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The estrogen receptor is a nuclear hormone receptor activated by the natural steroid hormone 17$\beta$-estradiol (E2). Fragment molecular orbital (FMO) calculations were performed which allowed us to obtain the interaction energy…
Estrogen receptors (ERs) are a group of proteins activated by 17$\beta$-estradiol. The endocrine-disrupting chemicals (EDCs) mimic estrogen action by bind directly to the ligand binding domain of ER. From this perspective, ER represent a…
Fragment molecular orbital (FMO) calculations were performed in aqueous media which allowed us to obtain the interaction energy between the human estrogen receptor $\alpha$ ligand-binding domain (ER) and the selected ligands (L):…
Understanding of the molecular interaction between asphaltenes and other molecules, which may act as its solvents, provides insights into the nature of its stability in petroleum fluids and its phase transitions. Molecular dynamics…
Ab initio molecular dynamics (AIMD) simulations have been performed on aqueous solutions of four simple sugars, {\alpha}-D-glucose, \b{eta}-D-glucose, {\alpha}-D-mannose and {\alpha}-D-galactose. Hydrogen bonding (HB) properties, such as…
A highly diluted aqueous solution of histamine was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
An approach has been proposed to characterize the competitive association of D2O and to study the heterogeneity of hydration water adsorbed by the protein, immunoglobulin G, using methodology for determining of non-freezing water in mixed…
The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a…
We have theoretically studied the uptake of a non-uniformly charged biomolecule, suitable to represent a globular protein or a drug, by a charged hydrogel carrier in the presence of a 1:1 electrolyte. Based on the analysis of a physical…
We used modified Arrhenius approximations to analyze the known temperature dependences (TDs) of water microstructure parameters and its dynamic characteristics. The analysis of activation energies showed a significant difference in the…
Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors. We present a set of C3-substituted (-)-stepholidine derivatives as…
Using modified Arrhenius approximations, the activation energies of water, alcohols, and hexane structure rearrangement reactions responsible for temperature dependences of their dynamic and dielectric characteristics were determined. The…
The existence of an isosbestic point in the OH bond vibration band of H2O molecules in solutions of strong electrolytes has been shown by many research groups but its physical meaning has been only recently read as the equilibrium point…
Chemical thermodynamic models of solvent and solute activities predict the equilibrium behaviour of aqueous solutions. How-ever, these models are semi-empirical. They represent micro-scale ion and solvent behaviours that control the…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Hypothesis: The structural details, viscosity trends and dynamic phenomena in t-butanol/water solutions are closely related on the molecular scales across the entire composition range. Utilizing the experimental small- and wide-angle x-ray…
The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…
Hydrogen bonding interactions between biological chromophores and their surrounding protein and solvent environment significantly affect the photochemical pathways of the chromophore and its biological function. A common first step in the…
In the present study, water is considered as a dynamic network between molecules at distances not exceeding 3.2 angstroms. The instantaneous configurations obtained by using the molecular dynamics method have been sequentially analyzed, the…