![]() ![]() ![]() The secondary structure of proteins was determined by the DSSP method by Kabsch and Sander. Mass spectrometric measurements were performed using the equipment of the “Human Proteome” Core Facility (IBMC, Moscow, Russia).įrom the obtained database, all the motifs with peptides under consideration were selected if the number of individual blocks of the protein molecule included motifs, where the first and last helices were in contact (d ≤ 14 Å). Peptides were loaded 2.5% acetonitrile, 0.1% formic acid, and 0.03% acetic acid at a flow rate of 20 μL/min for 4 min and separated in a linear gradient of mobile Phases A (water with 0.1% formic acid and 0.03% acetic acid) and B (acetonitrile with 0.1% formic acid and 0.03% acetic acid) at a flow rate of 0.3 μL/min using the following elution scheme: started at 2.5% of B for 3 min and was raised to 12% of B for the next 15 min, then to 37% of B for the next 27 min, and to 50% for the next 3 min, then rapid increase to 90% of B for 2 min maintained for 8 min at a flow rate of 0.45 μL/min, and columns system equilibration for the next 13 min in the initial gradient conditions. Peptides were separated on an Ultimate 3000 RSLC Nano UPLC system (Thermo Scientific, Waltham, MA, USA) with pre-installed enrichment column (Acclaim Pepmap ® (5 × 0.3 mm, 300 Å pore size, 5 µm particle size)) and analytical column (Acclaim Pepmap ® analytical column (75 µm × 150 mm, 1.8 µm particle size, 60 Å pore size)). These dynamic events largely consist of post-translational modifications (PTMs) of proteins. It is important to study dynamic (reversible) events at the molecular level, given that these events likely make a decisive contribution to the uncontrolled inversion of metabolic events during pathogenesis. Multidimensional omics data on the level of gene expression, transcript content, protein and metabolite composition and content provide a vast array of knowledge that requires further investigation to understand the molecular events accompanying the pathological process. Changes in cellular phenotype are among the most striking programmed biological events that occur in a healthy cell and include changes in the stages of the cell cycle from prophase to anaphase, de novo gluconeogenesis, differentiation and maturation of a cell into a mature phenotype, and the processes of cells along the path of pathogenesis. There has been a growing interest in understanding the processes that regulate signaling pathways and, as a consequence, determining the onset of metabolic pathway reprogramming and changes in the cell phenotype during ontogenesis. Systems biology enables the integration of data on molecular changes in the body in health and disease. ![]() The phenomenon of modification is accompanied, as a rule, by an increase in the area available for the solvent of the modified amino acid residue and its active environment. Results revealed that PTMs are localized in stable and compact space protein globule motifs that are exposed to a solvent. For proteins with PDB structures, a comparative analysis of the structural changes accompanying the modifications was performed. Fifteen proteins containing PTMs were identified in blood samples from patients with kidney cancer. The proteins were analyzed using ultra-high resolution HPLC-MS/MS and structural analysis was performed with the AMBER and GROMACS software packages. Conformational changes in proteins after modification were analyzed. We examined protein PTMs in the blood samples from patients with kidney cancer. It is likely that dysregulation of post-translational cellular signaling leads to abnormal proliferation and oncogenesis. Common PTMs are reversible and serve as a mechanism for modulating metabolic trans-formations in cells. Post-translational modification (PTM) leads to conformational changes in protein structure, modulates the biological function of proteins, and, consequently, changes the signature of metabolic transformations and the immune response in the body. ![]()
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