Publications by authors named "Kirill Nikolsky"
Metabolomics investigates final and intermediate metabolic products in cells. Assessment of the human metabolome relies principally on the analysis of blood, urine, saliva, sweat, and feces. Tissue biopsy is employed less frequently.
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- - The study aims to advance the diagnosis and treatment of schizophrenia by identifying blood biomarkers, moving away from solely subjective assessments of clinical symptoms.
- - Researchers conducted a detailed proteomic analysis of plasma samples from 48 schizophrenia patients and 50 healthy individuals, using advanced techniques to evaluate protein presence.
- - Findings revealed unique proteins in schizophrenia patients that are linked to key biological processes, enhancing the understanding of the disorder's molecular mechanisms and potential therapeutic targets.
The primary objective of analyzing the data obtained in a mass spectrometry-based proteomic experiment is peptide and protein identification, or correct assignment of the tandem mass spectrum to one amino acid sequence. Comparison of empirical fragment spectra with the theoretical predicted one or matching with the collected spectra library are commonly accepted strategies of proteins identification and defining of their amino acid sequences. Although these approaches are widely used and are appreciably efficient for the well-characterized model organisms or measured proteins, they cannot detect novel peptide sequences that have not been previously annotated or are rare.
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- Many studies show that post-translational modifications (PTMs) like phosphorylation influence protein function, but there's no agreement on how much they alter protein structure.
- The research specifically focuses on phosphorylation of serine, threonine, and tyrosine and examines how these modifications affect various geometric parameters of proteins.
- It was found that phosphorylation leads to varying degrees of structural changes in proteins, particularly around the modification site, and this can switch proteins from inactive to active states.
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- Researchers developed a new tool called SAFoldNet to improve the comparison and searching of 3D protein structures in structural biology.
- SAFoldNet combines neural networks with the BLAST algorithm and uses a multistage process involving geometry conversion, candidate structure formation, and structural alignment refinement.
- The tool's effectiveness was validated against current services, leading to a user-friendly web interface that allows for various protein structure analyses and provides similarity metrics.
Amino acid substitutions and post-translational modifications (PTMs) play a crucial role in many cellular processes by directly affecting the structural and dynamic features of protein interaction. Despite their importance, the understanding of protein PTMs at the structural level is still largely incomplete. The Protein Data Bank contains a relatively small number of 3D structures having post-translational modifications.
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- The study explores two types of protein structures, three-helix bundles and SH3-type barrels, across various organisms using a neural graph network to analyze their spatial folds.
- Molecular experiments were conducted on small proteins with these structures, evaluating parameters like stability and structural integrity at different temperatures (300K, 340K, and 370K).
- The research aims to show that it is possible to analyze these protein folds independently from their protein environment, leading to improved efficiency and reduced computation time without losing essential information.
Article Synopsis
- * Alpha-synuclein, which can aggregate and harm cells, interacts with cyclophilin A to prevent these destructive aggregations, highlighting the importance of chaperone proteins.
- * Using advanced molecular docking techniques, we identified how alpha-synuclein, cyclophilin A, and Anle138b can form a stable complex, primarily through hydrophobic and hydrogen bonding interactions.
A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs is important for developing a deeper understanding of the mechanisms of protein folding. Here, we propose a universal PSSNet machine-learning method for SSS recognition and segmentation.
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- * A study of 3,661 healthy athletes used various medical examinations and machine learning to analyze health indicators related to recovery post-competition.
- * Key findings indicated that muscle metabolism parameters (like aspartate aminotransferase and creatine kinase) and ornithine cycle parameters (like creatinine and urea) were crucial for distinguishing between catabolic and anabolic metabolism in athletes.
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- - This study examined how 3β-corner super-secondary structures maintain their stability in water, independent of protein globules, using molecular dynamics (MD) simulations.
- - Researchers analyzed various geometric parameters, like gyration radius and hydrogen bonds, and characterized a set of 3β-corner structures to show they consistently retained their formation.
- - The findings suggest that 3β-corners are stable in aqueous environments and could serve as essential building blocks for protein folding and offer a standalone focus for structural biology research.
Article Synopsis
- * JAK and STAT proteins play key roles in signaling processes related to inflammation and are important in autoimmune diseases like rheumatoid arthritis.
- * The study explored how the drug ruxolitinib interacts with JAK1 and JAK2, showing it binds selectively to these proteins with strong binding affinities, mainly through hydrophobic interactions.
Article Synopsis
- Protein post-translational modifications (PTMs) play a vital role in various cellular functions and their dysregulation is linked to diseases like rheumatoid arthritis (RA).
- The three key PTMs involved in RA include glycosylation, which influences antigen presentation, citrullination, which is closely linked to the presence of specific autoantibodies, and carbamylation.
- This study analyzed proteins with PTMs relevant to RA over the past 20 years, identifying target proteins, exploring their structural characteristics, and conducting molecular dynamics experiments to understand how these modifications may relate to the disease's development.
Article Synopsis
- Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes joint damage and significant disability, largely driven by cytokines and the JAK/STAT signaling pathway.
- The development of small molecule inhibitors targeting the JAK family has transformed RA treatment, with upadacitinib (Rinvoq) being a notable option due to its selectivity for JAK1 over JAK2 and JAK3.
- Research indicates that the binding characteristics of upadacitinib with JAK1 through hydrogen bonds provide insights into its mechanism of action and how it differs among various JAK isoforms.
Proteins expressed during the cell cycle determine cell function, topology, and responses to environmental influences. The development and improvement of experimental methods in the field of structural biology provide valuable information about the structure and functions of individual proteins. This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories for storage, as well as methods of molecular dynamics research.
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