KUROCHKIN Igor

Insulin-Degrading Enzyme in the Fight against Alzheimer's Disease

Published date : 29 Nov 2017

After decades of research and clinical trials there is still no cure for Alzheimer's disease (AD). While impaired clearance of amyloid beta (Aβ) peptides is considered as one of the major causes of AD, it was recently complemented by a potential role of other toxic amyloidogenic species. Insulin-degrading enzyme (IDE) is the proteolytic culprit of various β-forming peptides, both extracellular and intracellular.

type
Journal Paper
journal
Trends in Pharmacological Sciences, 10 Nov 2017, doi : 10.1016/j.tips.2017.10.008
Impact Factor
12.797

A novel community driven software for functional enrichment analysis of extracellular vesicles data

Published date : 26 May 2017

Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture “what the community needs in a tool”. Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes.

type
Journal Paper
journal
Journal of Extracellular Vesicles 2017, Vol. 6, 2017, Issue 1, doi: 10.1080/20013078.2017.1321455
Impact Factor
4.259

Genome-wide analysis of mRNAs associated with mouse peroxisomes

Published date : 22 Dec 2016

Background: RNA is often targeted to be localized to the specific subcellular compartments. Specific localization of mRNA is believed to be an important mechanism for targeting their protein products to the locations, where their function is required.

type
Journal Paper
journal
BMC Genomics 2016, 17 (Supp 13), 1028, doi: 10.1186/s12864-016-3330-x
Impact Factor
3.869

Towards allosterically increased catalytic activity of insulin degrading enzyme (IDE) against amyloid peptides

Published date : 03 Dec 2016

Physiological role of insulin degrading enzyme (IDE) in the intracytosolic clearance of amyloid beta (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial in the treatment of the late onset Alzhimer’s disease (AD). The major challenge towards this goal is to increase specific catalytic activity of IDE against the Aβ-substrate.

type
Journal Paper
journal
Biochemistry 2016, doi: 10.1021/acs.biochem.6b00783
Impact Factor
2.87

Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding

Published date : 30 Jun 2015

Aminoacyl-tRNA synthetases (ARSs) play an essential role in the protein synthesis by catalyzing an attachment of their cognate amino acids to tRNAs. Unlike their prokaryotic counterparts, ARSs in higher eukaryotes form a multiaminoacyl-tRNA synthetase complex (MARS), consisting of the subset of ARS polypeptides and three auxiliary proteins. The intriguing feature of MARS complex is the presence of only nine out of twenty ARSs, specific for Arg, Asp, Gln, Glu, Ile, Leu, Lys, Met, and Pro, regardless of the organism, cell, or tissue types.

type
Journal Paper
journal
Protein Science 24 (2015) Pg. 1475-1485, doi: 10.1002/pro.2735

Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

Published date : 29 May 2015

Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription characterized by pausing of RNA polymerase II (PolII) in both directions, at specific promoters, within 30 minutes of the OS response.

type
Journal Paper
journal
Scientific Reports 5,Article no: 9737, 2015, doi: 10.1038/srep09737

Long noncoding RNAs: a potential novel class of cancer biomarkers

Published date : 23 Apr 2015

Long noncoding RNAs (lncRNAs) are a novel class of RNA molecules defined as transcripts longer than 200 nucleotides that lack protein coding potential. They constitute a major, but still poorly characterized part of human transcriptome, however, evidence is growing that they are important regulatory molecules involved in various cellular processes. It is becoming increasingly clear that many lncRNAs are deregulated in cancer and some of them can be important drivers of malignant transformation.

type
Journal Paper
journal
Frontiers in Genetics, April 2015, Vol. 6, Article 145, doi:10.3389/fgene.2015.00145

Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles

Published date : 22 Dec 2014

Secreted membrane-enclosed vesicles, collectively called extracellular vesicles (EVs), which include exosomes, ectosomes, microvesicles, microparticles, apoptotic bodies and other EV subsets, encompass a very rapidly growing scientific field in biology and medicine. Importantly, it is currently technically challenging to obtain a totally pure EV fraction free from non-vesicular components for functional studies, and therefore there is a need to establish guidelines for analyses of these vesicles and reporting of scientific studies on EV biology.

type
Journal Paper
journal
Journal of Extracellular Vesicles 2014, 3: 26913 - http://dx.doi.org/10.3402/jev.v3.26913

HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

Published date : 08 Dec 2014

Background
Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies.

Results

type
Journal Paper
journal
BMC Genomics 2014, 15(Suppl 9):S7 doi:10.1186/1471-2164-15-S9-S7
Impact Factor
4.04

Understanding the Functions of Peroxisomal Proteins: The Peroxisomal Proteome, Peroxisomal Import, Proteases and Other Protein Families and Their Network Organization: What Has Computational Biology Contributed?

Published date : 22 May 2014

Computational studies based on high-throughput experimental datasets, some of which were even not generated in the context of peroxisome research, have considerably shaped the understanding of the peroxisomal proteome. Most importantly, this research revealed to a considerable extent how the total peroxisomal proteome is composed and what is its network and pathway structure. Computational prediction tools have been instrumental for finding proteins that are imported into peroxisomes via canonical import mechanisms.

type
Book/Book Chapter
journal
Molecular Machines Involved in Peroxisome Biogenesis and Maintenance, 2014, PG 187-232, doi: 10.1007/978-3-7091-1788-0_9