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Items: 1 to 50 of 58

1.

Modeling large protein-glycosaminoglycan complexes using a fragment-based approach.

Samsonov SA, Zacharias M, Chauvot de Beauchene I.

J Comput Chem. 2019 Feb 15. doi: 10.1002/jcc.25797. [Epub ahead of print]

PMID:
30768805
2.

[Single nucleotide polymorphisms of the CYP11B2, GNB3 and NOS3 genes in various ethnic groups of arctic zone of yakutia suffering from arterial hypertension].

Komzin KV, Petrova PG, Strekalovskaya AA, Samsonov SN, Parshina SS, Terentyeva YV.

Wiad Lek. 2018;71(9):1742-1748. Russian.

PMID:
30737933
3.

Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations.

Bojarski KK, Sieradzan AK, Samsonov SA.

Biopolymers. 2019 Jan 22:e23252. doi: 10.1002/bip.23252. [Epub ahead of print]

PMID:
30667535
4.

Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners.

Vallet SD, Miele AE, Uciechowska-Kaczmarzyk U, Liwo A, Duclos B, Samsonov SA, Ricard-Blum S.

Sci Rep. 2018 Aug 6;8(1):11768. doi: 10.1038/s41598-018-30190-6.

5.

Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems.

Kohut G, Liwo A, Bősze S, Beke-Somfai T, Samsonov SA.

J Phys Chem B. 2018 Aug 16;122(32):7821-7827. doi: 10.1021/acs.jpcb.8b03658. Epub 2018 Aug 8.

PMID:
30049211
6.

Molecular dynamics-based model of VEGF-A and its heparin interactions.

Uciechowska-Kaczmarzyk U, Babik S, Zsila F, Bojarski KK, Beke-Somfai T, Samsonov SA.

J Mol Graph Model. 2018 Jun;82:157-166. doi: 10.1016/j.jmgm.2018.04.015. Epub 2018 Apr 27.

PMID:
29738889
7.

Molecular interactions of the anticancer agent ellipticine with glycosaminoglycans by in silico analysis.

Zsila F, Samsonov SA.

Carbohydr Res. 2018 Jun 15;462:28-33. doi: 10.1016/j.carres.2018.03.014. Epub 2018 Apr 3.

PMID:
29655053
8.

Computational Analysis of Solvent Inclusion in Docking Studies of Protein-Glycosaminoglycan Systems.

Samsonov SA.

Methods Mol Biol. 2018;1762:445-454. doi: 10.1007/978-1-4939-7756-7_22.

PMID:
29594785
9.

The effect of interleukin-8 truncations on its interactions with glycosaminoglycans.

Nordsieck K, Baumann L, Hintze V, Pisabarro MT, Schnabelrauch M, Beck-Sickinger AG, Samsonov SA.

Biopolymers. 2018 Aug;109(10):e23103. doi: 10.1002/bip.23103. Epub 2018 Jan 27.

PMID:
29377072
10.

Sulfated Hyaluronan Derivatives Modulate TGF-β1:Receptor Complex Formation: Possible Consequences for TGF-β1 Signaling.

Koehler L, Samsonov S, Rother S, Vogel S, Köhling S, Moeller S, Schnabelrauch M, Rademann J, Hempel U, Pisabarro MT, Scharnweber D, Hintze V.

Sci Rep. 2017 Apr 26;7(1):1210. doi: 10.1038/s41598-017-01264-8.

11.

Sulfated Hyaluronan Alters Endothelial Cell Activation in Vitro by Controlling the Biological Activity of the Angiogenic Factors Vascular Endothelial Growth Factor-A and Tissue Inhibitor of Metalloproteinase-3.

Rother S, Samsonov SA, Moeller S, Schnabelrauch M, Rademann J, Blaszkiewicz J, Köhling S, Waltenberger J, Pisabarro MT, Scharnweber D, Hintze V.

ACS Appl Mater Interfaces. 2017 Mar 22;9(11):9539-9550. doi: 10.1021/acsami.7b01300. Epub 2017 Mar 13.

PMID:
28248081
12.

The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from a Combined Bioinformatical and Experimental Approach.

Anders G, Hassiepen U, Theisgen S, Heymann S, Muller L, Panigada T, Huster D, Samsonov SA.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jan-Feb;15(1):300-308. doi: 10.1109/TCBB.2016.2614821. Epub 2016 Oct 3.

PMID:
28113517
13.

Computational drill down on FGF1-heparin interactions through methodological evaluation.

Babik S, Samsonov SA, Pisabarro MT.

Glycoconj J. 2017 Jun;34(3):427-440. doi: 10.1007/s10719-016-9745-4. Epub 2016 Nov 17.

14.

Structural and functional insights into the interaction of sulfated glycosaminoglycans with tissue inhibitor of metalloproteinase-3 - A possible regulatory role on extracellular matrix homeostasis.

Rother S, Samsonov SA, Hofmann T, Blaszkiewicz J, Köhling S, Moeller S, Schnabelrauch M, Rademann J, Kalkhof S, von Bergen M, Pisabarro MT, Scharnweber D, Hintze V.

Acta Biomater. 2016 Nov;45:143-154. doi: 10.1016/j.actbio.2016.08.030. Epub 2016 Aug 18.

PMID:
27545813
15.

The HELIO-geophysical storminess health effects in the cardio-vascular system of a human in the middle and high latitudes.

Samsonov SN, Manykina VI, Kleimenova NG, Parshina SS, Strekalovskaya AA, Petrova PG.

Wiad Lek. 2016;69(3 pt 2):537-541.

PMID:
27717941
16.

Sulfated Hyaluronan Alters the Interaction Profile of TIMP-3 with the Endocytic Receptor LRP-1 Clusters II and IV and Increases the Extracellular TIMP-3 Level of Human Bone Marrow Stromal Cells.

Rother S, Samsonov SA, Hempel U, Vogel S, Moeller S, Blaszkiewicz J, Köhling S, Schnabelrauch M, Rademann J, Pisabarro MT, Hintze V, Scharnweber D.

Biomacromolecules. 2016 Oct 10;17(10):3252-3261. Epub 2016 Sep 20.

PMID:
27610455
17.

Computational analysis of interactions in structurally available protein-glycosaminoglycan complexes.

Samsonov SA, Pisabarro MT.

Glycobiology. 2016 Aug;26(8):850-861. doi: 10.1093/glycob/cww055. Epub 2016 Jun 24.

PMID:
27496767
18.

The structural investigation of glycosaminoglycan binding to CXCL12 displays distinct interaction sites.

Panitz N, Theisgen S, Samsonov SA, Gehrcke JP, Baumann L, Bellmann-Sickert K, Köhling S, Pisabarro MT, Rademann J, Huster D, Beck-Sickinger AG.

Glycobiology. 2016 Nov;26(11):1209-1221. doi: 10.1093/glycob/cww059. Epub 2016 Jun 24.

PMID:
27496764
19.

The HELIO-geophysical storminess health effects in the cardio-vascular system of a human in the middle and high latitudes.

Samsonov SN, Manykina VI, Kleimenova NG, Parshina SS, Strekalovskaya AA, Petrova PG.

Wiad Lek. 2016;69(3 pt 2):537-541.

PMID:
28478422
20.

Glycosaminoglycan derivatives: promising candidates for the design of functional biomaterials.

Scharnweber D, Hübner L, Rother S, Hempel U, Anderegg U, Samsonov SA, Pisabarro MT, Hofbauer L, Schnabelrauch M, Franz S, Simon J, Hintze V.

J Mater Sci Mater Med. 2015 Sep;26(9):232. doi: 10.1007/s10856-015-5563-7. Epub 2015 Sep 10.

PMID:
26358319
21.

Structural and functional insights into sclerostin-glycosaminoglycan interactions in bone.

Salbach-Hirsch J, Samsonov SA, Hintze V, Hofbauer C, Picke AK, Rauner M, Gehrcke JP, Moeller S, Schnabelrauch M, Scharnweber D, Pisabarro MT, Hofbauer LC.

Biomaterials. 2015 Oct;67:335-45. doi: 10.1016/j.biomaterials.2015.07.021. Epub 2015 Jul 15.

PMID:
26232882
22.

Antimicrobial Peptide LL-37 Is Both a Substrate of Cathepsins S and K and a Selective Inhibitor of Cathepsin L.

Andrault PM, Samsonov SA, Weber G, Coquet L, Nazmi K, Bolscher JG, Lalmanach AC, Jouenne T, Brömme D, Pisabarro MT, Lalmanach G, Lecaille F.

Biochemistry. 2015 May 5;54(17):2785-98. doi: 10.1021/acs.biochem.5b00231. Epub 2015 Apr 27.

PMID:
25884905
23.

Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry.

Hofmann T, Samsonov SA, Pichert A, Lemmnitzer K, Schiller J, Huster D, Pisabarro MT, von Bergen M, Kalkhof S.

Methods. 2015 Nov 1;89:45-53. doi: 10.1016/j.ymeth.2015.02.011. Epub 2015 Feb 26.

PMID:
25726910
24.

Insights into the preferential order of strand exchange in the Cre/loxP recombinase system: impact of the DNA spacer flanking sequence and flexibility.

Abi-Ghanem J, Samsonov SA, Pisabarro MT.

J Comput Aided Mol Des. 2015 Mar;29(3):271-82. doi: 10.1007/s10822-014-9825-0. Epub 2015 Jan 3.

PMID:
25555999
25.

Segmented lateral dyke growth in a rifting event at Bárðarbunga volcanic system, Iceland.

Sigmundsson F, Hooper A, Hreinsdóttir S, Vogfjörd KS, Ófeigsson BG, Heimisson ER, Dumont S, Parks M, Spaans K, Gudmundsson GB, Drouin V, Árnadóttir T, Jónsdóttir K, Gudmundsson MT, Högnadóttir T, Fridriksdóttir HM, Hensch M, Einarsson P, Magnússon E, Samsonov S, Brandsdóttir B, White RS, Ágústsdóttir T, Greenfield T, Green RG, Hjartardóttir ÁR, Pedersen R, Bennett RA, Geirsson H, La Femina PC, Björnsson H, Pálsson F, Sturkell E, Bean CJ, Möllhoff M, Braiden AK, Eibl EP.

Nature. 2015 Jan 8;517(7533):191-5. doi: 10.1038/nature14111. Epub 2014 Dec 15.

26.

Coarse-grained model of glycosaminoglycans.

Samsonov SA, Bichmann L, Pisabarro MT.

J Chem Inf Model. 2015 Jan 26;55(1):114-24. doi: 10.1021/ci500669w. Epub 2014 Dec 19.

PMID:
25490039
27.

Continuing megathrust earthquake potential in Chile after the 2014 Iquique earthquake.

Hayes GP, Herman MW, Barnhart WD, Furlong KP, Riquelme S, Benz HM, Bergman E, Barrientos S, Earle PS, Samsonov S.

Nature. 2014 Aug 21;512(7514):295-8. doi: 10.1038/nature13677. Epub 2014 Aug 13.

PMID:
25119028
28.

Sulfated glycosaminoglycans exploit the conformational plasticity of bone morphogenetic protein-2 (BMP-2) and alter the interaction profile with its receptor.

Hintze V, Samsonov SA, Anselmi M, Moeller S, Becher J, Schnabelrauch M, Scharnweber D, Pisabarro MT.

Biomacromolecules. 2014 Aug 11;15(8):3083-92. doi: 10.1021/bm5006855. Epub 2014 Jul 16.

PMID:
25029480
29.

Glycosaminoglycan monosaccharide blocks analysis by quantum mechanics, molecular dynamics, and nuclear magnetic resonance.

Samsonov SA, Theisgen S, Riemer T, Huster D, Pisabarro MT.

Biomed Res Int. 2014;2014:808071. doi: 10.1155/2014/808071. Epub 2014 Apr 7.

30.

Multipose binding in molecular docking.

Atkovska K, Samsonov SA, Paszkowski-Rogacz M, Pisabarro MT.

Int J Mol Sci. 2014 Feb 14;15(2):2622-45. doi: 10.3390/ijms15022622.

31.

Flexibility and explicit solvent in molecular-dynamics-based docking of protein-glycosaminoglycan systems.

Samsonov SA, Gehrcke JP, Pisabarro MT.

J Chem Inf Model. 2014 Feb 24;54(2):582-92. doi: 10.1021/ci4006047. Epub 2014 Feb 12.

PMID:
24479827
32.

Importance of IdoA and IdoA(2S) ring conformations in computational studies of glycosaminoglycan-protein interactions.

Samsonov SA, Pisabarro MT.

Carbohydr Res. 2013 Nov 15;381:133-7. doi: 10.1016/j.carres.2013.09.005. Epub 2013 Sep 16.

PMID:
24096273
33.

Investigation of lysine side chain interactions of interleukin-8 with heparin and other glycosaminoglycans studied by a methylation-NMR approach.

Möbius K, Nordsieck K, Pichert A, Samsonov SA, Thomas L, Schiller J, Kalkhof S, Teresa Pisabarro M, Beck-Sickinger AG, Huster D.

Glycobiology. 2013 Nov;23(11):1260-9. doi: 10.1093/glycob/cwt062. Epub 2013 Aug 27.

PMID:
23982278
34.

Binding of chondroitin 4-sulfate to cathepsin S regulates its enzymatic activity.

Sage J, Mallèvre F, Barbarin-Costes F, Samsonov SA, Gehrcke JP, Pisabarro MT, Perrier E, Schnebert S, Roget A, Livache T, Nizard C, Lalmanach G, Lecaille F.

Biochemistry. 2013 Sep 17;52(37):6487-98. doi: 10.1021/bi400925g. Epub 2013 Sep 4.

PMID:
23968158
35.

The promotion of osteoclastogenesis by sulfated hyaluronan through interference with osteoprotegerin and receptor activator of NF-κB ligand/osteoprotegerin complex formation.

Salbach-Hirsch J, Kraemer J, Rauner M, Samsonov SA, Pisabarro MT, Moeller S, Schnabelrauch M, Scharnweber D, Hofbauer LC, Hintze V.

Biomaterials. 2013 Oct;34(31):7653-61. doi: 10.1016/j.biomaterials.2013.06.053. Epub 2013 Jul 17.

PMID:
23871544
36.

Artificial extracellular matrix composed of collagen I and highly sulfated hyaluronan interferes with TGFβ(1) signaling and prevents TGFβ(1)-induced myofibroblast differentiation.

van der Smissen A, Samsonov S, Hintze V, Scharnweber D, Moeller S, Schnabelrauch M, Pisabarro MT, Anderegg U.

Acta Biomater. 2013 Aug;9(8):7775-86. doi: 10.1016/j.actbio.2013.04.023. Epub 2013 Apr 18.

PMID:
23602877
37.

Residue 75 of interleukin-8 is crucial for its interactions with glycosaminoglycans.

Nordsieck K, Pichert A, Samsonov SA, Thomas L, Berger C, Pisabarro MT, Huster D, Beck-Sickinger AG.

Chembiochem. 2012 Nov 26;13(17):2558-66. doi: 10.1002/cbic.201200467. Epub 2012 Oct 15.

PMID:
23070988
38.

The influence of glycosaminoglycans on IL-8-mediated functions of neutrophils.

Schlorke D, Thomas L, Samsonov SA, Huster D, Arnhold J, Pichert A.

Carbohydr Res. 2012 Jul 15;356:196-203. doi: 10.1016/j.carres.2012.02.025. Epub 2012 Mar 5.

PMID:
22444322
39.

SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds.

Teyra J, Samsonov SA, Schreiber S, Pisabarro MT.

BMC Bioinformatics. 2011 Oct 13;12:398. doi: 10.1186/1471-2105-12-398.

40.

Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular modeling.

Pichert A, Samsonov SA, Theisgen S, Thomas L, Baumann L, Schiller J, Beck-Sickinger AG, Huster D, Pisabarro MT.

Glycobiology. 2012 Jan;22(1):134-45. doi: 10.1093/glycob/cwr120. Epub 2011 Aug 26.

41.

Docking glycosaminoglycans to proteins: analysis of solvent inclusion.

Samsonov SA, Teyra J, Pisabarro MT.

J Comput Aided Mol Des. 2011 May;25(5):477-89. doi: 10.1007/s10822-011-9433-1. Epub 2011 May 20.

42.

A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia.

Słabicki M, Theis M, Krastev DB, Samsonov S, Mundwiller E, Junqueira M, Paszkowski-Rogacz M, Teyra J, Heninger AK, Poser I, Prieur F, Truchetto J, Confavreux C, Marelli C, Durr A, Camdessanche JP, Brice A, Shevchenko A, Pisabarro MT, Stevanin G, Buchholz F.

PLoS Biol. 2010 Jun 29;8(6):e1000408. doi: 10.1371/journal.pbio.1000408.

43.

Fluorine in protein environments: a QM and MD study.

Samsonov SA, Salwiczek M, Anders G, Koksch B, Pisabarro MT.

J Phys Chem B. 2009 Dec 24;113(51):16400-8. doi: 10.1021/jp906402b.

PMID:
19947631
44.

Position-dependent effects of fluorinated amino acids on the hydrophobic core formation of a heterodimeric coiled coil.

Salwiczek M, Samsonov S, Vagt T, Nyakatura E, Fleige E, Numata J, Cölfen H, Pisabarro MT, Koksch B.

Chemistry. 2009 Aug 3;15(31):7628-36. doi: 10.1002/chem.200802136.

PMID:
19579235
45.

Selection of a buried salt bridge by phage display.

Vagt T, Jäckel C, Samsonov S, Teresa Pisabarro M, Koksch B.

Bioorg Med Chem Lett. 2009 Jul 15;19(14):3924-7. doi: 10.1016/j.bmcl.2009.03.062. Epub 2009 Mar 21.

PMID:
19369078
46.

Analysis of the impact of solvent on contacts prediction in proteins.

Samsonov SA, Teyra J, Anders G, Pisabarro MT.

BMC Struct Biol. 2009 Apr 15;9:22. doi: 10.1186/1472-6807-9-22.

47.

A molecular dynamics approach to study the importance of solvent in protein interactions.

Samsonov S, Teyra J, Pisabarro MT.

Proteins. 2008 Nov 1;73(2):515-25. doi: 10.1002/prot.22076.

PMID:
18452208
48.

[Relations between CTR1 gene activity and copper status in different rat organs].

Samsonov SA, Platonova NA, Skvortsov AN, Tsymbalenko NV, Vasin AV, Puchkova LV.

Mol Biol (Mosk). 2006 Mar-Apr;40(2):239-51. Russian.

PMID:
16637264
49.

[Heliogeophysical disturbances and exacerbations of cardiovascular disease].

Samsonov SN, Petrova PG, Sokolov VD, Strekalovskaia AA, Makarov GA, Ivanov KI.

Zh Nevrol Psikhiatr Im S S Korsakova. 2005;(Suppl 14):18-22. Russian.

PMID:
16184849
50.

[Mitochondrial ceruloplasmin of mammals].

Vasin AV, Platonova NA, Povalikhin RG, Klotchenko SA, Samsonov SA, Tsymbalenko NV, Puchkova LV.

Mol Biol (Mosk). 2005 Jan-Feb;39(1):48-60. Russian.

PMID:
15773547

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