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Article ; Online: Modulation of extrinsic apoptotic pathway by intracellular glycosylation.

Seyrek, Kamil / Ivanisenko, Nikita V / König, Corinna / Lavrik, Inna N

2024

Abstract: The importance of post-translational modifications (PTMs), particularly O-GlcNAcylation, of cytoplasmic proteins in apoptosis has been neglected for quite a while. Modification of cytoplasmic proteins by a single N-acetylglucosamine sugar is a dynamic ... ...

Abstract	The importance of post-translational modifications (PTMs), particularly O-GlcNAcylation, of cytoplasmic proteins in apoptosis has been neglected for quite a while. Modification of cytoplasmic proteins by a single N-acetylglucosamine sugar is a dynamic and reversible PTM exhibiting properties more like phosphorylation than classical O- and N-linked glycosylation. Due to the sparse information existing, we have only limited understanding of how GlcNAcylation affects cell death. Deciphering the role of GlcNAcylation in cell fate may provide further understanding of cell fate decisions. This review focus on the modulation of extrinsic apoptotic pathway via GlcNAcylation carried out by O-GlcNAc transferase (OGT) or by other bacterial effector proteins.
Language	English
Publishing date	2024-02-08
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	30122-x
ISSN	1879-3088 ; 0962-8924
ISSN (online)	1879-3088
ISSN	0962-8924
DOI	10.1016/j.tcb.2024.01.003
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Article ; Online: Learning the changes of barnase mutants thermostability from structural fluctuations obtained using anisotropic network modeling.

Alemasov, Nikolay A / Ivanisenko, Nikita V / Ivanisenko, Vladimir A

Journal of molecular graphics & modelling

2020 Volume 97, Page(s) 107572

Abstract: In biotechnology applications, rational design of new proteins with improved physico-chemical properties includes a number of important tasks. One of the greatest practical and fundamental challenges is the design of highly thermostable protein enzymes ... ...

Abstract	In biotechnology applications, rational design of new proteins with improved physico-chemical properties includes a number of important tasks. One of the greatest practical and fundamental challenges is the design of highly thermostable protein enzymes that maintain catalytic activity at high temperatures. This problem may be solved by introducing mutations into the wild-type enzyme protein. In this work, to predict the impact of such mutations in barnase protein we applied the anisotropic network modeling approach, revealing atomic fluctuations in structural regions that are changed in mutants compared to the wild-type protein. A regression model was constructed based on these structural features that can allow one to predict the thermal stability of new barnase mutants. Moreover, the analysis of regression model provides a mechanistic explanation of how the structural features can contribute to the thermal stability of barnase mutants.
MeSH term(s)	Bacterial Proteins/genetics ; Enzyme Stability ; Hot Temperature ; Mutation ; Ribonucleases/genetics
Chemical Substances	Bacterial Proteins ; Ribonucleases (EC 3.1.-) ; Bacillus amyloliquefaciens ribonuclease (EC 3.1.27.-)
Language	English
Publishing date	2020-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2020.107572
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Article ; Online: Computer analysis of the relation between hydrogen bond stability in SOD1 mutants and the survival time of amyotrophic lateral sclerosis patients.

Alemasov, Nikolay A / Timofeev, Vladimir S / Ivanisenko, Nikita V / Kolchanov, Nikolay A / Ivanisenko, Vladimir A

Journal of molecular graphics & modelling

2021 Volume 110, Page(s) 108026

Abstract: Background and objective: Mutations in the SOD1 protein can lead to the death of motor neurons, which, in turn, causes an incurable disease called amyotrophic lateral sclerosis (ALS). At the same time, the mechanism of the onset and development of this ... ...

Abstract	Background and objective: Mutations in the SOD1 protein can lead to the death of motor neurons, which, in turn, causes an incurable disease called amyotrophic lateral sclerosis (ALS). At the same time, the mechanism of the onset and development of this disease is not fully understood and is often contradictory. Methods: Accelerated Molecular Dynamics as implemented in the OpenMM library, principal component analysis, regression analysis, random forest method. Results: The stability of hydrogen bonds in 72 mutants of the SOD1 protein was calculated. Principal component analysis was carried out. Based on ten principal components acting as predictors, a multiple linear regression model was constructed. An analysis of the correlation of these ten principal components with the initial values of the stability of hydrogen bonds made it possible to characterize the contribution of known structurally and functionally important sites in the SOD1 to the scatter of ALS patients' survival time. Conclusion: Such an analysis made it possible to put forward hypotheses about the relationship between the stabilizing and destabilizing effects of mutations in different structurally and functionally important regions of SOD1 with the patients's survival time.
MeSH term(s)	Amyotrophic Lateral Sclerosis/genetics ; Computers ; Humans ; Hydrogen Bonding ; Mutation ; Protein Conformation ; Superoxide Dismutase/genetics ; Superoxide Dismutase-1/genetics
Chemical Substances	SOD1 protein, human ; Superoxide Dismutase (EC 1.15.1.1) ; Superoxide Dismutase-1 (EC 1.15.1.1)
Language	English
Publishing date	2021-10-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2021.108026
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Article ; Online: PROSTATA: a framework for protein stability assessment using transformers.

Umerenkov, Dmitriy / Nikolaev, Fedor / Shashkova, Tatiana I / Strashnov, Pavel V / Sindeeva, Maria / Shevtsov, Andrey / Ivanisenko, Nikita V / Kardymon, Olga L

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 11

Abstract: Motivation: Accurate prediction of change in protein stability due to point mutations is an attractive goal that remains unachieved. Despite the high interest in this area, little consideration has been given to the transformer architecture, which is ... ...

Abstract	Motivation: Accurate prediction of change in protein stability due to point mutations is an attractive goal that remains unachieved. Despite the high interest in this area, little consideration has been given to the transformer architecture, which is dominant in many fields of machine learning. Results: In this work, we introduce PROSTATA, a predictive model built in a knowledge-transfer fashion on a new curated dataset. PROSTATA demonstrates advantage over existing solutions based on neural networks. We show that the large improvement margin is due to both the architecture of the model and the quality of the new training dataset. This work opens up opportunities to develop new lightweight and accurate models for protein stability assessment. Availability and implementation: PROSTATA is available at https://github.com/AIRI-Institute/PROSTATA and https://prostata.airi.net.
MeSH term(s)	Machine Learning ; Neural Networks, Computer ; Point Mutation ; Protein Stability
Language	English
Publishing date	2023-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad671
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Article ; Online: Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection.

Antropova, Evgeniya A / Khlebodarova, Tamara M / Demenkov, Pavel S / Volianskaia, Anastasiia R / Venzel, Artur S / Ivanisenko, Nikita V / Gavrilenko, Alexandr D / Ivanisenko, Timofey V / Adamovskaya, Anna V / Revva, Polina M / Kolchanov, Nikolay A / Lavrik, Inna N / Ivanisenko, Vladimir A

Journal of integrative bioinformatics

2023 Volume 20, Issue 3

Abstract: Hepatocellular carcinoma (HCC) has been associated with hepatitis C viral (HCV) infection as a potential risk factor. Nonetheless, the precise genetic regulatory mechanisms triggered by the virus, leading to virus-induced hepatocarcinogenesis, remain ... ...

Abstract	Hepatocellular carcinoma (HCC) has been associated with hepatitis C viral (HCV) infection as a potential risk factor. Nonetheless, the precise genetic regulatory mechanisms triggered by the virus, leading to virus-induced hepatocarcinogenesis, remain unclear. We hypothesized that HCV proteins might modulate the activity of aberrantly methylated HCC genes through regulatory pathways. Virus-host regulatory pathways, interactions between proteins, gene expression, transport, and stability regulation, were reconstructed using the ANDSystem. Gene expression regulation was statistically significant. Gene network analysis identified four out of 70 HCC marker genes whose expression regulation by viral proteins may be associated with HCC:
MeSH term(s)	Humans ; Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/metabolism ; Carcinoma, Hepatocellular/pathology ; Liver Neoplasms/genetics ; Liver Neoplasms/metabolism ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Hepacivirus/genetics ; Hepacivirus/metabolism ; Hepatitis C/complications ; Hepatitis C/genetics ; Virus Diseases ; Histone-Lysine N-Methyltransferase
Chemical Substances	Viral Nonstructural Proteins ; SMYD3 protein, human (EC 2.1.1.43) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43)
Language	English
Publishing date	2023-11-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2147212-9
ISSN	1613-4516 ; 1613-4516
ISSN (online)	1613-4516
ISSN	1613-4516
DOI	10.1515/jib-2023-0013
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Article ; Online: Correction to: selected articles from Belyaev Conference 2017: structural biology.

Alemasov, Nikolay A / Ivanisenko, Nikita V / Ramachandran, Srinivasan / Ivanisenko, Vladimir A

BMC structural biology

2018 Volume 18, Issue 1, Page(s) 3

Abstract: After publication of the article [1], it has been brought to our attention that there is a discrepancy between the publication date on the pdf and online formats. The date on the pdf is 6th February 2018 and online is 5th February 2018. The correct ... ...

Abstract	After publication of the article [1], it has been brought to our attention that there is a discrepancy between the publication date on the pdf and online formats. The date on the pdf is 6th February 2018 and online is 5th February 2018. The correct publication date is the one on the pdf, 6th February 2018.
Language	English
Publishing date	2018-03-21
Publishing country	England
Document type	Journal Article ; Published Erratum
ZDB-ID	2050440-8
ISSN	1472-6807 ; 1472-6807
ISSN (online)	1472-6807
ISSN	1472-6807
DOI	10.1186/s12900-018-0082-7
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Article ; Online: Pharmacological targeting of c-FLIP

König, Corinna / Hillert-Richter, Laura K / Ivanisenko, Nikita V / Ivanisenko, Vladimir A / Lavrik, Inna N

Scientific reports

2020 Volume 10, Issue 1, Page(s) 20823

Abstract: The development of efficient combinatorial treatments is one of the key tasks in modern anti-cancer therapies. An apoptotic signal can either be induced by activation of death receptors (DR) (extrinsic pathway) or via the mitochondria (intrinsic pathway). ...

Abstract	The development of efficient combinatorial treatments is one of the key tasks in modern anti-cancer therapies. An apoptotic signal can either be induced by activation of death receptors (DR) (extrinsic pathway) or via the mitochondria (intrinsic pathway). Cancer cells are characterized by deregulation of both pathways. Procaspase-8 activation in extrinsic apoptosis is controlled by c-FLIP proteins. We have recently reported the small molecules FLIPinB/FLIPinBγ targeting c-FLIP
MeSH term(s)	Aniline Compounds/pharmacology ; Antineoplastic Combined Chemotherapy Protocols/pharmacology ; Apoptosis/drug effects ; CASP8 and FADD-Like Apoptosis Regulating Protein/antagonists & inhibitors ; Caspase 8/metabolism ; Cell Survival/drug effects ; Death Domain Receptor Signaling Adaptor Proteins/metabolism ; Drug Delivery Systems ; Fas Ligand Protein/pharmacology ; HeLa Cells ; Humans ; Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors ; Sulfonamides/pharmacology
Chemical Substances	Aniline Compounds ; BCL2 protein, human ; CASP8 and FADD-Like Apoptosis Regulating Protein ; CFLAR protein, human ; Death Domain Receptor Signaling Adaptor Proteins ; Fas Ligand Protein ; Proto-Oncogene Proteins c-bcl-2 ; Sulfonamides ; CASP8 protein, human (EC 3.4.22.-) ; Caspase 8 (EC 3.4.22.-) ; navitoclax (XKJ5VVK2WD)
Language	English
Publishing date	2020-11-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-76079-1
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Article: The role of death domain proteins in host response upon SARS-CoV-2 infection: modulation of programmed cell death and translational applications.

Ivanisenko, Nikita V / Seyrek, Kamil / Kolchanov, Nikolay A / Ivanisenko, Vladimir A / Lavrik, Inna N

Cell death discovery

2020 Volume 6, Issue 1, Page(s) 101

Abstract: The current pandemic of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) poses a significant global public health threat. While urgent regulatory measures in control of the rapid spread of this virus are essential, scientists around the ... ...

Abstract	The current pandemic of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) poses a significant global public health threat. While urgent regulatory measures in control of the rapid spread of this virus are essential, scientists around the world have quickly engaged in this battle by studying the molecular mechanisms and searching for effective therapeutic strategies against this deadly disease. At present, the exact mechanisms of programmed cell death upon SARS-CoV-2 infection remain to be elucidated, though there is increasing evidence suggesting that cell death pathways play a key role in SARS-CoV-2 infection. There are several types of programmed cell death, including apoptosis, pyroptosis, and necroptosis. These distinct programs are largely controlled by the proteins of the death domain (DD) superfamily, which play an important role in viral pathogenesis and host antiviral response. Many viruses have acquired the capability to subvert the program of cell death and evade the host immune response, mainly by virally encoded gene products that control cell signaling networks. In this mini-review, we will focus on SARS-CoV-2, and discuss the implication of restraining the DD-mediated signaling network to potentially suppress viral replication and reduce tissue damage.
Keywords	covid19
Language	English
Publishing date	2020-10-10
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2058-7716
ISSN	2058-7716
DOI	10.1038/s41420-020-00331-w
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Article ; Online: Regression model for predicting pathogenic properties of SOD1 mutants based on the analysis of conformational stability and conservation of hydrogen bonds.

Alemasov, Nikolay A / Ivanisenko, Nikita V / Ivanisenko, Vladimir A

Journal of molecular graphics & modelling

2017 Volume 77, Page(s) 378–385

Abstract: Intracellular aggregation of proteins is thought to be involved in the aetiology of various neurodegenerative diseases. In particular, mutations in the SOD1 gene are linked to the familial form of amyotrophic lateral sclerosis (ALS). Recently, we ... ...

Abstract	Intracellular aggregation of proteins is thought to be involved in the aetiology of various neurodegenerative diseases. In particular, mutations in the SOD1 gene are linked to the familial form of amyotrophic lateral sclerosis (ALS). Recently, we developed a regression model for estimating the survival time of ALS patients carrying mutations in SOD1. This model was built based on an analysis of the stability of hydrogen bonds formed in SOD1 mutant proteins during a molecular dynamics (MD) simulation. In the present paper, the regression model was improved by taking into account a new hydrogen-bond property that reflects the conservation measure of a hydrogen bond in the space of protein conformational states. Conformational conservation of hydrogen bonds, being obtained with elastic network (EN) models, allowed us to find eight hydrogen bonds that might affect the pathogenic SOD1 mutants' properties in addition to the bonds that were found via MD in our previous work. The correlation coefficient between survival time of patients with ALS-linked mutations in SOD1 predicted within the improved model and that observed in the literature was 0.91. SOD1 amino acid residues forming these pathogenic hydrogen bonds are found in zinc-binding and electrostatic loops as well as at zinc-binding sites and are in contact with SOD1 aggregates, which implies that these regions are sensitive to perturbations from pathogenic mutations.
MeSH term(s)	Amyotrophic Lateral Sclerosis/drug therapy ; Amyotrophic Lateral Sclerosis/enzymology ; Binding Sites ; Humans ; Hydrogen Bonding/drug effects ; Molecular Dynamics Simulation ; Mutation ; Protein Aggregation, Pathological/drug therapy ; Protein Aggregation, Pathological/genetics ; Protein Conformation ; Superoxide Dismutase-1/antagonists & inhibitors ; Superoxide Dismutase-1/chemistry ; Superoxide Dismutase-1/genetics ; Zinc/chemistry
Chemical Substances	SOD1 protein, human ; Superoxide Dismutase-1 (EC 1.15.1.1) ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	2017-09-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2017.09.014
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Article ; Online: ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature.

Ivanisenko, Timofey V / Saik, Olga V / Demenkov, Pavel S / Ivanisenko, Nikita V / Savostianov, Alexander N / Ivanisenko, Vladimir A

BMC bioinformatics

2020 Volume 21, Issue Suppl 11, Page(s) 228

Abstract: Background: The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are ... ...

Abstract	Background: The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are highly effective in document search; however, they do not allow knowledge extraction. In contrast to the search engines, text-mining systems provide extraction of knowledge with representations in the form of semantic networks. Of particular interest are tools performing a full cycle of knowledge management and engineering, including automated retrieval, integration, and representation of knowledge in the form of semantic networks, their visualization, and analysis. STRING, Pathway Studio, MetaCore, and others are well-known examples of such products. Previously, we developed the Associative Network Discovery System (ANDSystem), which also implements such a cycle. However, the drawback of these systems is dependence on the employed ontologies describing the subject area, which limits their functionality in searching information based on user-specified queries. Results: The ANDDigest system is a new web-based module of the ANDSystem tool, permitting searching within PubMed by using dictionaries from the ANDSystem tool and sets of user-defined keywords. ANDDigest allows performing the search based on complex queries simultaneously, taking into account many types of objects from the ANDSystem's ontology. The system has a user-friendly interface, providing sorting, visualization, and filtering of the found information, including mapping of mentioned objects in text, linking to external databases, sorting of data by publication date, citations number, journal H-indices, etc. The system provides data on trends for identified entities based on dynamics of interest according to the frequency of their mentions in PubMed by years. Conclusions: The main feature of ANDDigest is its functionality, serving as a specialized search for information about multiple associative relationships of objects from the ANDSystem's ontology vocabularies, taking into account user-specified keywords. The tool can be applied to the interpretation of experimental genetics data, the search for associations between molecular genetics objects, and the preparation of scientific and analytical reviews. It is presently available at https://anddigest.sysbio.ru/ .
MeSH term(s)	Data Mining/methods ; Databases, Factual ; Internet ; PubMed ; Software
Language	English
Publishing date	2020-09-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-020-03557-8
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