Laboratory of Biopolymers Structure | Intercollegiate Faculty of Biotechnology UG&MUG

Laboratory of Biopolymers Structure

Last modified: 
2018, May 18 - 12:51pm

PROFILE

Research areas:

  • Temperature influence on structure and biological activity of small proteins and peptides
  • Development of coarse-grained force-field unres and its application to study biochemical processes
  • Experimental and theoretical study on mechanism of protein folding
  • Theoretical studies on role of the myoglobin in unsaturated fatty acids metabolism
  • Experimental and theoretical studies on transition metal ion complexes formed by biologically active peptides

RESEARCH TEAM

Laboratory of Biopolymers Structure

Intercollegiate Faculty of Biotechnology UG&MUG
Abrahama 58 Street, 80-307 Gdańsk, Poland

tel.: +48 58 523 6428

team prof. Ołdziej

STAFF LIST

Head: Assoc. Prof. Stanisław Ołdziej
tel.: +48 58 523 6428 [e-mail] 

List of PhD and PhD students:

dr Wioletta Żmudzińska [link]
tel.: +48 58 523 6434 [e-mail]

MSc Aleksandra Lewandowska
tel.: +48 58 523 6434 [e-mail]
MSc Marcel Thiel
tel.: +48 58 523 6434
MSc Anna Fel
tel.: +48 58 523 6434

PUBLICATION

  1. Lewandowska Aleksandra Ewa, Macur Katarzyna, Czaplewska Paulina, Liss Joanna, Łukaszuk Krzysztof, Ołdziej Stanisław. Human follicular fluid proteomic and peptidomic composition quantitative studies by SWATH-MS methodology. Applicability of high pH RP-HPLC fractionation. Journal of Proteomics 2018, (w druku) (doi: 10.1016/j.jprot.2018.03.010)
  2. Lewandowska Aleksandra EwaMacur KatarzynaCzaplewska Paulina, Liss Joanna, Łukaszuk Krzysztof, Oldziej Stanislaw. Qualitative and quantitative analysis of proteome and peptidome of human follicular fluid using multiple samples from single donor with LC-MS and SWATH methodology. Journal of Proteome Research 2017, 16(8): pp 3053–3067 (doi: 10.1021/acs.jproteome.7b00366)
  3. Krupa Pawel, Hałabis AnnaŻmudzińska WiolettaOłdziej Stanisław, Scheraga Harold Abraham, Liwo Adam. Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics. Journal of Chemical Information and Modeling2017, 57(9): 2364-2377 (doi: 10.1021/acs.jcim.7b00254)
  4. Uber Dorota, Wyrzykowski Dariszu, Tiberi Caterina, Sabatino Giuseppina, Żmudzińska Wioletta, Chmurzyński Lech, Papini Anna Maria, Makowska Joanna. Conformation-dependent affinity of Cu(II) ions peptide complexes derived from the human Pin1 protein. Journal  of Thermal Analysis and Calorimetry 2017, 127(2):  1431–1443 (doi: 10.1007/s10973-016-5387-9).
  5. Spodzieja Marta, Kalejta Katarzyna, Kołodziejczyk Aleksandra S., Maszota‐Zieleniak Martyna, Rodziewicz‐Motowidło Sylwia, Żmudzińska Wioletta,  Czaplewska Paulina. Characteristics of C‐terminal, β‐amyloid peptide binding fragment of neuroprotective protease inhibitor, cystatin C. Journal of Molecular Recognition2017, 30: e2581 (doi: 10.1002/jmr.2581)
  6. Jaworski Paweł, Donczew Rafał,  Mielke Thorsten, Thiel MarcelOłdziej Stanisław, Weigel Christoph, Pawlik Anna Magdalena. Unique and universal features of Epsilonproteobacterial origins of chromosome replication and DnaA-DnaA box interactions. Frontiers in Microbiology2016, 7: 15555 (doi: 10.3389/fmicb.2016.01555)
  7. Makowska Joanna, Żamojć Krzysztof, Wyrzykowski Dariusz, Żmudzińska Wioletta, Uber Dorota, Wierzbicka Małgorzata, Wiczk Wiesław, Chmurzyński Lech.Probing the binding of Cu2 + ions to a fragment of the Aβ(1–42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations. Biophysical Chemistry 2016 (w druku)  (doi: 10.1016/j.bpc.2016.06.006)​​
  8. Uber Dorota, Wyrzykowski Dariszu, Tiberi Caterina, Sabatino Giuseppina, Żmudzińska Wioletta, Chmurzyński Lech, Papini Anna Maria, Makowska Joanna. Conformation-dependent affinity of Cu(II) ions peptide complexes derived from the human Pin1 protein. Journal  of Thermal Analysis and Calorimetry 2016 (w druku)  (doi:10.1007/s10973-016-5387-9)
  9. Łodyga-Chruścińska Elżbieta, Symonowicz Marzena, Sykuła Anna, Bujacz Anna, Garribba Eugenio, Rowińska-Żyrek Magdalena, Ołdziej Stanisław, Klewicka Elżbieta, Janicka Magdalena, Królewska Karolina, Cieślak Marcin, Brodowska Katarzyna, Chruścinski Longin. Chelating ability and biological activity of hesperetin Schiff base. Journal of Inorganic Biochemistry 2015, 143: 34-47 (doi: 10.1016/j.jinorgbio.2014.11.005).
  10. Wiśniewska Marta, Sobolewski EmilOłdziej Stanisław, Liwo Adam, Scheraga Harold A., Makowski Mariusz. Theoretical studies of interactions between O-phosphorylated and standard amino-acid side-chain models in water. Journal of Physical Chemistry B 2015, 119(27): 8526-8534 (doi: 10.1021/acs.jpcb.5b04782).
  11. Yu Hyun Young, Ziegelhoffer Thomas, Osipiuk Jerzy, Ciesielski Szymon J., Baranowski Maciej, Zhou Min, Joachimiak Andrzej, Craig Elizabeth A. Roles of Intramolecular and Intermolecular Interactions in Functional Regulation of the Hsp70 J-protein Co-Chaperone Sis1. Journal of Molecular Biology 2015, 427(7): 1632-1643 (doi: 10.1016/j.jmb.2015.02.007).
  12. Zaborowski Bartłomiej, Jagieła Dawid, Czaplewski Cezary, Hałabis AnnaLewandowska AgnieszkaŻmudzińska WiolettaOłdziej Stanisław, Karczyńska Agnieszka, Omieczynski Christian, Wirecki Tomasz, Liwo Adam. A Maximum-Likelihood Approach to Force-Field Calibration. Journal of Chemical Information and Modeling 2015, przyjęta do druku (doi: 10.1021/acs.jcim.5b00395).
  13. Liwo Adam, Baranowski Maciej, Czaplewski Cezary, Gołaś Ewa, He Yi, Jagieła Dawid, Krupa Paweł, Maciejczyk Maciej, Makowski Mariusz, Mozolewska Magdalena A., Niadzvedtski Andrei, Ołdziej Stanisław, Scheraga Harold A., Sieradzan Adam K., Ślusarz Rafał, Wirecki Tomasz, Yin Yanping, Zaborowski Bartłomiej. A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions. Journal of Molecular Modeling 2014, 20(8): art. no 2306 (1-15) (doi: 10.1007/s00894-014-2306-5).
  14. Makowska Joanna, Uber Dorota, Żmudzińska Wioletta, Chmurzyński Lech. Conformational analysis of fragment of human Pin1 WW domain: influence of charged amino-acid residues on β-hairpin structure. TASK Quarterly 2014, 18(4): 343-349.
  15. Makowska Joanna, Żmudzińska Wioletta, Uber Dorota, Chmurzyński Lech. A study of the influence of charged residues on b-Hairpin formation by nuclear magnetic resonance and molecular dynamics. Protein Journal 2014, 33(6): 525-535 (doi: 10.1007/s10930-014-9585-7).
  16. He Yi, Maciejczyk Maciej, Ołdziej Stanisław, Scheraga Harold A., Liwo Adam. Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix. Physical Review Letters 2013, 110(9): art. no 098101 (1-5).
  17. He Yi, Mozolewska Magdalena A., Krupa Paweł, Sieradzan Adam K., Wirecki Tomasz K., Liwo Adam, Kachlishwili Khatuna, Rackovsky Shalom, Jagieła Dawid, Ślusarz Rafał, Czaplewski Cezary R., Ołdziej Stanisław, Scheraga Harold A. Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(37): 14936-14941.
  18. Janicka-Klos Anna, Porciatti Elena, Valensin Daniela, Conato Chiara, Remelli Maurizio, Ołdziej Stanisław, Valensinb Gianni, Kozlowski Henryk. The unusual stabilization of the Ni2+ and Cu2+ complexes with NSFRY. Dalton Transactions 2013, 42(2): 448-458.
  19. Krupa Paweł, Sieradzan Adam K., Rackovsky S., Baranowski MaciejOłdziej Stanisław, Scheraga Harold A., Liwo Adam, Czaplewski Cezary. Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States. Journal of Chemical Theory and Computation 2013, 9(10): 4620-4632.
  20. Sahi Chandan, Kominek Jacek, Ziegelhoffer Thomas, Yu Hyun-Young, Baranowski MaciejMarszałek Jarosław, Craig Elizabeth A. Sequential Duplications of an Ancient Member of the DnaJ-Family Expanded the Functional Chaperone Network in the Eukaryotic Cytosol. Molecular Biology and Evolution 2013, 30(5): 985-998.
  21. Gołaś Ewa, Maisuradze Gia G., Senet Patrick, Ołdziej Stanisław, Czaplewski Cezary, Scheraga Harold A., Liwo Adam. Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. Journal of Chemical Theory and Computation 2012, 8(5): 1750-1764.
  22. Hałabis AnnaŻmudzińska Wioletta, Liwo A., Ołdziej S. Conformational dynamics of the trp-cage miniprotein at its folding temperature. Journal of Physical Chemistry B 2012, 116(23): 6898-6907.
  23. Makowska Joanna, Liwo Adam, Żmudzińska WiolettaLewandowska Agnieszka, Chmurzyński Lech, Scheraga Harold A. Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal. Biopolymers 2012, 97(4): 240-249.
  24. Ołdziej Stanisław, Czaplewski Cezary, Liwo Adam, Vila JA., Scheraga Harold A. 1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins. W: Comprehensive biophysics (1 Edycja). Red. Edward Egelman. Academic Press 2012 (ISBN 9780123749208) 1: 494-513.
  25. Sobolewski E.Ołdziej S., Wiśniewska M., Liwo A., Makowski M. Toward temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. II. Molecular dynamics study of pairs of different types of interactions in water at various temperatures. Journal of Physical Chemistry B 2012, 116(23): 6844-6853.
  26. Łodyga-Chruścińska E., Ołdziej S., Sochacka E., Korzycka K., Chruściński L., Micera G., Sanna D., Turek M., Pawlak J. Impact of histidine residue on chelating ability of 2′-deoxyriboadenosine. Journal of Inorganic Biochemistry 2011, 105(9): 1212-1219.
  27. Makowski M., Liwo A., Sobolewski E., Scheraga H.A. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains. Journal of Physical Chemistry B 2011, 115(19): 6119-6129.
  28. Śladewska Anna, Szymańska Aneta, Kordalska Marlena, Lewandowska Agnieszka, Kołodziejczyk Aleksandra S., Paraschiv Gabriela, Przybylski Michael, Czaplewska Paulina. Identification of the epitope for anti-cystatin C antibody. Journal of Molecular Recognition 2011, 24(4): 687-699.
  29. Czaplewski C., Liwo A., Makowski M., Ołdziej S., Scheraga H. A. Coarse-grained models of proteins: theory and applications. W: Multiscale approaches to protein modeling. Ed. A. Kolinski, Springer, London 2010 (ISBN-13: 978-1-4419-6888-3) Chapter 3: 35-84.
  30. Brasun Justyna, Matera-Witkiewicz Agnieszka, Kamysz Elżbieta, Kamysz Wojciech, Ołdziej Stanisław. The influence of the cyclopeptide sequence on its coordination abilities towards Cu(II). Polyhedron 2010, 29(6): 1535-1542.
  31. Kozak Maciej, Lewandowska AgnieszkaOłdziej Stanisław, Rodziewicz-Motowidło Sylwia, Liwo Adam. Combination of SAXS and NMR techniques as a tool for the determination of peptide structure in solution. Journal of Physical Chemistry Letters 2010, 1(20): 3128-3131.
  32. Lewandowska AgnieszkaOłdziej Stanisław, Liwo Adam, Scheraga Harold A. beta-hairpin-forming peptides; models of early stages of protein folding. Biophysical Chemistry 2010, 151(1-2): 1-9.
  33. Lewandowska AgnieszkaOłdziej Stanisław, Liwo Adam, Scheraga Harold A. Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions. Proteins-Structure Function and Bioinformatics 2010, 78(3): 723-737.
  34. Lewandowska AgnieszkaOłdziej Stanisław, Liwo Adam, Scheraga Harold A. Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein. Biopolymers 2010, 93(5): 469-480.
  35. Liwo Adam, Ołdziej Stanisław, Czaplewski Cezary, Kleinerman Dana S., Blood Philip, Scheraga Harold A. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems: Toward millisecond-scale simulations of protein structure, dynamics, and thermodynamics. Journal of Chemical Theory and Computation 2010, 6(3): 890-909.
  36. Maisuradze Gia G., Liwo Adam, Ołdziej Stanisław, Scheraga Harold A. Evidence, from Simulations, of a Single State with Residual Native Structure at the Thermal Denaturation Midpoint of a Small Globular Protein. Journal of the American Chemical Society 2010, 132(27): 9444-9452.
  37. Ołdziej Stanisław, Czaplewski Cezary, Liwo Adam, Scheraga Harold A. Towards temperature dependent coarse-grained potential of side-chain interactions for protein folding simulations. II. Simple functional forms for the side-chain-interaction potential: Effect on simulated heat capacity and radius of gyration of staphyloco. W: 10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2010, Philadelphia, Pennsylvania, USA, May 31-June 3 2010. IEEE Computer Society 2010 (ISBN 978-0-7695-4083-2) 5521680: 263-266.
  38. Brasuń J., Matera A., Ołdziej S., Pratesi A., Ginanneschi M., Messori L. Impact of ring size on the copper(II) coordination abilities of cyclic tetrapeptides. Journal of Inorganic Biochemistry 2009, 103(5): 813-817.
  39.  Łodyga-Chruścińska E., Ołdziej S., Sanna D., Micera G., Chruściński L., Kaczmarek K., Nachman R.J., Zabrocki J., Sykuła A. Coordination ability of insect kinin analogs. Polyhedron 2009, 28(3): 485-492.
  40. Mrozek J., Lewandowska A., Guzow K., Malicka J., Banecki B., Wiczk W. Influence of Dab2 and Pro3 configuration of [Leu]-enkephalins on the interactions with β-cyclodextrin studied by fluorescence spectroscopy, microcalorimetry and 1H NMR spectroscopy. Journal of Inclusion Phenomena and Macrocyclic Chemistry 2009, 65(3-4): 361-375.
  41. Rodziewicz-Motowidło S., Iwaszkiewicz J., Sosnowska R., Czaplewska, P., Sobolewski E., Szymańska A., Stachowiak A., Liwo A. The Role of the Val57 Amino-Acid Residue in the Hinge Loop of the Human Cystatin C. Conformational Studies of the Beta2-L1-Beta3 Segments of Wild-Type Human Cystatin C and Its Mutants. Biopolymers 2009, 91(5): 373-383.
  42. Skwierawska A., Makowska, J., Ołdziej S., Liwo A., Scheraga H.A. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure. Proteins-Structure Function and Bioinformatics 2009, 75(4): 931-953.
  43. Skwierawska A.Ołdziej S., Liwo A., Scheraga H.A. Conformational Studies of the C-Terminal 16-Amino-Acid-Residue Fragment of the B3 Domain of the Immunoglobulin Binding Protein G from StreptococcusBiopolymers 2009, 91(1): 37-51.
  44. Skwierawska AgnieszkaŻmudzińska WiolettaOłdziej Stanisław, Liwo Adam, Scheraga Harold A. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation. Proteins-Structure Function and Bioinformatics 2009, 76(3): 637-654.
  45. Sobolewski E., Makowski M., Ołdziej S., Czaplewski C., Liwo A., Scheraga H.A.,. Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures. Protein Engineering Design & Selection 2009, 22(9): 547-552.