Vol 44, No 4 (2018)

Over the past decade, tools of omics technologies have generated a large amount of data in various repositories, which are of interest for meta-analysis today. Now, researchers in the field of proteomics and peptidomics focus not on sequencing, but on functions performed by molecules and metabolic interactions, in which the proteins or peptides participate. As a result of a single LC-MS/MS analysis, several thousand unique peptides can be identified, each of which may be bioactive. A classic technique for determining the peptide function is a direct experiment. Bioinformatics approaches as a preliminary analysis of potential biological functions are an important step and are able to significantly reduce time and cost of experimental verification. This article provides an overview of computational methods for predicting biological functions of peptides. Approaches based on machine learning, which are the most popular today, algorithms using structural, evolutionary, or statistical patterns, as well as methods based on molecular docking, are considered. Databases of bioactive peptides are reported, providing information necessary to construct new algorithms for predicting biological functions. Attention is paid to the characteristics of peptides, on the basis of which it is possible to draw conclusions about their bioactivity. In addition, the report provides a list of online services that may be used by researchers to analyze potential activities of peptides with which they work.

Alginate lyases catalyze degradation of alginic acids and their salts, alginates, which are one of the main components of brown algae cell walls and comprise up to 40% algae’s dry weight. Alginates are interesting due to their high biological activity, particularly the ability of charged groups to bind tightly to oppositecharged protein amino acid residues, and chelating and jelling properties in presence of bivalent metal cations. Alginate lyases can digest substrates by β-elimination. They can be classified by the type of cleaved bonds. For today, more than 50000 amino acid sequences are referred to alginate lyases, 47000 of them belonging to bacterial genomes. Alginate lyases are one of the most common tools for degrading biofilms. Alginate digestion products display antitumor, anti-inflammatory, and antioxidant properties.

Immonium ions and immonium-related ions commonly appear in the mass spectra of peptide precursor ions. An overall understanding of the variation of the abundance of these ions is beneficial for the identification of unknown peptides. Here, four peptides from mass spectrometry (MS) of sucrose phosphorylase were selected as precursor ions, and the frequency of immonium ions and immonium-related ions in a dataset containing 130 MS/MS spectra were examined. Immonium ions and immonium-related ions were mainly produced from the further fragmentation of a-, b-, and y-ions. At the optimal collision energy (CE), the immonium ions of leucine at m/z 86, isoleucine at m/z 86, glutamine at m/z 101, arginine at m/z 129, tryptophan at m/z 159, proline at m/z 70, valine at m/z 72, glutamic acid at m/z 102, phenylalanine at m/z 120, and tyrosine at m/z 136, as well as the immonium-related ions of methionine at m/z 61, lysine at m/z 84, glutamine at m/z 84, and tyrosine at m/z 91 existed in higher abundance and had higher confidence level, therefore suggesting the presence of corresponding amino acid residues well. However, the immonium ions of serine at m/z 60 and threonine at m/z 74, although showing lower abundance, were stable at high CE and had higher confidence level, indicating the presence of serine and threonine residues, respectively. The immonium ion of asparagine at m/z 87 also was a good indicator for the existence of asparagine residue.

To improve the diagnostics of pseudotuberculosis by ELISA, a genetically engineered hybrid bifunctional protein (CmAP/OmpF) was obtained based on the pore-forming protein of the outer membrane of human pathogenic bacterium Yersinia pseudotuberculosis (OmpF) and the highly active alkaline phosphatase of marine bacterium Cobetia amphilecti KMM 296 (CmAP). The OmpF module in the fusion protein retains the properties of the diagnostic antigen of the pseudotuberculosis pathogen, and the CmAP module is an enzyme label for detecting porin complexes with specific antibodies. The CmAP/OmpF activity was successfully confirmed by the binding of antibodies to OmpF porin in murine antisera, as well as in the sera of patients with pseudotuberculosis. The use of hybrid complex CmAP/OmpF for the diagnostics of pseudotuberculosis will eliminate the use of enzyme-labeled secondary antibodies, usually necessary for detecting specific antibodies in the blood serum of patients, and thus simplify the procedure and shorten the analysis time.

The article draws the attention of chemists to the literature data reporting the discovery of new targets for growth inhibition of Mycobacterium tuberculosis, namely, diterpene cyclase (Rv3377c) and tuberculosinol phosphatase (Rv3378c), which produce diterpenoids of tuberculosinols in the cell membrane of M. tuberculosis, and these diterpenoids ensure the pathogenicity and the virulence of M. tuberculosis. For the first time, by the example of diterpenoid of isosteviol, its binuclear derivatives, triterpenoid betulinic, oleanolic, and ursolic acids, it has been shown by the molecular docking method that the antitubercular activity of natural terpenoids is caused by their ability to bind to the active site of tuberculosinol phosphatase (Rv3378c) of M. tuberculosis. It is suggested that natural and semisynthetic terpenoids represent a promising platform for design of a new generation of antitubercular agents that affect this enzyme.

2-Hetaryl- and 2-acyl-9,10,12,13-tetramethoxy-3-methyl-4,5-dihydro-3H-phenanthro[1,2-d]-azepines have been synthesized from 8,9,11,12-tetramethoxy-2-methyl-3,4-dihydronaphtho[2,1-f]isoquinolinium perchlorate by pyridine-azepine recyclization. The resulting compounds have revealed a pronounced antibacterial activity against Staphylococcus aureus (strain P-209) and Escherichia coli (field strain 078). Some of these compounds have a moderate fungistatic activity against Peniciliium italicum fungi. Two compounds have shown a certain activity in relation to the Colpoda steinii protozoa.

Recent studies revealed that about 80% of the eukaryotic genome is biochemically active; it produces not solely mRNA but also a large number of noncoding RNAs (ncRNAs). Thus, a large fraction of “ribonome” (the total cellular complement of RNAs and their regulatory factors) of the cell consists of a variety of noncoding RNAs (ncRNAs), while mRNAs occupy only a small part of it. It is well known that long noncoding RNAs (lncRNAs) are involved in the regulation of protein-coding gene expression by altering the chromatin structure, transcription regulation, and pre-mRNA splicing. MicroRNAs and small interfering RNAs trigger the RNA interference mechanism involved in the transcriptional and post-transcriptional regulation of gene expression. However, our knowledge of the role of noncoding part of the genome in proteome diversification and plasticity is scarce. In this mini-review, we discuss new data obtained over the past few years, which change our view of the role of noncoding part of the genome in the cell proteome formation.

Using atomic force microscopy (AFM), the formation of nanosized silica structures on a substrate, catalyzed by the recombinant silicatein LoSilA1 from the marine sponge Latrunculia oparinae, was studied. It has been shown that at room temperature under neutral conditions, recombinant silicatein immobilized on a mica substrate causes the rapid polycondensation of tetrakis(2-hydroxyethyl) orthosilicate to form spherical particles. Thus, immobilized silicatein may acts as a catalyst in the preparation of ordered silica structures on various surfaces.

Page 37, left column, last sentence should read:

The concentration of the recombinant PT1 preparation, which causes 50% inhibition of the currents mediated by P2X3 receptors in the rate-sensor neurons (IC₅₀), was 12 ± 2 nM at Hill coefficient (n_H) 1.1 ± 0.2 (for RO-85 IC₅₀ relative to recombinant rat receptors was ~31 nM) [15].

Section REFRENCES, add reference:

15. Esipov, R.S., Stepanenko, V.N., Vasilevskii, A.A., Korol’kova, Yu.V., and Grishin, E.V., Method for obtaining recombinant analgesic peptide, RF Patent no. 2571942, Byul. Izobret., 2015, no. 36.

Add section ACKNOWLEDGMENTS:

The works comparing recombinant and natural PT1 were carried out by A.A. Vasilevskii (Institute of Bioorganic Chemistry, Russian Academy of Sciences), G.A. Savchenko and O.A. Kryshtal’ (Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine).

This work was supported by the State Contract dated June 14, 2012, No. 16.N08.12.1023 “Preclinical Studies on Polypeptide Analgesic Selectively Interacting with Purinergic Receptors”.

The original article can be found online at DOI: 10.1134/S1068162018010065.