Projects funded by the NCN

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Information of the project and the call

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Modeling of glycosaminoglycan-induced formation of protein structure and enhancement of biologically relevant protein-ligand interactions

2018/30/E/ST4/00037

Keywords:

molecular dynamics glycosaminoglycans protein-saccharide interactions molecular docking coarse-grain modeling

Descriptors:

  • ST4_15: Colloid chemistry
  • NZ1_3: Biophysics
  • NZ1_4: Structural biology

Panel:

ST4 - Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development

Host institution :

Uniwersytet Gdański, Wydział Chemii

woj. pomorskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Sergey Samsonov 

Number of co-investigators in the project: 4

Call: SONATA BIS 8 - announced on 2018-06-15

Amount awarded: 2 477 304 PLN

Project start date (Y-m-d): 2019-06-03

Project end date (Y-m-d): 2024-06-02

Project duration:: 60 months (the same as in the proposal)

Project status: Project completed

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (41)
  • Book publications / chapters in book publications (3)
  1. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach.
    Authors:
    Glashagen G., de Vries S., Uciechowska-Kaczmarzyk U., Samsonov S.A., Murail S., Tuffery P., Zacharias M.
    Academic press:
    Proteins (rok: 2019, tom: 88, strony: 1018–1028), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.25860 - link to the publication
  2. Computational insights into the calcium ions role in protein-glycosaminoglycan systems.
    Authors:
    Kogut M.M., Maszota-Zieleniak M., Marcisz M., Samsonov S.A.
    Academic press:
    Phys Chem Chem Phys (rok: 2021, tom: 23, strony: 3519–3530), Wydawca: Royal Society of Chemistry (United Kingdom)
    Status:
    Published
    DOI:
    10.1039/D0CP05438K - link to the publication
  3. Cyclic peptidic furin inhibitors developed by combinatorial chemistry
    Authors:
    Gitlin-Domagalska A., Dębowki D., Maciejewska A., Samsonov S.A., Maszota-Zieleniak M., Ptaszyńska N., Łęgowska A., Rolka K.
    Academic press:
    ACS Medicinal Chemistry Letters (rok: 2023, tom: 14, strony: 458-465), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acsmedchemlett.3c00008 - link to the publication
  4. In silico insights into procathepsin S maturation mediated by glycosaminoglycans
    Authors:
    Bojarski K.K., Samsonov S.A.
    Academic press:
    Journal of Molecular Graphics and Modeling (rok: 2023, tom: 120, strony: 108406), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2023.108406 - link to the publication
  5. Interplay of heparan sulfate chains with the core proteins of syndecans 2 and 4
    Authors:
    Maszota-Zieleniak M., Liwo A., Ricard-Blum S., Samsonov S.A.
    Academic press:
    Proteoglycan Research (rok: 2023, tom: 1, strony: e10), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pgr2.10 - link to the publication
  6. Studying specificity in protein-glycosaminoglycan recognition with umbrella sampling
    Authors:
    Marcicz M., Anila S., Gaardløs M., Zacharias M., Samsonov S.A.
    Academic press:
    Beilstein Journal of Organic Chemistry (rok: 2023, tom: 19, strony: 1933-1946), Wydawca: The Beilstein Institute
    Status:
    Published
    DOI:
    10.3762/bjoc.19.144 - link to the publication
  7. Theory and practice of coarse-grained molecular dynamics of biologically important systems.
    Authors:
    Liwo A., Czaplewski C., Sieradzan A.K., Lipska A.G., Samsonov S.A., Murarka R.K.
    Academic press:
    Biomolecules (rok: 2021, tom: 11, strony: 1347), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom11091347 - link to the publication
  8. Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans.
    Authors:
    Marcisz M., Maszota-Zieleniak M., Huard B., Samsonov S.A.
    Academic press:
    Biomolecules (rok: 2021, tom: 11, strony: 1349), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom11091349 - link to the publication
  9. Binding of fluorescent dansyl amino acids in albumin: when the access to the protein cavity is more important than the strength of binding.
    Authors:
    Bertozo L. C., Maszota-Zieleniak M., Bolean M., Ciancaglini P., Samsonov S.A., Ximenes V.F.
    Academic press:
    Dyes and Pigments (rok: 2021, tom: 188, strony: 109195), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.dyepig.2021.109195 - link to the publication
  10. Further analyses of APRIL/APRIL-Receptor/Glycosaminoglycan interactions by biochemical assays linked to computational studies.
    Authors:
    Marcisz M., Huard B., Lipska A.G., Samsonov S.A.
    Academic press:
    Glycobiology (rok: 2021, tom: 31, strony: 772-786), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/glycob/cwab016 - link to the publication
  11. Induced Circular Dichroism as a Tool to Monitor the Displacement of Ligands Between Albumins
    Authors:
    Bertozo L., Kogut M., Maszota-Zieleniak A., Samsonov S.A., Ximenez V.F.
    Academic press:
    Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (rok: 2022, tom: 278, strony: 121374), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.saa.2022.121374 - link to the publication
  12. Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4
    Authors:
    Gaardløs M., Samsonov S.A., Sletmoen M., Sætrom G.I., Hjørnevik M., Sletta H., Tøndervik A., Aachmann F.L.
    Academic press:
    Glycobiology (rok: 2021, tom: Epub, strony: Epub), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/glycob/cwab025 - link to the publication
  13. Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment.
    Authors:
    Antoniak A., Biskupek I., Bojarski K.K., Czaplewski C., Giełdoń A., Kogut M., Kogut M.M., Krupa P., Lipska A.G., Liwo A., Lubecka E.A., Marcisz M., Maszota-Zieleniak M., Samsonov S.A., Sieradzan A.K., Ślusarz M.J., Ślusarz R., Wesołowski P.A., Ziȩba K.
    Academic press:
    J Mol Graph Mod. (rok: 2021, tom: 108, strony: 108008), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2021.108008 - link to the publication
  14. Modulation of the expression and activity of cathepsin S in reconstructed human skin by neohesperidin dihydrochalcone
    Authors:
    Sage J., Renault J., Domain R., Bojarski K.K., Chazeirat T., Saidi A., Leblanc E., Nizard C., Samsonov S.A., Kurfurst R., Lalmanach G., Lecaille F.
    Academic press:
    Matrix Biology (rok: 2022, tom: 107, strony: 97-112), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.matbio.2022.02.003 - link to the publication
  15. Rat cathepsin K: enzymatic specificity and regulation of its collagenolytic activity.
    Authors:
    Lecaille F., Chazeirat T., Bojarski K.K., Renault J., Saidi A., Prasad V.G.N.V, Samsonov S.A., Lalmanach G.
    Academic press:
    BBA – Proteins and Proteomics (rok: 2019, tom: 1868, strony: 140318), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bbapap.2019.140318 - link to the publication
  16. The abnormal accumulation of heparan sulfate in patients with mucopolysaccharidosis prevents the elastolytic activity of cathepsin V.
    Authors:
    Chazeirat T., Denamur S., Bojarski K.K., Andrault P.-M., Sizaret D., Zhang F., Saidi A., Tardieu M., Linhardt R.J., Labarthe F., Brömme D., Samsonov S.A., Lalmanach G., Lecaille F.
    Academic press:
    Carbohydrate Polymers (rok: 2020, tom: 253, strony: 117261), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.carbpol.2020.117261 - link to the publication
  17. Insights into the interaction of Human Serum Albumin with Ionic Liquids – Thermodynamic, spectroscopic and molecular modelling studies
    Authors:
    Kowalska D., Dołżonek J., Żamojć K., Samsonov S.A., Maszota-Zieleniak M., Makowska J., Stepnowski P., Białk-Bielińska A., Wyrzykowski D.
    Academic press:
    International Journal of Biological Macromolecules (rok: 2023, tom: 249, strony: 125883), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ijbiomac.2023.125883 - link to the publication
  18. A case of Parkinson's disease with early onset in a heterozygous carrier of mutation in Atp7b gene.
    Authors:
    Ilyechova E., Miliukhina I., Karpenko M., Orlov I., Puchkova L., Samsonov S.A.
    Academic press:
    Journal of Personalized Medicine (rok: 2019, tom: 9, strony: 41), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/jpm9030041 - link to the publication
  19. Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L:consequences in mucopolysaccharidosis
    Authors:
    Denamur S., Chazeirat T., Masztoa-Zieleniak M., Vives R., Saidi A., Zhang F., Linhardt R.J., Labarthe F., Samsonov S.A., Lalmanach G., Lecaille F.
    Academic press:
    Carbohydrate Polymers (rok: 2022, tom: 293, strony: 119734), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.carbpol.2022.119734 - link to the publication
  20. Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13.
    Authors:
    Karczyńska A., Zięba K., Uciechowska U., Mozolewska, M., Krupa P., Lubecka E., Lipska A., Sikorska C., Samsonov S., Sieradzan A., Gieldon A., Liwo A., Ślusarz R., Ślusarz M., Lee, J., Joo K., Czaplewski C.
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2020, tom: 60, strony: 1844–1864), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.9b00864 - link to the publication
  21. Mind your dye: the amyloid sensor thioflavin T interacts with sulfated glycosaminoglycans used to induce cross-β-sheet motifs.
    Authors:
    Zsila F., Samsonov S.A., Maszota-Zieleniak M.
    Academic press:
    J Phys Chem B (rok: 2020, tom: 124, strony: 11625-11633), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.0c08273 - link to the publication
  22. Probing proton-loading site of cytochrome c oxidase by time-resolved Fourier transform infrared spectroscopy.
    Authors:
    Gorbikova E., Samsonov S.A., Kalendar R.
    Academic press:
    Molecules (rok: 2020, tom: 25, strony: 3393), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/molecules25153393 - link to the publication
  23. Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability.
    Authors:
    Gitlin-Domagalska A., Dębowski D., Gucwa K., Starego D., Ptaszyńska N., Sieradzan A., Karczyńska A., Samsonov S.A., Mangold M., Gütschow M., Łęgowska A., Rolka K.
    Academic press:
    Biochemie (rok: 2020, tom: 171–172, strony: 178–186), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.biochi.2020.03.006 - link to the publication
  24. Acute phase α1-acid glycoprotein as a siderophore-capturing component of the human plasma: a molecular modeling study.
    Authors:
    Samsonov S.A., Zsila F., Maszota-Zieleniak M.
    Academic press:
    J Mol Graph Mod. (rok: 2021, tom: 105, strony: 107861), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2021.107861 - link to the publication
  25. Affinity and putative entrance mechanisms of alkyl sulfates into the β-CD cavity
    Authors:
    Kogut M.M., Grabowska O., Wyrzykowski D., Samsonov S.A.
    Academic press:
    Journal of Molecular Liquids (rok: 2022, tom: 364, strony: 119978), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.molliq.2022.119978 - link to the publication
  26. Analysis of procollagen C-proteinase enhancer-1/glycosaminoglycan binding sites and of the potential role of calcium ions in the interaction.
    Authors:
    Potthoff J., Bojarski K.K., Kohut G., Lipska A.G., Liwo A., Kessler E., Ricard-Blum S., Samsonov S.A.
    Academic press:
    International Journal of Molecular Sciences (rok: 2019, tom: 20, strony: 5021), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms20205021 - link to the publication
  27. Computational insights into heparin-small molecule interactions: evaluation of the balance between stacking and non-stacking binding modes.
    Authors:
    Maszota-Zieleniak M., Zsila F., Samsonov S.A.
    Academic press:
    Carbohydrate Research (rok: 2021, tom: 507, strony: 108390), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.carres.2021.108390 - link to the publication
  28. Effect of Tetraphenylborate on Physicochemical Properties of Bovine Serum Albumin.
    Authors:
    Grabowska O., Kogut M.M., Żamojć K., Samsonov S.A., Makowska J., Tesmar A., Chmur K., Wyrzykowski D., Chmurzyński L.
    Academic press:
    Molecules (rok: 2021, tom: 26, strony: 6565), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/molecules26216565 - link to the publication
  29. Evaluation of Replica Exchange with Repulsive Scaling Approach for Docking Glycosaminoglycans.
    Authors:
    Maszota-Zieleniak M., Marcisz M., Kogut M.M., Siebenmorgen T., Zacharias M., Samsonov S.A.
    Academic press:
    J Comp Chem (rok: 2021, tom: 42, strony: 1040-1053), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/JCC.26496 - link to the publication
  30. Explicit Solvent Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) in Molecular Modeling of Protein-Glycosaminoglycan Complexes
    Authors:
    Marcisz M., Gaardløs M., Bojarski K.K., Siebenmorgen T., Zacharias M., Samsonov S.A.
    Academic press:
    J Comp Chem (rok: 2022, tom: 43, strony: 1633-1640), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.26965 - link to the publication
  31. Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis
    Authors:
    Kogut M.M., Danielsson A., Ricard-Blum S., Samsonov S.A.
    Academic press:
    Computational Biology and Chemistry (rok: 2022, tom: 99, strony: 107727), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.compbiolchem.2022.107727 - link to the publication
  32. Modeling protein-glycosaminoglycan complexes: does the size matter?
    Authors:
    Marcisz M., Zacharias M., Samsonov S.A.
    Academic press:
    J Chem Inf Mod. (rok: 2021, tom: 61, strony: 4475-4485), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.1c00664 - link to the publication
  33. Molecular Dynamics Approaches Dissect Molecular Mechanisms Underlying Methylene Blue–Glycosaminoglycan Interactions
    Authors:
    Maszota-Zieleniak M., Zsila F., Samsonov S.A.
    Academic press:
    Molecules (rok: 2022, tom: 27, strony: 2654), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.1016/j.saa.2022.121374 - link to the publication
  34. Physicochemical nature of sodium dodecyl sulfate interactions with bovine serum albumin revealed by interdisciplinary approaches.
    Authors:
    Tesmar A., Kogut M.M., Żamojć K., Grabowska O., Chmur K., Samsonov S.A., Makowska J., Wyrzykowski D., Chmurzyński L.
    Academic press:
    Journal of Molecular Liquids (rok: 2021, tom: 340, strony: 117185), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.molliq.2021.117185 - link to the publication
  35. In silico and in vitro mapping of specificity patterns of glycosaminoglycans towards cysteine cathepsins B, L, K, S and V
    Authors:
    Bojarski K.K., Sage J., Lalmanach G., Lecaille F., Samsonov S.A.
    Academic press:
    J Mol Graph Mod (rok: 2022, tom: 113, strony: 108153), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2022.108153 - link to the publication
  36. Modeling glycosaminoglycan-protein complexes
    Authors:
    Kogut M.M., Marcisz M., Samsonov S.A.
    Academic press:
    Current Opinion in Structural Biology (rok: 2022, tom: 73, strony: 102332), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.sbi.2022.102332 - link to the publication
  37. Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment.
    Authors:
    Lubecka E.A., Karczynska A.S., Lipska A.G., Sieradzan A.K., Zieba K., Sikorska C., Uciechowska U., Samsonov S.A., Krupa P., Mozolewska M.A., Golon L., Gieldon A., Czaplewski C., Slusarz R., Slusarz M., Crivelli S.N., Liwo A.
    Academic press:
    Journal of Molecular Graphics and Modeling (rok: 2019, tom: 92, strony: 154–166), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2019.07.013 - link to the publication
  38. Investigation of the Structure of Regulatory Proteins Interacting with Glycosaminoglycans by Combining NMR Spectroscopy and Molecular Modeling – The Beginning of a Wonderful Friendship.
    Authors:
    Künze G., Huster D., Samsonov S.A.
    Academic press:
    Biological Chemistry (rok: 2021, tom: 402, strony: 1337-1355.), Wydawca: Walter de Gruyter
    Status:
    Published
    DOI:
    10.1515/hsz-2021-0119 - link to the publication
  39. Solvent models benchmark for molecular dynamics of glycosaminoglycans
    Authors:
    Marcisz M., Samsonov S.A.
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2023, tom: 63, strony: 2147-2157), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.2c01472 - link to the publication
  40. The potential role of glycosaminoglycans in serum amyloid A fibril formation by in silico approaches.
    Authors:
    Maszota-Zieleniak M., Danielsson A., Samsonov S.A.
    Academic press:
    Matrix Biology Plus (rok: 2021, tom: 12, strony: 1000080), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.mbplus.2021.100080 - link to the publication
  41. The role of glycosaminoglycans in procathepsin B maturation – molecular mechanism elucidated by a computational study.
    Authors:
    Bojarski K.K., Karczyńska A.S., Samsonov S.A.
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2020, tom: 60, strony: 2247–2256), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.0c00023 - link to the publication
  1. Molecular dynamics simulation-based prediction of glycosaminoglycan interactions with drug molecules
    Authors:
    Maszota-Zieleniak M., Samsonov S.A.
    Book:
    Computational Drug Discovery and Design (2nd Ed.). Methods in Molecular Biology Series (rok: 2023, tom: 2714, strony: 143-153), Wydawca: Springer
    Status:
    Published
  2. Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
    Authors:
    Liwo A., Sieradzan A.K., Karczyńska A.S., Lubecka E.A., Samsonov S.A., Czaplewski C., Krupa P., Mozolewska M.
    Book:
    Practical Aspects of Computational Chemistry (rok: 2022, tom: V, strony: 31-69), Wydawca: Springer Nature Switzerland AG
    Status:
    Published
  3. Repulsive Scaling Replica Exchange Molecular Dynamics in Modeling Protein-Glycosaminoglycan Complexes
    Authors:
    Marcisz M., Maszota-Zieleniak M., Samsonov S.A.
    Book:
    Proteoglycans: Methods and Protocols, Methods in Molecular Biology Series (rok: 2023, tom: 2619, strony: 153–167), Wydawca: Springer
    Status:
    Published

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