: Structure – activity relationships of aminoethyl substituted cyclohexanes

2021

Abstract Depending on the substitution pattern and stereochemistry, 1,3-dioxanes 1 with an aminoethyl moiety in 4-position represent potent σ1 receptor antagonists. In order to increase the stability, a cyclohexane ring first replaced the acetalic 1, 3-dioxane ring of 1. A large set of aminoethyl substituted cyclohexane derivatives was prepared in a six-step synthesis. All enantiomers and diastereomers were separated by chiral HPLC at the stage of the primary alcohol 7, and their absolute configuration was determined by CD spectroscopy. Neither the relative nor the absolute configuration had a large impact on the σ1 affinity. The highest σ1 affinity was found for cis-configured benzylamines…