[Comparative Analysis of the Performance of Mascot and IdentiPy Algorithms on a Benchmark Dataset Obtained by Tandem Mass Spectrometry Analysis of Testicular Biopsies].

Proteome profiling of human testicular biopsies was performed using tandem mass spectrometry with electrospray ionization. Protein identification results were compared for the Mascot commercial search engine, the SearchGUI noncommercial package, and their analog IdentiProt based on the open-source IdentiPy algorithm (http://hg.theorchromo.

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project.

Protein interactomics based on direct molecular fishing on paramagnetic particles: practical realization and further SPR validation.

There is increasing evidence that proteins function in the cell as integrated stable or temporally formed protein complexes, interactomes. Previously, using model systems we demonstrated applicability of direct molecular fishing on paramagnetic particles for protein interactomics (Ershov et al. Proteomics, 2012, 12, 3295).

Protein interactomics based on direct molecular fishing on paramagnetic particles: experimental simulation and SPR validation.

We describe an experimental approach for direct molecular fishing of prey protein on the surface of two types of paramagnetic particles (PMP) having different size and composition. Human microsomal cytochrome b(5) (b(5)) and its known partner human cytochrome P450 3A5 (CYP3A5) were used as bait and prey proteins, respectively. For assessing the level of unspecific binding of background proteins, α-fetoprotein (aFP) was used.

Protein-protein interactions as new targets for drug design: virtual and experimental approaches.

Protein-protein and protein-ligand interactions play a central role in biochemical reactions, and understanding these processes is an important task in different fields of biomedical science and drug discovery. Proteins often work in complex assemblies of several macromolecules and small ligands. The structural and functional description of protein-protein interactions (PPI) is very important for basic-, as well as applied research.

YC-1-like potentiation of NO-dependent activation of soluble guanylate cyclase by derivatives of protoporphyrin IX.

The influence of protoporphyrin IX derivatives--2,4-di(1-methoxyethyl)-deuteroporphyrin IX disodium salt (dimegin) and hematoporphyrin IX (HP)--on the activation of human platelet soluble guanylate cyclase by sodium nitroprusside was investigated. Dimegin and HP, like 1-benzyl-3-(hydroxymethyl-2-furyl)indazole (YC-1), produce synergistic effects on the activation of soluble guanylate cyclase by sodium nitroprusside. The synergistic activation of the enzyme by the combination of 10 microM sodium nitroprusside and 5 microM dimegin (or 5 microM HP) was 190 +/- 19 and 134 +/- 10%, respectively.

[Antioxidant properties of a leaf extract from Aronia (Aronia melanocarba) containing proanthocyanidins].

Antioxidant capacity of a procyanidin-containing extract from Aronia melanocarpa leaves has been studied in vitro and in vivo. Using the chemiluminescence technique, the effective content of antioxidants and its reactivity towards peroxyl radicals have been measured in a model reaction of initiated oxidation of hydrocarbon for the whole extract and two of its chromatographic fractions separated by HPLC. The results indicate that the extract contains a combination of antioxidants with different radical scavenging activities.

[Bacterial L-asparaginase and glutamin(asparagin)ase: some properties, structure and anti-tumor activity].

Experimental material on structurally and functional organization, regulation of biosynthesis and activity, mechanism of action, genetic determinants, heterologous expression of bacterial L-asparaginases is accumulated. The modern approaches to isolation and purification of these enzymes, some questions of practical using in oncology in the schedules combined chemotherapy of leukemia the native and modified forms of L-asparaginases are discussed. The some results before carried out in the IBMC RAMS and number institutes of the Russia on study bacterial L-asparaginases and glutamine(asparagine)ases are summarized.