Publications by authors named "S V Samsonov"

Article Synopsis
  • Heparin is a key polysaccharide that regulates cellular activities by interacting with proteins like growth factors and cytokines, but studying its effects on larger scales is challenging with traditional molecular dynamics.
  • Coarse-grained models simplify these systems by reducing complexity, allowing for better exploration of protein/heparin interactions over extended time frames and larger sizes.
  • A new coarse-grained model has been developed and validated with UNRES software, showing strong alignment with experimental results, making it suitable for investigating complex biological processes involving heparin.
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The objective of this study was to examine the interactions between anionic surfactants, specifically 1-alkylsulfonates (KXS) and 1-alkylsulfates (SXS) ions, with human serum albumin (HSA). A combination of experimental techniques, including isothermal titration calorimetry (ITC), steady-state fluorescence spectroscopy (SF), and molecular dynamics-based approaches was employed to gain a comprehensive understanding of these processes. It has been demonstrated that the subtle variations in the charge distribution on the anionic surfactant headgroups have a significant impact on the number of binding sites, the stoichiometry of the resulting complexes, and the strength of the interactions between the surfactants and the protein.

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Glycosaminoglycans (GAGs) play a key role in a variety of biological processes in the extracellular matrix (ECM) via interactions with their protein targets. Due to their high flexibility, periodicity and electrostatics-driven interactions, GAG-containing complexes are very challenging to characterize both experimentally and in silico. In this study, we, for the first time, systematically analyzed the interactions of endostatin, a proteolytic fragment of collagen XVIII known to be anti-angiogenic and anti-tumoral, with heparin (HP) and representative heparan sulfate (HS) oligosaccharides of various lengths, sequences and sulfation patterns.

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Acridinium esters, due to their capability for chemiluminescence (CL), are employed as indicators and labels in biomedical diagnostics and other fields. In this work, the influence of ionic surfactants, hexadecyltrimethylammonium chloride and bromide (CTAC and CTAB, cationic) and sodium dodecyl sulphate (SDS, anionic) on the CL parameters and mechanism of representative emitter, 10-methyl-9-[(2-methylphenoxy)carbonyl]acridinium trifluoromethanesulphonate (2MeX) in a HO/NaOH environment, is studied. Our investigations revealed that the type of surfactant and its form in solution have an impact on the CL kinetic constants and integral efficiencies, while changes in those emission properties resulting from the type of ion (Cl vs.

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Article Synopsis
  • * The study updates the Cyclic Peptide Matching program (cPEPmatch) to identify cyclic peptides that mimic the GAG-binding sites of antithrombin III (ATIII), a key anticoagulant.
  • * By using computational tools and experimental validation methods, researchers identified a promising cyclic peptide binder, demonstrating their potential for new therapeutic applications targeting GAGs.
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