Instruct will be represented by its director, prof. David Stuart from Oxford University, and representatives from other member states.

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1 CONFERENCE MULTIDISCIPLINARY APPROACH TO STRUCTURAL BIOLOGY FROM MACROMOLECULES TO CELLS Poznan Science Center Wieniawskiego 17/19, Poznan, Poland March 6 7, 2015 Department of Crystallography - Center for Biocrystallographic Research at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznan organises on 6-7 March 2015 a conference Multidisciplinary Approach to Structural Biology. From Macromolecules to Cells. The meeting will bring together representatives of leading Polish research institutions dedicated to various aspects of structural biology and using state-of-the-art techniques. The purpose of the conference is to take stock of structural biology in Poland, as well as a presentation of our research community and infrastructure to the European consortium Instruct, with the prospect of joining the consortium. Instruct provides researches with access to modern infrastructure and expertise throughout Europe and encourages multi-disciplinary approach in order to build an integrated model of the cell. Presently, Instruct has 2618 members and 16 Instruct Centres in 11 countries. It also provides short-term internships for young scientists in leading research laboratories. Instruct will be represented by its director, prof. David Stuart from Oxford University, and representatives from other member states. For detailed information about Instruct please go to: Organising Committee Wojciech Rypniewski, Mariusz Jaskólski, Michał M. Sikorski Department of Crystallography Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland Contact: wojtekr@ibch.poznan.pl and mmsik@ibch.poznan.pl

2 MULTIDISCIPLINARY APPROACH TO STRUCTURAL BIOLOGY FROM MACROMOLECULES TO CELLS Poznan Science Center Wieniawskiego 17/19, March 6 7, 2015 Invited Speakers Prof. David Stuart - special Instruct guest - Oxford University, London, UK Prof. Marek Figlerowicz - Director of the Institute of Bioorganic Chemistry, Polish Academy of Sciences Dr. Krzysztof Brzeziński - University of Bialystok, Białystok, Poland Dr. Honorata Czapińska - International Institute of Molecular and Cell Biology, Warszawa, Poland Prof. Michał Dadlez - Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland Dr. Grzegorz Dubin - Jagiellonian University, Kraków, Poland Prof. Tadeusz Holak - Jagiellonian University, Kraków, Poland Dr. Agnieszka Kiliszek - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Prof. Maciej Kozak - Adam Mickiewicz University, Poznan, Poland Prof. Paweł P. Liberski - Medical University of Lodz, Łódź, Poland Prof. Barbara Nawrot - Department of Bioorganic Chemistry, Polish Academy of Sciences, Łódź, Poland Dr. Izabela Sierocka - Adam Mickiewicz University, Joanna Śliwiak - Institute of Bioorganic Chemistry, Polish Academy of Sciences Dr. Anna Urbanowicz - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Prof. Krzysztof Woźniak - Warsaw University, Warszawa, Poland Dr. Mirosław Zarębski - Jagiellonian University, Kraków, Poland Organized by: Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland Department of Crystallography Center for Biocrystallographic Research Conference web page: Sponsors: LKB Biotech

3 MULTIDISCIPLINARY APPROACH TO STRUCTURAL BIOLOGY FROM MACROMOLECULES TO CELLS P R O G R A M M E Friday, March 6, :30 8:45 Wojciech Rypniewski - General remarks 08:45 9:00 Marek Figlerowicz - Director of the Institute - Research at the Institute of Bioorganic Chemistry 09:00 9:30 David Stuart - special Instruct guest 09:30 10:00 Maciej Kozak - Polish synchrotron SOLARIS and its potential in Bio-SAXS applications 10:00 10:30 Honorata Czapińska - Structural studies of restriction-modification systems 10:30 10:50 Coffee break 10:50 11:20 Krzysztof Woźniak - Crystallography beyond Independent Atom Model 11:20 11:50 11:50 12:20 Michał Dadlez - Approach to structures of difficult protein targets by hydrogen-deuterium exchange/mass spectrometry analysis - new clothes for the old emperor Tadeusz Holak - Monitoring the Antagonist-Protein and Protein-Protein Interactions with NMR Spectroscopy: Inhibitors of the p53-mdm2 Interaction 12:20 12:50 Barbara Nawrot - Synthetic oligonucleotides as molecular tools for applications in cell biology 12:50 14:00 Lunch 14:00 14:30 Paweł P. Liberski - Prions, prionoids and misfolded proteins 14:30 14:50 Mirosław Zarębski - Subcellular Cytometry - Quantitative 3-D Analysis of Discrete Subcellular Structures and Events 14:50 15:10 Grzegorz Dubin - Structural and functional analysis of Spl proteases form S. aureus 15:10 15:30 Joanna Śliwiak - Protein-ligand- interactions - structural and biophysical studies 15:30 15:50 Agnieszka Kiliszek - Crystallographic studies of toxic RNA 15:50 16:10 Izabela Sierocka - High-throughput platforms for RNA analyses in the Institute of Molecular Biology and Biotechnology at the Faculty of Biology, Adam Mickiewicz University, Poznan 16:10 16:30 Coffee break 16:30 16:50 16:50 17:10 Anna Urbanowicz - TROSPA from Ixodes ricinus - the first intrinsically disordered protein involved in specific vector-microbe recognition Krzysztof Brzeziński - Structural and biochemical characterization of archaeal type S-adenosyl-Lhomocysteine hydrolases 17:10 18:00 Discussion

4 POSTERS POSTER NUMBER AUTHOR(S)/ AFFILIATION PROTEINS TITLE Aleksandra Pawela, Joanna Banasiak Department of Natural Products Biochemistry, Group of Plant Molecular Physiology, IBCh, PAS Wanda Biała, Michał Jasiński Department of Natural Products Biochemistry Group of Plant Molecular Physiology, IBCh, PAS Karolina Jarzyniak Department of Natural Products Biochemistry, Group of Plant Molecular Physiology, IBCh, PAS Dominik Lewandowski Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Aleksander Tworak Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Michał Taube, Artur Jarmołowski, Maciej Kozak Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Przemysław Wieczorek Department of Gene Expression, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland Mateusz Bajczyk Department of Gene Expression, Adam Mickiewicz University, Weronika Andrzejewska Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Witold Gospodarczyk Department: Macromolecular Physics Department, Faculty of Physics, Adam Mickiewicz University, ABA transport as an essential regulatory factor in nodulation process Functional analysis of MtABCG transporters - in search of endogenous substrates Unravelling the role of Medicago truncatula ABCG/PDR transporters in nodulation TROSPA - an intrinsically disordered protein involved in the tick colonization by Borrelia Dicer-like proteins in Medicago truncatula, a model legume plant Structural studies of the plant HSP90-SGT1- ADP complex in solution Structural study of the human SGT1 protein in solution Novel proteins interacting with the SERRATE protein in Arabidopsis thaliana The study of complexation process between cationic gemini surfactants and DNA using structural and spectoscopic methods. Microfluidic system for amyloids formation analysis 1

5 11 12 Marta Grzechowiak Protein Engineering Laboratory, Department of Crystallography CBB, Institute of Bioorganic Chemistry, PAS, Miłosz Ruszkowski, Joanna Śliwiak, Agnieszka Ciesielska, Jakub Barciszewski, Michał Sikorski, Mariusz Jaskólski Protein Engineering Laboratory, Department of Crystallography CBB, Institute of Bioorganic Chemistry, PAS, Inorganic pyrophosphatase (PPase) from a higher plant Specific plant hormone binding proteins with PR-10 fold - structural and thermodynamic studies NUCLEIC ACIDS Ewelina Małecka Department of Biochemistry, Adam Mickiewicz University, Agnieszka Stefaniak Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, PAS, Magdalena Małgowska Institute of Bioorganic Chemistry, PAS, Poznań, Poland Tadeusz Kuliński Department of Chemical Biology, Institute of Bioorganic Chemistry, PAS, Jolanta Lisowiec Department: Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, PAS, Marta Szabat Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, PAS, Anna Pasternak, Kotkowiak Weronika Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, PAS, VIRUSES Aleksander Jan Strugała Department of molecular and systems biology, Institute of Bioorganic Chemistry, PAS, Agata Groszewska Department of Biochemistry, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Daria Sobańska Department of Biochemistry,, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland The unique mode of binding of bacterial srnas to the distal side of the Hfq protein RNA Chaperone activity of retroviral proteins Distinctive structural motifs of RNA G- quadruplexes composed of AGG, CGG and UGG trinucleotide repeats Structural propensities of RNA motifs Structural Determinants of Alternative Splicing Regulations of the MAPT pre-mrna Thermodynamic and structural features of beta-l-rna Unlocked nucleic acids: implications of increased conformational flexibility for RNA/DNA triplex formation BMV- and RCNMV- based virus like particles as carriers of biologically active substances. Competition among srnas for access to Hfq affects the rates of association and dissociation of the complex of DsrA srna with rpos mrna The rates of srna association to mrna correlate with Hfq-dependent translation repression. 2

6 23 Joanna Mazur Department of Biochemistry, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, The role of Mg 2+ ions for E.coli srna MgrR binding to eptb mrna and to the Hfq protein. NUCLEOTIDE ANALOGUES Dorota Magner Dept of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, PAS, Lucyna Budźko Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, PAS, Grzegorz Framski Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland Dagmara Sara Baraniak Institute of Bioorganic Chemistry Polish Academy of Sciences, Justyna Gołębiewska Department of Nucleic Acids Chemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, Agnieszka Szymańska-Michalak Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań Krystian Kołodziej Group of Nucleotide Stereochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Magdalena Materna Department: Department of Nucleic Acids Chemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, SNP alleles expression differentiation on mrna level using modified antisense oligonucleotides Deamination of methylated and non-methylated cytidines by human AID New applications of 6-alkyl-2,3- dihydrofurano[2,3-d]pyrimidin-2(1h)-one and 6- alkyl-2,3-dihydropyrrolo[2,3-d]pyrimidin- 2(3H,7H)-one nucleosides: anticancer properties Synthesis and Cytotoxic Evaluation of Novel Proparagyl Derivatives of 5-Fluoro-2 - deoxyuridine Nucleosides Studies on the synthesis and biological properties of nucleosid-5 -yl phosphoramidates. Cell cycle arrest, apoptosis and anti-proliferative activity of new 3'-O-acyl-2'-deoxy-5-fluorouridine derivatives The Loss of TEAH + Cation From Certain Nucleotide Analogues N-Oxides in the synthesis of nucleotide analogues 3

7 ALPHABETICAL LIST OF PARTICIPANTS 1. Andrzejewska Weronika 2. Bajczyk Mateusz 3. Banasiak Joanna 4. Baraniak Dagmara S. 5. Barciszewski Jakub 6. Barciszewski Jan 7. Bejger Magdalena 8. Belter Agnieszka 9. Biała Wanda 10. Boryski Jerzy 11. Brzeziński Krzysztof 12. Brzęk Aleksandra 13. Budźko Lucyna 14. Czapik Tomasz 15. Czapińska Honorata 16. Dadlez Michał 17. Daenke Susan 18. Dubin Grzegorz 19. Fedoruk-Wyszomirska Agnieszka 20. Femiak Iwona 21. Figlerowicz Marek 22. Framski Grzegorz 23. Gawron Marian 24. Gdaniec Zofia 25. Gołębiewska Justyna 26. Gospodarczyk Witold 27. Groszewska Agata 28. Grzechowiak Marta 29. Handschuh Luiza 30. Holak Tadeusz 31. Imiołczyk Barbara 32. Jarzyniak Karolina 33. Jasiński Michał 34. Jaskólski Mariusz 35. Kamel Karol 36. Kasperska Alina 37. Kasprzak Joanna 38. Kiliszek Agnieszka 39. Kołodziej Krystian 40. Koralewska Natalia 41. Kotkowiak Weronika 42. Kozak Maciej

8 43. Krzywda Szymon 44. Kuliński Tadeusz 45. Lewandowski Dominik 46. Liberski Paweł P. 47. Lisowiec Jolanta 48. Magner Dorota 49. Małecka Ewelina 50. Małgowska Magdalena 51. Manszewski Tomasz 52. Marcinkowska-Swojak Małgorzata 53. Materna Magda 54. Mazur Joanna 55. Milewski Marek Cezary 56. Nawrot Barbara 57. Nowak Karolina 58. Pasternak Anna 59. Pawela Aleksandra 60. Philips Anna 61. Pokornowska Maria 62. Rypniewski Wojciech 63. Sierocka Izabela 64. Sikorski Michał M. 65. Sobańska Daria 66. Stefaniak Agnieszka Katarzyna 67. Stelmaszczuk Michał 68. Stróżycki Paweł 69. Strugała Aleksander 70. Stuart David 71. Szabat Marta 72. Szpotkowski Kamil 73. Szymanska-Michalak Agnieszka 74. Śliwiak Joanna 75. Taube Michał 76. Teubert Anna 77. Tworak Aleksander 78. Urbanowicz Anna 79. Wieczorek Przemysław 80. Woźniak Krzysztof 81. Wyszko Eliza 82. Zarębski Mirosław

9 The Conference accompanying event Microscape Joanna Hoffmann-Dietrich Sound composition: Andre Bartetzki Joanna Hoffmann, a renowned Polish artist sharing her life between Poznan & Berlin. She is Professor (Dr.hab) of the University of Arts in Poznan and leader of the Studio for Transdisciplinary Projects and Research. She is also the Chair of Art & Science Node in Berlin. Joanna Hoffmann's transdisciplinary works combine art, science and technology. Her use of multimedia installations, 3d stereoscopy, experimental video animation and other media explore the visualization of molecular as well as cosmic space. Her work relates to advanced scientific research on the phenomenon of life and to the interplay between scientific and cultural, sensual and illusive, digital and biological, natural and synthetic. Microscape brings together a few threads of artistic research being developed within the frame of the long-term project Hidden Topologies of Being inspired by the origin and complex geometry of protein molecules, named "basic bricks of life". Proteins are associated mostly with cellular robots. For me however, as an assembly of proteins a protein molecule became a key to explore relations between micro and macro scales of my existence, a unique unite of my spacetime [ ] The artistic presentation Microscape accompanying the Conference "Multidisciplinary Approach to Structural Biology. From Macromolecules to Cells" embraces: πρωτεο/ Proteo hologram-like animation The work s title refers to the Greek root of the word protein (Gr. πρωτεῖος the first, in the lead) as well as to the philosophical tradition of searching for arche the essence of the physical world. Πρωτεο / Proteo is an animation portraying a cloud of particles creating a mini-universe folded in the form of Calabi-Yau space, in which, according to superstring theory, successive dimensions of our world are curled up at the subatomic level. Giving birth to a convoluted protein molecule and its dynamic molecular 'dance of life', it brings to mind a question about the relations between the energy, matter and form. If the scientific hypothesis about multi-dimensional nature of the world is true, then these hidden spaces are everywhere, in each point of the space outside as well as inside us. ( ) One day, maybe, our brain will be able to perceive how we exist in the multidimensional universe. For the time being, we have only our imagination in command and enormous diversity of protein globules, each of them suggesting, in other scale, a blister of some world." Microscape 3D multimedia installation The 3D multimedia installation is based on scientific data of molecular structures and transcribed by the artist into a computer animation. The work, in tandem with Andre Bartetzki s sound composition, relates specifically to the viewer s body and present itself as an artistic study on space and existence. By using technologies as diverse as Pepper's ghost (a forerunner of holography) and 3D video, Hoffmann's work merges interpretations of scientific data, image, sound and poetry. Microscape poses questions about the challenges and boundaries of our cognition creating an emotional bridge between our sensual experiences and abstractness of contemporary science. Conference room nr 312, Science Center, Wieniawskiego 17/19, Poznań March 6, 2015 at 9:00 20:00h