Protein-glycosaminoglycan interactions: computational approaches

  • New research project!
  • Our research will be continued and extended within the National Science Centre Programme SONATA BIS project "Modeling of glycosaminoglycan-induced formation of protein structure and enhancement of biologically relevant protein-ligand interactions " in the next 5 years!


  • Presentation at the Hosting Institution 25.04.2019
  • Polonez project. Summary" at the Department of Theoretical Chemistry at the University of Gdańsk. Sergey Samsonov.


  • Invited talk 19.04.2019
  • Modeling protein-glycosaminoglycan interactions" at International Sakharov Environmental Institute, Minsk, Belarus. Sergey Samsonov.


  • 8-10.04.2019 Conference participation
  • 33th Molecular Modelling Workshop 2019 (Erlangen, Germany). Presentation "Computational insights into procathepsin maturation mediated by glycosaminoglycans" by Krzysztof Bojarski.


  • 28.03.2019 Presentation at the Hosting Institution
  • Presentation of the overview and first results within the subproject "Computational insights into procathepsin maturation mediated by glycosaminoglycans" at the Department of Theoretical Chemistry at the University of Gdańsk. Krzysztof Bojarski.


  • 11-14.03.2019
  • Krzysztof participated in School in molecular computational biochemistry, which took place in Jerzy Haber Institute of Catalysis and Surface Chemistry, PAS, Kraków, Poland.


  • 29.03.2019 Webinar
  • Protein-ligand Interaction Energy-based Entropy Calculations: Fundamental Challenges For Flexible Systems. Webinar for Institute of Physics (Polish Academy of Sciences) and Thai Nguyen University (Vietnam). Together with Gergely Kohut from Hyngarian Academy of Sciences.


  • Science Popularization Event 05.03.2019
  • Krzystof Bojarski and Sergey Samsonov organized introductory lessons about molecular modeling under the title "From atoms to planets: towards the understanding of the structure of materia" for the 7th classes at the school of Gościcino (Wejherowo Region). In Polish.


  • Visiting Student 25.02.2019
  • Jan Potthoff from the Free University of Berlin is joining our project within the Erasmus Programme until the end of the project. He is going to contribute to the protein-GAG interactions study.


  • Invited talk 29.01.2019
  • Computational approaches to model interactions between proteins and glycosaminoglycans" at the Institute of Physics of Kazimierz Wielki Universit, Bydgoszcz, Sergey Samsonov


  • Workshop participation 12-13.01.2019
  • Workshop for POLONEZ Fellows: Management (Warsaw, Poland). Sergey Samsonov. The workshop was organized by VITAE - The Career Development Organisatio


  • Workshop participation 01-02.12.2018
  • Workshop for POLONEZ Fellows: Working with others (Warsaw, Poland). Sergey Samsonov. The workshop was organized by VITAE - The Career Development Organisation


  • Workshop participation 03-04.11.2018
  • Workshop for POLONEZ Fellows: Self Effectiveness (Warsaw, Poland). Sergey Samsonov. The workshop was organized by VITAE - The Career Development Organisation


  • Habilitation defence
  • 11.12.2018 Sergey Samsonov obtained the title of dr. habil. (HDR) at the University of Tours, France.


  • Invited talk 07.12.2018
  • Computational approaches to study glycosaminoglycan mediation of biologically relevant protein-ligand interactions" at the University of Reims, France, Sergey Samsonov


  • Scientific visit within Polonez Funding Programme 2-12.12.2018
  • Krzysztof Bojarski visited laboratory of Dr Fabien Lecaille at University of Tours France. He was trained in spectrofluorometer technics to measure specific protease activity with fluorogenic substrates. He gave also an oral presentation that covered his current PhD’s work.


  • Hosting a visit from a collaboration partner 16-17.10.2018
  • We hosted Prof. Daniel Huster, the Director of Institute of Medical Physics and Biophysics at Leipzig University (Germany). Within his visit, Prof. Huster gave a talk "Structural Dynamics of G-Protein‐Coupled Receptorsand Mutated Amyloid β-Fibrils" at the Faculty of Chemistry. We also discussed ongoing and future common projects.


  • Scientific visit within Polonez Funding Programme 24-28.09.2018 and invited talk
  • "Modeling of glycosaminoglycan-induced formation of protein structure and enhancement of biologically relevant protein-ligand interactions" at Institute for Medical Physics and Biophysics, Leipzig University, Germany. Sergey Samsonov


  • Conference participation 09-13.09.2018
  • 4-th Polish - Korean Conference on Protein Folding. Talk: "Computational insights into the glycosaminoglycan-mediated molecular mechanisms underlying cell signaling" Sergey Samsonov. PKC2018


  • Conference participation 09-13.09.2018
  • 4-th Polish - Korean Conference on Protein Folding. Poster presentation: "Computational analysis of interactions of endostatin with glycosaminoglycans" Urszula Uciechowska-Kaczmarzyk. PKC2018


  • Conference participation 09-13.09.2018
  • 4-th Polish - Korean Conference on Protein Folding. Poster presentation: "Computational study on phospholyrated glycosaminoglycans" Krzysztof Bojarski. PKC2018


  • Conference participation 14-19.07.2018
  • 29th International Carbohydrate Symposium Lisboa. Poster presentation: "Computational analysis of interactions of endostatin with glycosaminoglycans" Urszula Uciechowska-Kaczmarzyk. ICS 2018 .


  • Invited talk 16.07.2018.
  • "Modeling protein-glycosaminoglycan interactions" at Research Institute of Influenza, Saint-Petersburg, Russia, Sergey Samsonov.


  • Conference participation 24-28.06.2018
  • Modeling and Design of Molecular Materials 2018 (Polanica Zdrój, Poland). Talk and Poster presentation: “Microsecond scale MD study of a protein-heparin complex”. Krzysztof Bojarski. Poster Award MDM 2018.


  • Workshop participation 23-24.06.2018
  • Workshop for POLONEZ Fellows: Communication (Warsaw, Poland). Sergey Samsonov. The workshop was organized by VITAE - The Career Development Organisation: CRAC.


  • Workshop participation 16-17.06.2018
  • Workshop for POLONEZ Fellows: Intellectual Properties (Warsaw, Poland). Sergey Samsonov. The workshop was organized by VITAE - The Career Development Organisation: CRAC.


  • Conference participation 11-12.06.2018
  • POLONEZ Fellows Forum (Kraków, Poland). Poster presentation: “Computational approaches to study protein-glycosaminoglycan interactions”. Sergey Samsonov. POLONEZ Fellows.


  • Presentation at the Hosting Institution 22.05.2018.
  • Presentation “Computational analysis of FGF-Heparin system” at the Department of Theoretical Chemistry at the University of Gdańsk. Krzysztof Bojarski.


  • Conference participation 12-14.03.2018.
  • 32thMolecular Modelling Workshop 2018 (Erlangen, Germany). Presentation “Impact of chondroitin sulfate-4 on human and rat cathepsin K collagenolytic activity” by Krzysztof Bojarski.


  • CAPRI 44 predictions March 2018.
  • We participate in CAPRI 44 (Critical Assessment of Prediction of Interactions) context, we analyzed target T135.


  • Visiting Reasearcher 12.02.2018
  • Gergely Kohut from Biomolecular Self-assembly Research Group Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences joined our project team for the next 2.5 months. Gergely is going to apply molecular dynamics and molecular docking techniques to study the intrinsically disordered peptide CM15, which can be considered as a potential drug carrier against mycobacterium tuberculosis.


  • ISMS Newsletter 05.02.2018
  • The information about our project was published in the ISMB (International Society of Matrix Biology) Newsletter 27 (October 2017). ISMB_October2017


  • Conference participation 27.11.2017
  • VI Ogólnokrajowa Konferencja Młodzi Naukowcy w Polsce – Badania i Rozwój (Gdańsk, Poland). Presentation “Computational analysis of cathepsin V interactions with glycosaminoglycans” by Krzysztof Bojarski.


  • Invited talk and presentation of the results within the collaboration 16-17.10.2017.
  • Computational approaches to study interactions in protein-glycosaminoglycan molecular systems” at Institute for Molecular and Supramolecular Chemistry and Biochemistry, University of Lyon, France. Urszula Uciechowska-Kaczmarzyk and Sergey Samsonov.


  • Presentation of common results by our collaborators 09-10.10.2017.
  • Regulation of cathepsin V activity by heparan sulfate: putative pathophysiological consequences in mucopolysaccharidoses". Sergey Samsonov is a co-author of the presented work within the collaboration with Dr. Lecaille (Tours University, France) https://gagosciences.ibs.fr


  • Conference participation 07.10.2017.
  • Coarse graining of biomolecules and beyond: theory and applications (Warsaw, Poland). Poster presentations “AMBER-compatible coarse-grained model of glycosaminoglycans” by Sergey Samsonov and “Effect of restraint type and strength on the quality of protein models obtained with homology-restrained UNRES simulations” by Krzysztof Bojarski.


  • Scientific visit within Polonez Funding Programme and oral presentation 03-06.10.2017.
  • “Computational analysis of protein-GAG interactions” at Department of Biochemistry, University of Tours, France. 5 October 2017. Sergey Samsonov.


  • Invited talk 22.09.2017.
  • Interactions in protein-glycosaminoglycan systems: computational approaches” at the Institute of Materials and Environmental Chemistry, Hungarian Academy of Science, Budapest, Hungary. Sergey Samsonov.


  • CAPRI predictions August-September 2017.
  • We participate in CAPRI (Critical Assessment of PRediction of Interactions) context within the prediction team of Prof. Zachariashttp://www.ebi.ac.uk/msd-srv/capri/


  • Presentation of common results by our collaborators 09-14.07.2017
  • Actinides 2017 (Sendai, Japan). Talk by Prof. Tsushima: “Site-specific binding affinity of Eu(III) towards Ca-binding protein calmodulin: A combined spectroscopic and theoretical study”. Sergey Samsonov is a co-author of the presented work within the collaboration with Prof. Tsushima (Helmholtz-Zentrum Dresden-Rossendorf, Germany). http://actinides2017.jp


  • Conference participation 02-06.07.2017.
  • 19th European Carbohydrate Symposium (Barcelona, Spain). Poster presentation: “Computational analysis of interactions in protein-glycosaminoglycan complexes available in the PDB”. Sergey Samsonov. http://www.eurocarb2017.com


  • Presentation at the Hosting Institution 10.07.2017.
  • Presentation of the overview and first results within the subproject “Interactions of cathepsin proteases with glycosaminoglycans” at the Department of Theoretical Chemistry at the University of Gdańsk. Krzysztof Bojarski.


  • New Project Member 01.07.2017
  • Urszula Uciechowska-Kaczmarzyk joined the project.


  • Conference participation 13-15.06.2017
  • Systems Glycomics Beilstein Glyco-Bioinformatics Symposium 2017 (Berlin, Germany). Flash talk and poster presentation: “Evaluation of computational approaches for the analysis of FGF1-heparin interactions”. Sergey Samsonov.http://www.beilstein-institut.de/en/symposia/glyco-bioinfo


  • Presentation at the Hosting Institution 05.06.2017.
  • Presentation of the overview and first results of the Polonez project “Computational approaches to study protein-glycosaminoglycan interactions” at the Department of Theoretical Chemistry at the University of Gdańsk. Sergey Samsonov.


  • New Project Member 01.06.2017.
  • Krzysztof Bojarski joined the project.


  • Science Popularization Event 26.05.2017.
  • We took part in the organization and conducting of the workshops for kindergarten and school children at XIV Baltic Festival of Science at the Faculty of Chemistry at the University of Gdańsk. http://chemia.ug.edu.pl/wspolpraca/popularyzacja_nauki/baltycki_festiwal_nauki/xiv_bfn_2017


  • Presentation of common results by our collaborators 09-11.05.2017.
  • 20th Congress of the GGMM (Reims, France). Poster by Dr. Chauvot de Beauchêne “Fragment-based modeling of protein-GAG complexes”. Sergey Samsonov is a co-author of the presented work within the collaboration with Dr. Chauvot de Beauchêne (CNRS, LORIA, Nancy, France) and Prof. Zacharias (Technical Univeristy of Munich, Germany).https://ggmm2017.sciencesconf.org/


  • Project start 01.05.2017.
  • Our project started!


    This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665778.