Giatagana E-M., Berdiaki A., Gaardløs M., Tsatsakis A., Samsonov S.A., Nikitovic D. Rapamycin- induced autophagy in osteosarcoma cells is mediated via the biglycan/Wnt/β-catenin signaling axis American Journal of Physiology-Cell Physiology. 2022. Epub.
https://doi.org/10.1152/ajpcell.00368.2022

Kogut M.M., Grabowska O., Wyrzykowski D., Samsonov S.A. Affinity and putative entrance mechanisms of alkyl sulfates into the β-CD cavity Journal of Molecular Liquids. 2022. Vol. 364: 119978.
https://doi.org/10.1016/j.molliq.2022.119978

Kogut M.M.Danielsson A., Ricard-Blum S., Samsonov S.A. Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis Computational Biology and Chemistry. 2022. Vol. 99: 107727.
https://doi.org/10.1016/j.compbiolchem.2022.107727

Marcisz M., Gaardløs M.Bojarski K.K., Siebenmorgen T., Zacharias M., Samsonov S.A. Explicit Solvent Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) in Molecular Modeling of Protein-Glycosaminoglycan Complexes J Comp Chem. 2022. Vol. 43: 1633–1640.
https://doi.org/10.1002/jcc.26965

Danielsson A.Kogut M.M.Maszota-Zieleniak M., Chopra P., Boons G.J., Samsonov S.A. Molecular Dynamics-based descriptors of 3-O-Sulfated Heparan Sulfate as Contributors of Protein Binding Specificity Computational Biology and Chemistry. 2022. Vol. 99: 107716.
https://doi.org/10.1016/j.compbiolchem.2022.107716

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. Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L:consequences in mucopolysaccharidosis Carbohydrate Polymers. 2022. Vol. 293: 119734.
https://doi.org/10.1016/j.carbpol.2022.119734

Lipska A.G., Anoniak A. M., Wesolowski P., Warszawski A., Samsonov S.A., Sieradzan A.K. Coarse- grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins Journal of Molecular Modeling. 2022. Vol. 293: 119734.
https://doi.org/10.1016/j.carbpol.2022.119734

Bertozo L., Kogut M., Maszota-Zieleniak A.Samsonov S.A., Ximenez V.F. Induced Circular Dichroism as a Tool to Monitor the Displacement of Ligands Between Albumins Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2022. Vol. 278: 121374.
https://doi.org/10.1016/j.saa.2022.121374

Maszota-Zieleniak M., Zsila F., Samsonov S.A. Molecular Dynamics Approaches Dissect Molecular Mechanisms Underlying Methylene Blue–Glycosaminoglycan Interactions Molecules. 2022. Vol. 27: 2654.
https://doi.org/10.3390/molecules27092654

Giatagana E-M., Berdiaki A., Gaardløs M.Samsonov S.A., Tzanakakis G.N., Nikitovic D. Biglycan interacts with type I insulin-like receptor (IGF-IR) signaling pathway to regulate osteosarcoma progression and response to chemotherapy Cancers. 2022. Vol 14: 1196.
https://doi.org/10.3390/cancers14051196

Bojarski K.K., Sage J., Lalmanach G., Lecaille F., Samsonov S.A. In silico and in vitro mapping of specificity patterns of glycosaminoglycans towards cysteine cathepsins B, L, K, S and V J Mol Graph Mod. 2022. Vol. 113: 108153
https://doi.org/10.1016/j.jmgm.2022.108153

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. Modulation of the expression and activity of cathepsin S in reconstructed human skin by neohesperidin dihydrochalcone Matrix Biology. 2022. Vol. 107: 97-112
https://doi.org/10.1016/j.matbio.2022.02.003

Kogut M.M.Marcisz M.Samsonov S.A. Modeling glycosaminoglycan-protein complexes Current Opinion in Structural Biology. 2022.
https://doi.org/10.1016/j.sbi.2022.102332

Liwo A., Sieradzan A.K., Karczyńska A.S., Lubecka E.A., Samsonov S.A., Czaplewski C., Krupa P., Mozolewska M. Practical Aspects of Computational Chemistry V. Chapter: Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry Springer Nature Switzerland AG. 2022.
https://doi.org/10.1007/978-3-030-83244-5_2

Grabowska O., Kogut M.M., Żamojć K., Samsonov S.A., Makowska J., Tesmar A., Chmur K., Wyrzykowski D., Chmurzyński L. Effect of Tetraphenylborate on Physicochemical Properties of Bovine Serum Albumin Molecules. 2021. Vol. 26: 6565
https://doi.org/10.3390/molecules26216565

Marcisz M.Maszota-Zieleniak M., Huard B., Samsonov S.A. Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans Biomolecules. 2021. Vol. 11: 1349.
https://doi.org/10.3390/biom11091349

Liwo A., Czaplewski C., Sieradzan A.K., Lipska A.G., Samsonov S.A., Murarka R.K. Theory and practice of coarse-grained molecular dynamics Biomolecules. 2021. Vol. 11: 1347.
https://doi.org/10.3390/biom11091347

Lensink M.F., Brysbaert G., Mauri T., Nadzirin N., Velankar S., Chaleil R.A.G., Clarence T., Bates P.A., Kong R., Liu B., Yang G., Liu M., Shi H., Lu X., Chang S., Roy R.S., Quadir F., Liu J., Cheng J., Antoniak A., Czaplewski C., Giełdoń A., Kogut M., Lipska A.G., Liwo A., Lubecka E.A., Maszota-Zieleniak M., Sieradzan A.K., Ślusarz R., Wesołowski P.A., Zięba K., De Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment Proteins. 2021.
https://doi.org/10.1002/prot.26222

Marcisz M., Zacharias M., Samsonov S.A. Modeling protein-glycosaminoglycan complexes: does the size matter? J Chem Inf Mod. 2021. Vol. 61: 4475–4485.
https://doi.org/10.1021/acs.jcim.1c00664

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. Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment J Mol Graph Mod. 2021. 108:108008
https://doi.org/10.1016/j.jmgm.2021.108008

Tesmar A., Kogut M.M., Żamojć K., Grabowska O., Chmur K., Samsonov S.A., Makowska J., Wyrzykowski D., Chmurzyński L. Physicochemical nature of sodium dodecyl sulfate interactions with bovine serum albumin revealed by interdisciplinary approaches Journal of Molecular Liquids. 2021. Vol. 340: 117185
https://doi.org/10.1016/j.molliq.2021.117185

Maszota-Zieleniak M.Danielsson A.Samsonov S.A. The potential role of glycosaminoglycans in serum amyloid A fibril formation by in silico approaches Matrix Biology Plus. 2021. Vol. 12: 100008
https://doi.org/10.1016/j.mbplus.2021.100080

Maszota-Zieleniak M., Zsila F., Samsonov S.A. Computational insights into heparin-small molecule interactions: evaluation of the balance between stacking and non-stacking binding modes. Carbohydrate Research Carbohydrate Research. 2021. Vol. 507: 108390
https://doi.org/10.1016/j.carres.2021.108390

Künze G., Huster D., Samsonov S.A. Investigation of the Structure of Regulatory Proteins Interacting with Glycosaminoglycans by Combining NMR Spectroscopy and Molecular Modeling – The Beginning of a Wonderful Friendship Biological Chemistry. 2021.
https://doi.org/10.1515/hsz-2021-0119

Gaardløs M., Samsonov S.A. , Sletmoen M., Sætrom G.I., Hjørnevik M., Sletta H., Tøndervik A., Aachmann F.L. Insights into the roles of charged residues in binding and processivity of mannuronan C-5 epimerase AlgE4 Glycobiology. 2021.
https://doi.org/10.1093/glycob/cwab025/

Marcisz M., Huard B., Lipska A.G., Samsonov S.A. Further analyses of APRIL/APRIL- Receptor/Glycosaminoglycan interactions by biochemical assays linked to computational studies Glycobiology. 2021.
https://doi.org/10.1093/glycob/cwab016

Bertozo L. C., Maszota-Zieleniak M., Bolean M., Ciancaglini P., Samsonov S.A., Ximenes V.F. Binding of fluorescent dansyl amino acids in albumin: when the access to the protein cavity is more important than the strength of binding Dyes and Pigments. 2021. Vol. 188: 109195
https://doi.org/10.1016/j.dyepig.2021.109195

Maszota-Zieleniak M.Marcisz M.Kogut M.M., Siebenmorgen T., Zacharias M., Samsonov S.A. Evaluation of Replica Exchange with Repulsive Scaling Approach for Docking Glycosaminoglycans J Comp Chem. 2021. Vol. 42: 1040–1053
https://doi.org/10.1002/JCC.26496

Samsonov S.A., Zsila F., Maszota-Zieleniak M. Acute phase α1-acid glycoprotein as a siderophore-capturing component of the human plasma: a molecular modeling study J Mol Graph Mod. 2021. 105:107861
https://doi.org/10.1016/j.jmgm.2021.107861

Kogut M.M.Maszota-Zieleniak M.Marcisz M.Samsonov S.A. Computational insights into the calcium ions role in protein-glycosaminoglycan systems. Phys Chem Chem Phys. 2021. Vol. 23: 3519–3530.
https://doi.org/10.1039/D0CP05438K

Bojarski K.K.Samsonov S.A. Role of oligosaccharide chain polarity in protein-glycosaminoglycan interactions. J Chem Inf Mod. 2021. Vol. 61: 455–466.
https://doi.org/10.1021/acs.jcim.0c01402

Zsila F., Samsonov S.A.Maszota-Zieleniak M. Mind your dye: the amyloid sensor thioflavin T interacts with sulfated glycosaminoglycans used to induce cross-β-sheet motifs. J Phys Chem B. 2020. Vol. 124: 11625–11633.
https://doi.org/10.1021/acs.jpcb.0c08273

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. The abnormal accumulation of heparan sulfate in patients with mucopolysaccharidosis prevents the elastolytic activity of cathepsin V. Carbohydrate Polymers. 2020. Vol. 253:117261.
https://doi.org/10.1016/j.carbpol.2020.117261

Gorbikova E., Samsonov S.A., Kalendar R. Probing proton-loading site of cytochrome c oxidase by time-resolved Fourier transform infrared spectroscopy. Molecules. 2020. Vol. 25:3393.
https://doi.org/10.3390/molecules25153393

Bojarski K.K., Karczyńska A.S., Samsonov S.A. The role of glycosaminoglycans in procathepsin B maturation – molecular mechanism elucidated by a computational study. J Chem Inf Mod. 2020. Vol. 60:2247–2256.
https://pubs.acs.org/doi/10.1021/acs.jcim.0c00023

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. Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability. Biochemie. Vol. 171–172:178–186.
https://doi.org/10.1016/j.biochi.2020.03.006

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. Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13. J Chem Inf Mod. 2020. Vol. 60:1844–1864.
https://pubs.acs.org/doi/10.1021/acs.jcim.9b00864

Glashagen G., de Vries S., Uciechowska-Kaczmarzyk U.Samsonov S.A., Murail S., Tuffery P., Zacharias M. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins. 2019. Vol. 88:1018–1028. https://doi.org/10.1002/prot.25860

Lecaille F., Chazeirat T., Bojarski K.K., Renault J., Saidi A., Prasad V.G.N.V, Samsonov S.A., Lalmanach G. Rat cathepsin K: enzymatic specificity and regulation of its collagenolytic activity. BBA – Proteins and Proteomics. 2019, Vol. 1868:140318.
https://doi.org/10.1016/j.bbapap.2019.140318

Plotnikova M.A., Klotchenko S.A., Kiselev A.A., Gorshkov A.N., Shurygina A.S., Vasilyev K.A., Uciechowska-Kaczmarzyk U.Samsonov S.A., Kovalenko A.L., Vasin A.V. Meglumine acridone acetate, the ionic salt of CMA and N-methylglucamine, induces apoptosis in human PBMCs via the mitochondrial pathway. Sci Rep. 2019, Vol. 9:18240.
https://doi.org/10.1038/s41598-019-54208-9

Lensink M.F., Brysbaert G., Nadzirin N., Velankar S., Chaleil R.A.G., Gerguri T., Bates P.A., Laine E., Carbone A., Grudinin S., Kong R., Liu R.R., Xu X.M., Shi H., Chang S., Eisenstein M., Karczynska A., Czaplewski C., Lubecka E., Lipska A., Krupa P., Mozolewska M., Golon Ł., Samsonov S., Liwo A., Crivelli S., Pagès G., Karasikov M., Kadukova M., Yan Y., Huang S.Y., Rosell M., Rodríguez-Lumbreras L.A., Romero-Durana M., Díaz-Bueno L., Fernandez-Recio J., Christoffer C., Terashi G., Shin W.H., Aderinwale T., Maddhuri Venkata Subraman S.R., Kihara D., Kozakov D., Vajda S., Porter K., Padhorny D., Desta I., Beglov D., Ignatov M., Kotelnikov S., Moal I.H., Ritchie D.W., Chauvot de Beauchêne I., Maigret B., Devignes M.D., Ruiz Echartea M.E., Barradas-Bautista D., Cao Z., Cavallo L., Oliva R., Cao Y., Shen Y., Baek M., Park T., Woo H., Seok C., Braitbard M., Bitton L., Scheidman-Duhovny D., Dapkūnas J., Olechnovič K., Venclovas Č., Kundrotas P.J., Belkin S., Chakravarty D., Badal V.D., Vakser I.A., Vreven T., Vangaveti S., Borrman T., Weng Z., Guest J.D., Gowthaman R., Pierce B.G., Xu X., Duan R., Qiu L., Hou J., Ryan Merideth B., Ma Z., Cheng J., Zou X., Koukos P.I., Roel-Touris J., Ambrosetti F., Geng C., Schaarschmidt J., Trellet M.E., Melquiond A.S.J., Xue L., Jiménez-García B., van Noort C.W., Honorato R.V., Bonvin A.M.J.J., Wodak S.J. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins. 2019, Vol. 87:1200–1221.
https://doi.org/10.1002/prot.25838

Potthoff J.Bojarski K.K., Kohut G., Lipska A.G., Liwo A., Kessler E., Ricard-Blum S., Samsonov S.A. Analysis of procollagen C-proteinase enhancer-1/glycosaminoglycan binding sites and of the potential role of calcium ions in the interaction. Int J Mol Sci, Special Issue: “Recent Developments on Protein–Ligand Interactions: From Structure, Function to Applications”. 2019, Vol. 20:5021.
https://doi.org/10.3390/ijms20205021

Ilyechova E., Miliukhina I., Karpenko M., Orlov I., Puchkova L., Samsonov S.A. A case of Parkinson’s disease with early onset in a heterozygous carrier of mutation in Atp7b gene. J Pers Med. 2019, Vol. 9:41.
https://doi.org/10.3390/jpm9030041

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.
https://doi.org/10.1039/C9CP03750K

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. Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. J Mol Graph Mod. 2019, Vol. 92:154–166.
https://doi.org/10.1016/j.jmgm.2019.07.013

Bojarski K.K., Becher J., Riemer T., Lemmnitzer K., Möller 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.
https://doi.org/10.1016/j.molstruc.2019.07.064

Samsonov S.A., Freza 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. https://doi.org/10.1016/j.carres.2019.107742

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.
https://doi.org10.1093/glycob/cwz047

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.
https://doi.org/10.1039/C9CP00471H

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.
https://doi.org/10.1016/j.jmgm.2019.04.001

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.
https://doi.org/10.1002/bip.23269

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.
https://doi.org/10.1002/jcc.25797

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.
https://doi.org/10.1002/bip.23252

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, No. 32:7821–7827.
https://doi.org/10.1021/acs.jpcb.8b03658

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.
https://doi.org/10.1038/s41598-018-30190-6

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.
https://doi.org/10.1016/j.jmgm.2018.04.015

Zsila F., Samsonov S.A. Molecular interactions of the anticancer agent ellipticine with glycosaminoglycans by in silico analysis. Carb Res. 2018. 462:28–33.
https://doi.org/10.1016/j.carres.2018.03.014

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:e23103.
https://doi.org/10.1002/bip.23103

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. 1762:445–454.
https://doi.org/10.1007/978-1-4939-7756-7_22