Direct molecular fishing in molecular partners investigation in protein–protein and protein–peptide interactions

An original experimental method of direct molecular fishing has been developed for identification of potential partners of protein–protein and protein–peptide interactions. It is based on combination of surface plasmon resonance technology (SPR), size exclusion and affinity chromatography and mass spectrometric identification of proteins (LC-MS/MS). Previously, we demonstrated applicability of this method for protein interactomics using experimental model system, as well as in the pilot study in the frame of the Human Proteome Project (HPP). In the present paper, this method was successfully applied to identify possible molecular partners of 7 target proteins encoded by genes of 18 chromosome (also in the frame of the HPP). Fishing on the affinity sorbents with immobilized target proteins as ligands was carried out using total lysate of human liver tissue as well as pooled sets of fractions (individual for each bait-protein) obtained by means of a combination of size exclusion chromatography and SPR analysis for the presence of potential prey-proteins in each fraction. As a result we obtained lists of possible molecular partners of all 7 proteins and performed a comparative evaluation of direct fishing specificity for these target proteins. Direct molecular fishing was also successfully used for search of potential protein partners interacting with different isoforms of amyloid-beta peptide, playing a key role in the development of Alzheimer’s disease. The synthetic peptides that are analogues of the metal-binding domain isoforms of beta-amyloid were used as molecular baits and the fishing was performed in various fractions of immortalized human neural cells. As a result, 13 potential partner proteins were identified in the cytosol fraction of the cells by fishing on amyloid-beta peptide (1-16).     

Cloning and detailed mapping of the fra-ymt region of the Yersinia pestis pFra plasmid]

The genetical libraries of the pFra plasmid of Yersinia pestis genes were obtained by insertion into the PstI, SalGI, EcoRI, XhoI restriction sites of the cosmid vector pHC79. The immunochemical analysis of the recombinant clones has revealed the clones synthesizing the antigen Fl (fraction I) and mouse toxin (Ymt--Yersinia pestis murine toxin). The restriction analysis of the plasmids from antigen synthesizing clones has permitted to construct the detailed physical map of the fra-ymt region of the pFra plasmid the size of 22 kb. The recombinant F1 positive clones of Escherichia coli are able to form at 37 degrees C the capsule-like structure peculiar for Yersinia pestis. The antigen F1 and the mouse toxin were isolated, purified and characterized. The antigen F1 is an 1-2 Md polymer containing a 16 kDa protein subunit. The mouse toxin a 240 kDa protein consisting of 61 kDa subunits. The nucleotide sequence of ymt gene has been defined.     

Molecular mobility of soluble collagen

Conformation structure of soluble collagen in anhydrous form, films and gels was studied by broad line NMR. An analysis of spectra points to partial ordering of polymer chains in the films and possible formation of secondary structure of collagen molecules by alpha-helix type. Distinction of gel spectra from those of films is explained by unordered rotation movements of the chain fragments at the expense of "superspiralization" of collagen molecules.     

Suppression of Lewis carcinoma metastasis in mice by an interferon-inducing vasodilator curantil

The intravascular (iv) or intramuscular (im) inoculations of a suspension of Lewis carcinoma cells induced metastatic tumor nodules in the lungs of C57Bl/6 mice. The administration of curantil (dipyridamole) (500 mg per 20 g-mouse, per os) once a week beginning one day after iv tumor cells inoculation (2 X 10(5) cells) reduced 4-fold the number of tumor nodules. The administration of curantil one day after im tumor cells inoculation (2 X 10(6) cells) reduced 2-fold the number of tumor nodules. The combined treatment of curantil (4-, 10-days after inoculation) and well-known inducer of interferon poly I:poly C (50 mg per 20 g-mouse, 1-, 7-, 14-days after inoculation tumor cells) had no synergistic effect.     

SARS-COV-2 Coronavirus Papain-like Protease PLpro as an Antiviral Target for Inhibitors of Active Site and Protein–Protein Interactions

Biophysics - The papain-like protease PLpro of the SARS-CoV-2 coronavirus is a multifunctional enzyme that catalyzes the proteolytic processing of two viral polyproteins, pp1a and pp1ab. PLpro also...     

Genomic and Physiological Characterization of Halophilic Bacteria of the Genera Halomonas and Marinobacter from Petroleum Reservoirs

Microbiology - During the exploitation of oil reservoirs with highly mineralized waters, water separated from oil is pumped back into the reservoirs, which in some cases leads to an increase in...     

Dinuclear versus mononuclear ruthenium(II) and osmium(II) complexes as potent mediators of glucose oxidase; crystal structure of [OsCl(4,4′-bpy)(bpy)<Subscript>2</Subscript>]BF<Subscript>4</Subscript>

New and known homo- and heterodinuclear Ru^II and Os^II complexes with 4,4-bipyridine (4,4-bpy), pyrazine, and 4-pyCH=CHpy-4 as bridging ligands (LL) of the type [Cl(bpy)₂M(LL)MCl(bpy)₂]X₂ (bpy=2,2-bipyridine; X=PF₆ or BF₄) have been studied in their capacity to exchange electrons with a reduced active site of glucose oxidase (GO) from Aspergillus niger. Cyclic voltammograms (CVs) of the dimers in the aqueous buffered solution, when compared with CVs of the parent monomeric species [MCl(LL)(bpy)₂]BF₄ and [MCl₂(bpy)₂] which could be generated at pH7, if the dimers undergo monomerization, indicate that the dimers are the dominating species under such conditions. All electrochemically oxidized dinuclear complexes studied show high rates of oxidation of GO reduced by d-glucose and the corresponding observed second-order rate constants are in the range (5–64)×10⁵ M^–1 s^–1 at 25 °C. However, these values are lower than that for the mononuclear complex [OsCl(4,4-bpy)(bpy)₂]BF₄ (1.1×10⁷ M^–1 s^–1), suggesting that potentially two-electron dimeric mediators have no advantage compared with corresponding monomeric complexes of Ru^II and Os^II. The structure of [OsCl(4,4-bpy)(bpy)₂]BF₄ was confirmed by X-ray crystallography. The monodentate 4,4-bpy ligand is coordinated cis to the chloride. Its higher reactivity toward reduced GO is accounted for in terms of the antenna effect of the monodentate 4,4-bpy ligand. The antenna length equals 9.2 Å and matches the depth of the enzyme active site pocket of ca. 10 Å. The mechanism of the antenna effect is discussed     

Cycloferon--a new domestic preparation for the prophylaxis of influenza and other acute respiratory viral infections

The results of the placebo-controlled multicenter study of the epidemiological efficiency of the preparation Cycloferon for the prophylaxis of acute respiratory viral infections in children and adolescents are presented. A total of 16,000 children and adolescents were selected for the study. The epidemiological efficiency of the preparation manifested in 1.5- 2.9-fold decreased morbidity level with a protection index equal to 41 - 90%, was demonstrated.