Protein-glycosaminoglycan interactions: computational approaches

2019:

1. Drobot B., Schmidt M., Mochizuki Y., Abe T., Okuwaki K., Brulfert F., Falke S., Samsonov S. A., Komeiji Y., Betzel C., Stumpf T., Raff J., Tsushima S. Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin. Phys Chem Chem Phys. 2019, Vol. 21: 21213-21222.

2. Bojarski K. K., Becher J., Riemer T., Lemmnitzer K., Moeller S., Schiller J., Schnabelrauch M., Samsonov S.A. Synthesis and in silico characterization of artificially phosphorylated glycosaminoglycans. J Mol Struct. 2019, Vol. 1197:401-416.

3. Samsonov S. A., Feza S., Zsila F. In silico analysis of heparin and chondroitin sulfate binding mechanisms of the antiprotozoal drug berenil and pentamidine. Carb Res. 2019, 482:107742.

4. Penk A., Baumann L., Huster D., Samsonov S. A. NMR and Molecular Modeling Reveal Specificity of the Interactions between CXCL14 and Glycosaminoglycans. Glycobiology, 2019, Vol. 29: 715-725.

5. Kohut G., Sieradzan A., Zsila F., Tunde J., Bosze S., Liwo A., Samsonov S. A., Beke-Somfai T. The Molecular Mechanism of Structural Changes in the Antimicrobial Peptide CM15 Upon Complex Formation with Drug Molecule Suramin: a Computational Analysis. Phys Chem Chem Phys. 2019, Vol.21: 10644-10659.

6. Uciechowska-Kaczmarzyk U., Chauvot de Beauchene I., Samsonov S. A. Docking software performance in protein-glycosaminoglycan systems. J Mol Graph Mod. 2019, Vol. 90:42-50.

7. Samsonov S. A., Zacharias M., Chauvot de Beauchene I. Modeling large protein-glycosaminoglycan complexes using a fragment-based approach. J Comp Chem. 2019, Vol. 40:1429-1439.

8. Samsonov S. A., Lubecka E. A., Bojarski K. K. , Ganzynkowicz R., Liwo A. Local and Long Range Potentials for Heparin-Protein Systems for Coarse-Grained Simulations. Biopolymers. 2019, Vol. 110:e23269.

9. Bojarski K. K., Sieradzan A.K.,Samsonov S. A., Molecular Dynamics Insights into Protein-Glycosaminoglycan Systems from Microsecond-Scale Simulations. Biopolymers. 2019, Vol. 110:e23252.


2018:

1. Kohut G., Liwo A., Bosze S., Beke-Somfai T., Samsonov S. A. Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges for Flexible Systems. J Phys Chem B. 2018. Vol. 122:7821-7827.

2. Vallet S.D., Miele A.E., Uciechowska-Kaczmarzyk U., Liwo A., Duclos B., Samsonov S. A. , Ricard-Blum S. Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners. Sci Rep. 2018. Vol. 8:11768.

3. Uciechowska-Kaczmarzyk U., Babik S., Zsila F., Bojarski K.K., Beke-Somfai T., Samsonov S. A. Molecular Dynamics-Based Model of VEGF-A and Its Heparin Interactions. J Mol Graph Mod. 2018. Vol 82:157-166.

4. Zsila F., Samsonov S. A., Molecular interactions of the anticancer agent ellipticine with glycosaminoglycans by in silico analysis. Carbohydarate Research. 2018. 462:28-33.

5. Samsonov S. A. Computational analysis of solvent inclusion in docking studies of protein-glycosaminoglycan systems. Computational Drug Discovery and Design. Methods in Molecular Biology Series. Springer. 2018, Vol 1762:445-454.

6. Nordsieck K., Baumann L., Hintze V., Pisabarro M. T., Schnabelrauch M., Beck-Sickenger A. G., Samsonov S. A. The effect of interleukin-8 truncations on its interactions with glycosaminoglycans. Biopolymers. 2018. 109(10):e23103.

7. Bojarski K. K., Samsonov S. A. Glycosaminoglycans mediate the function of cathepsin proteases. Review. ‘VII All Polish Conference: Young Scientists in Poland – Research and Development’. Wydawnictwo Młodzi Naukowcy ,2018. [PDF]

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.