Effect of ergosterol on the fungal membrane properties. All-atom and coarse-grained molecular dynamics study.

Cell membranes are complex multicomponent systems consisting of thousands of different lipids with numerous embedded membrane proteins and many types of sterols. We used all-atom and coarse-grained molecular dynamics simulations to study the structural and dynamical properties of phospholipid bilayers containing four types of phospholipids and different amount of ergosterol, main sterol component in the fungal membranes. To characterize the influence of ergosterol on the membrane properties we analyzed the surface area per lipid, bilayer thickness, area compressibility modulus, mass density profiles, deuterium order parameters, and lateral diffusion coefficients.

Interaction of Scots Pine Defensin with Model Membrane by Coarse-Grained Molecular Dynamics.

Plant defensins are a part of the innate immune system of plants that acts against a broad range of pathogens. Many plant defensins, including pine defensins, show strong antifungal activity that is associated with their ability to penetrate into the fungal cell membrane. However, the exact molecular mechanism of their action remains poorly defined.

Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition.

Translational diffusion is the most fundamental form of transport in chemical and biological systems. The diffusion coefficient is highly sensitive to changes in the size of the diffusing species; hence, it provides important information on the variety of macromolecular processes, such as self-assembly or folding-unfolding. Here, we investigate the behavior of the diffusion coefficient of a macromolecule in the vicinity of heat-induced transition from folded to unfolded state.

Structural insight into the glucokinase-ligands interactions. Molecular docking study.

Glucokinase (GK) plays a key role in the regulation of hepatic glucose metabolism. Inactivation of GK is associated with diabetes, and an increase of its activity is linked to hypoglycemia. Possibility to regulate the GK activity using small chemical compounds as allosteric activators induces the scientific interest to the study of the activation mechanism and to the development of new allosteric glucokinase activators.

Influence of zinc nanoparticles on survival of worms Eisenia fetida and taxonomic diversity of the gut microflora.

The study was conducted to examine the effect of zinc nanoparticles on survival of worms Eisenia fetida and composition of the gut microflora. Analysis of the survival data has shown that the introduction of high doses of the nanoparticles causes death of worms in the second group with 35 % mortality rate and activates protective mechanisms realized as mucous film. DNA from the worm guts was extracted and 16S metagenomic sequencing was fulfilled using MiSeq (Illumina).

Structure of Scots pine defensin 1 by spectroscopic methods and computational modeling.

Defensins are part of the innate immune system in plants with activity against a broad range of pathogens, including bacteria, fungi and viruses. Several defensins from conifers, including Scots pine defensin 1 (Pinus sylvestris defensin 1, (PsDef1)) have shown a strong antifungal activity, however structural and physico-chemical properties of the family, needed for establishing the structure-dynamics-function relationships, remain poorly characterized. We use several spectroscopic and computational methods to characterize the structure, dynamics, and oligomeric state of PsDef1.

Effect of ligand binding on the dynamics of trypsin. Comparison of different approaches.

The intramolecular signal transduction induced by the binding of ligands to trypsin was investigated by molecular dynamics simulations. Ligand binding changes the residue-residue interaction energies and suppresses the mobility of loops that are in direct contact with the ligand. The reduced mobility of these loops results in the altered flexibility of the nearby loops and thereby transmits the information from ligand binding site to the remote sites.

Brownian dynamics simulation of substrate motion near active site of enzyme entrapped inside reverse micelle.

Brownian dynamics simulation has been applied to analyze the influence of the electrostatic field of a reverse micelle on the enzyme-substrate complex formation inside a micelle. The probability that the enzyme-substrate complex will form from serine protease (trypsin) and the specific hydrophilic cationic substrate Nalpha-benzoyl-L: -arginine ethyl ester has been studied within the framework of the encounter complex formation theory. It has been shown that surfactant charge, dipole moments created by charged surfactant molecules and counterions, and permittivity of the inner core of reverse micelles can all be used as regulatory parameters to alter the substrate orientation near the active site of the enzyme and to change the probability that the enzyme-substrate complex will form.

Brownian dynamics simulation of the competitive reactions: binase dimerization and the association of binase and barstar.

A comparative study of the competitive reactions-the association reaction of binase with polypeptide inhibitor barstar and the reaction of binase dimerization-has been performed by the Brownian dynamics simulation method. It was shown that three types of the binase dimers could be formed and the dimerization reaction could compete with the inhibition reaction. The first type of the dimers leaves the active centre of binase free.

Lysozyme dimerization: Brownian dynamics simulation.

The lysozyme dimerization reaction has been studied within the framework of encounter-complex (EC) formation theory using the MacroDox software package. Two types of energetically favorite ECs were determined. In the first of them, active-center amino acids of lysozyme take part in the complex formation or the second molecule blocks accessibility to active center sterically.