Reactivity of Ala-Gly dipeptide with β-turn secondary structure

An accurate DFT study within conformational survey of the D-form serine-alanine protected dipeptide

The conformational analysis of N-formyl-D-serine-D-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD-γL, is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γD-γL includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n* of intra‒ligand alanine moiety of dipeptide structure.

Extracts from Frangula alnus Mill. and Their Effects on Environmental and Probiotic Bacteria

The bark of Frangula alnus Mill (FAM), the so-called alder buckthorn, has been widely investigated for its medicinal properties, especially its laxative effects and the bioactive properties of the plant material extract. Still, there is no wider study devoted to its antibacterial properties. This is important in the context of its impact on probiotic gut bacteria. The aim of the research was to recognize the effect of FAM extract on bacterial cells, and to determine how the bioactive properties and composition of the extract are influenced by the type of solvent used for the extraction. To find the most suitable conditions for the FAM extraction, we used four solvent solutions with different polarities, including water, methanol, ethanol, and isopropanol. We assessed the quality and composition of the extracts with spectral analysis, using spectrophotometric (FTIR, UV-Vis) and chromatographic methods (GC-MS). Finally, we analyzed the extractant impact of the extracts on the selected bacterial cells. The results showed that the chemical diversity of the extracts increased with the increase in solvent polarity, in which the abundance of frangulin, the main bioactive compound in buckthorn bark, was confirmed. Pseudomonas fluorescens ATCC 17400 was particularly sensitive to the action of extracts, whereas other strains of the Pseudomonas genus showed practically no adverse effects. Ethanolic extracts had the strongest effect on most of the selected bacteria strains. We found that the probiotic Lactobacillus strain, which represents intestinal microflora, has no direct effect on probiotic microorganisms. The research shown FAM extracts can be safe for probiotic bacteria present in human gut microflora. Moreover, the study indicated that contact with the extracts may reduce the total permeability of the bacterial membranes. This opens up the possibility of using FAM extracts as a factor regulating transport into cells, which may be used to support the action of other bioactive substances.

A reconnaissance DFT study of the full conformational analysis of N-formyl-L-serine-L-alanine-NH2 dipeptide

Theoretical conformational analysis of N-formyl-L-serine-L-alanine-NH₂ dipeptide model was investigated using B3LYP/6-311+G(d,p) and M06-2X/6-311+G(d,p) calculations. In this research, 243 total possible conformations of the dipeptide model were optimized including 87 stable conformers and the other disappeared ones migrated to more stable geometries. Migration pattern suggests more stability of the dipeptide model with the serine (ser) in β_L, γ_L, and γ_D and the alanine (ala) in γ_D and γ_L configurations, along with 26 of the found conformers having β-turn structures. Our calculations reveal that the most stable conformer, γ_L⁺γ_D, is in β-turn region of Ramachandran map; therefore, serine-alanine (ser-ala) dipeptide model should be adopted with a β-turn conformation. The atoms in molecules (AIM) topological analysis was carried out to characterize the nature of the intramolecular hydrogen bonding in β-turn structures. The γ_L⁺γ_D, including three hydrogen bonds, has the highest stability, while α_L^aγ_L as the most unstable β-turn conformer bears two and one hydrogen bonds at the B3LYP/6-311+G(d,p) and M06-2X/6-311+G(d,p) levels of theory, respectively. Graphical abstract.