In situ proteolysis for protein crystallization and structure determination

We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.     

Diversity of the bphA1 Genes in a Microbial Community from Anthropogenically Contaminated Soil and Isolation of New Pseudomonads Degrading Biphenyl/Chlorinated Biphenyls

Microbiology - Molecular biological and cultivation-based approaches were used to investigate the microbial community of tehnogenic soil contaminated with poorly degradable toxic (chlorinated)...     

Characterization of Pectobacterium carotovorum subsp. carotovorum Bacteriophage PP16 Prospective for Biocontrol of Potato Soft Rot

Microbiology - Phages of the phytopathogenic Pectobacteriaceae species causing black leg and soft rot of potato were investigated. These phages are promising as biocontrol agents to prevent the...     

Synthetic Oligopeptides Mimicking γ-Core Regions of Cysteine-Rich Peptides of Solanum lycopersicum Possess Antimicrobial Activity against Human and Plant Pathogens

Plant cysteine-rich peptides (CRPs) represent a diverse group of molecules involved in different aspects of plant physiology. Antimicrobial peptides, which directly suppress the growth of pathogens, are regarded as promising templates for the development of next-generation pharmaceuticals and ecologically friendly plant disease control agents. Their oligopeptide fragments are even more promising because of their low production costs. The goal of this work was to explore the antimicrobial activity of nine short peptides derived from the γ-core-containing regions of tomato CRPs against important plant and human pathogens. We discovered antimicrobial activity in peptides derived from the defensin-like peptides, snakins, and MEG, which demonstrates the direct involvement of these CRPs in defense reactions in tomato. The CRP-derived short peptides appeared particularly active against the gram-positive bacterium Clavibacter michiganensis, which causes bacterial wilt—opening up new possibilities for their use in agriculture to control this dangerous disease. Furthermore, high inhibitory potency of short oligopeptides was demonstrated against the yeast Cryptococcus neoformans, which causes serious diseases in humans, making these peptide molecules promising candidates for the development of next-generation pharmaceuticals. Studies of the mode of action of the two most active peptides indicate fungal membrane permeabilization as a mechanism of antimicrobial action.     

A switch from α‐helical to β‐strand conformation during co‐translational protein folding

Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ribosome. Here, we combine biophysical methods with cryo‐EM structure determination to show that folding of a β‐barrel protein begins with formation of a dynamic α‐helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N‐terminal part of the nascent chain refolds to a β‐hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α‐helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl‐transferase center suggest that protein folding could modulate ribosome activity.     

Secretion-fiber transformation in fibroin of the natural silk by polarization-optical methods

Structural changes in fibroin molecules upon transformation of the secret into a fiber were studied by the methods of birefringence in a longitudinal hydrodynamic field, optical rotatory dispersion, and circular dichroism. Fibroin fibers were obtained by drawing out the secret from the silk-secreting gland of silkworm moth Bombux mori. In this process, the formation of a longitudinal hydrodynamic field inside the gland was observed. The experimental data obtained make it possible to assess the degree of orientation and unfolding of macromolecules, as well as the conditions of the alpha-beta structural transition in fibroin chains.     

Regulatory contribution of heterotrimeric G-proteins to oocyte maturation in the sea urchin

Regulation of animal oocyte maturation is hypothesized to involve heterotrimeric G-proteins. It is difficult to test this hypothesis though without knowing what G-proteins are present in these cells and where are they localized. We set out to test the hypothesis that G-proteins regulate maturation in the sea urchin oocyte by identifying resident G-proteins in oocytes and eggs, and then investigating their function. We find four families of G-protein alpha-subunits (Galphai, Galphaq, Galphas, and Galpha12) present in both oocytes and eggs of the sea urchin. Three of them, Galphai, Galphaq, and Galphas are present on the plasma membrane of the oocyte, while the fourth is located on cytoplasmic vesicles. Upon oocyte maturation, these proteins remain in eggs, and continue to be expressed in embryonic tissues. To test the functional contribution of the G-proteins to the regulation of oocyte maturation, we employ specific intervening reagents, including antibodies and competitor peptides to each Galpha subunit, and specific Galpha toxins. We find that Gi is a main candidate for a positive regulator of sea urchin oocyte maturation. These studies provide a foundation to further test specific hypotheses of the G-protein mediated regulation of oocyte maturation, fertilization, and early development in the sea urchin.     

Similarity between the association factor of ribosomal subunits and the protein Stm1p from Saccharomyces cerevisiae

A ribosome association factor (AF) was isolated from the yeast Sacchharomyces cerevisiae. Partial amino acid sequence of AF was determined from its fragment of 25 kDa isolated by treating AF with 2-(2-nitrophenylsulfenyl)-3-methyl-3'-Bromoindolenine (BNPS-skatole). This sequence has a 86% identity to the product of the single-copy S. cerevisiae STM1 gene that is apparently involved in several events like binding to quadruplex and triplex nucleic acids and participating in apoptosis, stability of telomere structures, cell cycle, and ribosomal function. Here we show that AF and Stm1p share some characteristics: both bind to quadruplex and Pu triplex DNA, associates ribosomal subunits, and are thermostable. These observations suggest that these polypeptides belong to a family of proteins that may have roles in the translation process.     

KatG Ser3 15Thr mutation as the main reason of isoniazid resistance in Mycobacterium tuberculosis isolated in the Novosibirsk and Kemerovo Regions

KatG Ser3 15Thr mutation is one of the main reasons of resistance to isoniazid in Mycobacterium tuberculosis isolates. The frequency rate of the above mutation among isoniazid-resistant isolates made 94% in Novosibirsk Region and 93% in Kemerovo Region. The use of PCR-restriction fragment length polymorphism (PCR-RFLP) can be regarded as an adequate method for rapid screening of isoniazid resistance in Mycobacterium tuberculosis isolated in the West-Siberian Region.