Biomeditsinskaya khimiya最新文献

Registration of activity of a single molecule of horseradish peroxidase using a detector based on a solid-state nanopore. 使用基于固态纳米孔的检测器登记单分子辣根过氧化物酶的活性。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005349

Yu D Ivanov, A N Ableev, A V Vinogradova, E D Nevedrova, I D Shumov, V S Ziborov, A F Kozlov, I A Ivanova, N V Vaulin, D V Lebedev, A S Bukatin, I S Mukhin, E A Ponomarenko, A I Archakov

{"title":"Registration of activity of a single molecule of horseradish peroxidase using a detector based on a solid-state nanopore.","authors":"Yu D Ivanov, A N Ableev, A V Vinogradova, E D Nevedrova, I D Shumov, V S Ziborov, A F Kozlov, I A Ivanova, N V Vaulin, D V Lebedev, A S Bukatin, I S Mukhin, E A Ponomarenko, A I Archakov","doi":"10.18097/PBMC20247005349","DOIUrl":"https://doi.org/10.18097/PBMC20247005349","url":null,"abstract":"This work demonstrates the use of a solid-state nanopore detector to monitor the activity of a single molecule of a model enzyme, horseradish peroxidase (HRP). This detector includes a measuring cell, which is divided into cis- and trans- chambers by a silicon nitride chip (SiN structure) with a nanopore of 5 nm in diameter. To entrap a single HRP molecule into the nanopore, an electrode had been placed into the cis-chamber; HRP solution was added into this chamber after application of a negative voltage. The reaction of the HRP substrate, 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), oxidation by the enzyme molecule was performed in the presence of hydrogen peroxide. During this reaction, the functioning of a single HRP molecule, entrapped in the nanopore, was monitored by recording the time dependence of the ion current flowing through the nanopore. The approach proposed in our work is applicable for further studies of functioning of various enzymes at the level of single molecules, and this is an important step in the development of single-molecule enzymology.","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":"70 5","pages":"349-355"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The human proteome size as a technological development function. 作为技术发展功能的人类蛋白质组规模。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005364

E V Sarygina, A S Kozlova, E A Ponomarenko, E V Ilgisonis

{"title":"The human proteome size as a technological development function.","authors":"E V Sarygina, A S Kozlova, E A Ponomarenko, E V Ilgisonis","doi":"10.18097/PBMC20247005364","DOIUrl":"https://doi.org/10.18097/PBMC20247005364","url":null,"abstract":"Changes in information on the number of human proteoforms, post-translational modification (PTM) events, alternative splicing (AS), single-amino acid polymorphisms (SAP) associated with protein-coding genes in the neXtProt database have been retrospectively analyzed. In 2016, our group proposed three mathematical models for predicting the number of different proteins (proteoforms) in the human proteome. Eight years later, we compared the original data of the information resources and their contribution to the prediction results, correlating the differences with new approaches to experimental and bioinformatic analysis of protein modifications. The aim of this work is to update information on the status of records in the databases of identified proteoforms since 2016, as well as to identify trends in changes in the quantities of these records. According to various information models, modern experimental methods may identify from 5 to 125 million different proteoforms: the proteins formed due to alternative splicing, the implementation of single nucleotide polymorphisms at the proteomic level, and post-translational modifications in various combinations. This result reflects an increase in the size of the human proteome by 20 or more times over the past 8 years.","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":"70 5","pages":"364-373"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detection of low-copy proteins in proteomic studies: issues and solutions. 蛋白质组研究中低拷贝蛋白质的检测：问题与解决方案。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005342

A I Archakov, N E Vavilov, V G Zgoda

{"title":"Detection of low-copy proteins in proteomic studies: issues and solutions.","authors":"A I Archakov, N E Vavilov, V G Zgoda","doi":"10.18097/PBMC20247005342","DOIUrl":"https://doi.org/10.18097/PBMC20247005342","url":null,"abstract":"Detection of low-copy proteins in complex biological samples is one of the most important issues of modern proteomics. The main reason for inefficient detection of low protein concentrations is the insufficient sensitivity of mass spectrometric detectors and the high dynamic range of protein concentrations. In this study we have investigated the possibilities and limitations of a targeted mass spectrometric analysis using the reconstructed system of standard proteins UPS1 (Universal Proteomic Standard 1) as an example. The study has shown that the sensitivity of the method is affected by the concentration of target proteins of the UPS1 system, as well as by a high level of biological noise modelled by proteins of whole E. coli cell lysate. The limitations of the method have been overcome by concentrating and pre-fractionating the sample peptides in a reversed phase chromatographic system under alkaline elution conditions. Proteomic analysis of the biological sample (proteins of the human hepatocellular carcinoma cell line HepG2 encoded by genes of human chromosome 18) showed an increase in the sensitivity of the method as compared to the standard targeted mass spectrometric analysis. This culminated in registration of 94 proteins encoded by genes located on human chromosome18.","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":"70 5","pages":"342-348"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nanowire-based biosensors for solving biomedical problems. 解决生物医学问题的纳米线生物传感器。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005304

K V Goldaeva, T O Pleshakova, Yu D Ivanov

引用次数: 0

In silico and in cellulo approaches for functional annotation of human protein splice variants. 人类蛋白质剪接变体功能注释的硅学和细胞学方法。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005315

O I Kiseleva, V A Arzumanian, I Yu Kurbatov, E V Poverennaya

{"title":"In silico and in cellulo approaches for functional annotation of human protein splice variants.","authors":"O I Kiseleva, V A Arzumanian, I Yu Kurbatov, E V Poverennaya","doi":"10.18097/PBMC20247005315","DOIUrl":"https://doi.org/10.18097/PBMC20247005315","url":null,"abstract":"The elegance of pre-mRNA splicing mechanisms continues to interest scientists even after over a half century, since the discovery of the fact that coding regions in genes are interrupted by non-coding sequences. The vast majority of human genes have several mRNA variants, coding structurally and functionally different protein isoforms in a tissue-specific manner and with a linkage to specific developmental stages of the organism. Alteration of splicing patterns shifts the balance of functionally distinct proteins in living systems, distorts normal molecular pathways, and may trigger the onset and progression of various pathologies. Over the past two decades, numerous studies have been conducted in various life sciences disciplines to deepen our understanding of splicing mechanisms and the extent of their impact on the functioning of living systems. This review aims to summarize experimental and computational approaches used to elucidate the functions of splice variants of a single gene based on our experience accumulated in the laboratory of interactomics of proteoforms at the Institute of Biomedical Chemistry (IBMC) and best global practices.","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":"70 5","pages":"315-328"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biosensing platforms for DNA diagnostics based on CRISPR/Cas nucleases: towards the detection of nucleic acids at the level of single molecules in non-laboratory settings. 基于 CRISPR/Cas 核酸酶的 DNA 诊断生物传感平台：在非实验室环境中实现单分子水平的核酸检测。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005287

S A Khmeleva, K G Ptitsyn, L K Kurbatov, O S Timoshenko, E V Suprun, S P Radko, A V Lisitsa

{"title":"Biosensing platforms for DNA diagnostics based on CRISPR/Cas nucleases: towards the detection of nucleic acids at the level of single molecules in non-laboratory settings.","authors":"S A Khmeleva, K G Ptitsyn, L K Kurbatov, O S Timoshenko, E V Suprun, S P Radko, A V Lisitsa","doi":"10.18097/PBMC20247005287","DOIUrl":"https://doi.org/10.18097/PBMC20247005287","url":null,"abstract":"The use of CRISPR/Cas nucleases for the development of DNA diagnostic systems in out-of-laboratory conditions (point-of-need testing, PONT) has demonstrated rapid growth in the last few years, starting with the appearance in 2017-2018 of the first diagnostic platforms known as DETECTR and SHERLOCK. The platforms are based on a combination of methods of nucleic acid isothermal amplification with selective CRISPR/Cas detection of target amplicons. This significantly improves the sensitivity and specificity of PONT, making them comparable with or even superior to the sensitivity and specificity of polymerase chain reaction, considered as the \"gold standard\" of DNA diagnostics. The review considers modern approaches to the coupling of CRISPR/Cas detection using Cas9, Cas12a, Cas12b, Cas13a, Cas14, and Cas3 nucleases to various methods of nucleic acid isothermal amplification, with an emphasis on works in which sensitivity at the level of single molecules (attomolar and subattomolar concentrations of the target) is achieved. The properties of CRISPR/Cas nucleases used for targeted DNA diagnostics and the features of methods of nucleic acid isothermal amplification are briefly considered in the context of the development of diagnostic biosensing platforms. Special attention is paid to the most promising directions for the development of DNA diagnostics using CRISPR/Cas nuclease.","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":"70 5","pages":"287-303"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteome of plasma extracellular vesicles as a source of colorectal cancer biomarkers. 作为结直肠癌生物标志物来源的血浆细胞外囊泡蛋白质组。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005356

N A Soloveva, S E Novikova, T E Farafonova, O V Tikhonova, V G Zgoda, A I Archakov

{"title":"Proteome of plasma extracellular vesicles as a source of colorectal cancer biomarkers.","authors":"N A Soloveva, S E Novikova, T E Farafonova, O V Tikhonova, V G Zgoda, A I Archakov","doi":"10.18097/PBMC20247005356","DOIUrl":"https://doi.org/10.18097/PBMC20247005356","url":null,"abstract":"The search for minimally invasive methods for diagnostics of colorectal cancer (CRC) is the most important task for early diagnostics of the disease and subsequent successful treatment. Human plasma represents the main type of biological material used in the clinical practice; however, the complex dynamic range of substances circulating in it complicates determination of CRC protein markers by the mass spectrometric (MS) method. Studying the proteome of extracellular vesicles (EVs) isolated from human plasma represents an attractive approach for the discovery of tissue-secreted CRC markers. We performed shotgun mass spectrometry analysis of EV samples obtained from plasma of CRC patients and healthy volunteers. This MS analysis resulted in identification of 370 proteins (which were registered by at least two peptides). Stable isotope-free relative quantitation identified 55 proteins with altered abundance in EV samples obtained from plasma samples of CRC patients as compared to healthy controls. Among the EV proteins isolated from blood plasma we found components involved in cell adhesion and the VEGFA-VEGFR2 signaling pathway (TLN1, HSPA8, VCL, MYH9, and others), as well as proteins expressed predominantly by gastrointestinal tissues (polymeric immunoglobulin receptor, PIGR). The data obtained using the shotgun proteomic profiling may be added to the panel for targeted MS analysis of EV-associated protein markers, previously developed using CRC cell models.","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":"70 5","pages":"356-363"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Clinical metabolomics: current state and prospects in Russia. 临床代谢组学：俄罗斯的现状与前景。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005329

P G Lokhov, E E Balashova, O P Trifonova, D L Maslov, A P Lokhov, E A Ponomarenko, A V Lisitsa, M V Ugrumov, I S Stilidi, N E Kushlinskii, D B Nikityuk, V A Tutelyan, M V Shestakova, I I Dedov, A I Archakov

{"title":"Clinical metabolomics: current state and prospects in Russia.","authors":"P G Lokhov, E E Balashova, O P Trifonova, D L Maslov, A P Lokhov, E A Ponomarenko, A V Lisitsa, M V Ugrumov, I S Stilidi, N E Kushlinskii, D B Nikityuk, V A Tutelyan, M V Shestakova, I I Dedov, A I Archakov","doi":"10.18097/PBMC20247005329","DOIUrl":"https://doi.org/10.18097/PBMC20247005329","url":null,"abstract":"Using analytical technologies it is possible now to measure the entire diversity of molecules even in a small amount of biological samples. Metabolomic technologies simultaneously analyze thousands of low-molecular substances in a single drop of blood. Such analytical performance opens new possibilities for clinical laboratory diagnostics, still relying on the measurement of only a limited number of clinically significant substances. However, there are objective difficulties hampering introduction of metabolomics into clinical practice. The Institute of Biomedical Chemistry (IBMC), consolidating the efforts of leading scientific and medical organizations, has achieved success in this area by developing a clinical blood metabogram (CBM). CBM opens opportunities to obtain overview on the state of the body with the detailed individual metabolic characteristics of the patient. A number of scientific studies have shown that the CBM is an effective tool for monitoring the state of the body, and based on the CBM patterns (signatures), it is possible to diagnose and monitor the treatment of many diseases. Today, the CBM creation determines the current state and prospects of clinical metabolomics in Russia. This article, dedicated to the 80th anniversary of IBMC, is a review of these achievements focused on a discussion of their implementation in clinical practice.","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":"70 5","pages":"329-341"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fundamentals of protein chemistry at the Institute of Biomedical Chemistry. 生物医学化学研究所的蛋白质化学基础。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005263

A V Kolesnichenko, T O Pleshakova

引用次数: 0

AFM-fishing technology for protein detection in solutions. 用于检测溶液中蛋白质的原子力显微镜捕鱼技术。

Biomeditsinskaya khimiya Pub Date : 2024-09-01 DOI: 10.18097/PBMC20247005273

T O Pleshakova, M O Ershova, A A Valueva, I A Ivanova, Yu D Ivanov, A I Archakov

引用次数: 0