Go!RNA Structural Biology Group

    patent applications

    Górna M, Nowacka M, Izert M, Kowalska M, Karolak N, Klimecka M, Młynarczyk K. Sposób selekcji i/lub wzbogacania RNA, cząsteczka RNA oraz jej zastosowanie (A method of RNA selection and/or enrichment, a RNA molecule and use thereof). P.430151 (05.06.2019), PCT/IB2020/055263 (04.06.2020) WO/2020/245755, US17616459 (03.12.2021), EP20743765.8 (04.01.2022)

    Górna M, Izert M, Klimecka M, Szybowska P, Antosiewicz A, Twardowski P. Konstrukty peptydowe do celowanej degradacji białek (Peptide constructs for targeted protein degradation). P.439032 (24.09.2021), PCT/IB2022/059128 (26.09.2022) WO/2023/047376

    PREPRINTS

    Merski M, Górna MW. Thiamin-Diphosphate Enzymes Are an Ancient Family of Repeat Proteins. bioRxiv 2021.03.21.436335; DOI: 10.1101/2021.03.21.436335

    Merski M, Górna MW. Repeating Sequence Motifs are a Conserved Aspect of the Patatin and Patatin-Like Family of Proteins. SSRN 2023.10.25 DOI: 10.2139/ssrn.4613199

    IN PRESS

    Go!RNA lab publications

    1. Kramer S Karolak NK Odenwald J Gabiatti B Castañeda Londoño PA Zavřelová A Freire ER Almeida KS Braune S Moreira C Eder A Goos C Field M Carrington M Holetz F Górna MW Zoltner M 2023 A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res 51147520-7540
    2. Danazumi AU Ishmam IT# Idris S# Izert MA Balogun EO Górna MW 2023 Targeted Protein Degradation Might Present a Novel Therapeutic Approach in the Fight Against African Trypanosomiasis. Eur J Pharm Sci 186106451
    3. Pinto SM Subbannayya Y Kim H Hagen L Górna MW Nieminen AI Bjørås M Espevik T Kainov D Kandasamy RK 2023 MultiOMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience 261105895
    4. Aminu S Danazumi AU Alhafiz ZA Gorna MW Ibrahim MA 2023 β-Sitosterol could serve as a dual inhibitor of Trypanosoma congolense sialidase and phospholipase A2: in vitro kinetic analyses and molecular dynamic simulations. Mol Divers 2741645-1660
    5. Budniak UA Karolak NK Kulik M Młynarczyk K Górna MW Dominiak PM 2022 The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method. J Phys Chem B 126459152-9167
    6. Nowacka M# Latoch P# Izert MA Karolak NK Tomecki R Koper M Tudek A Starosta AL Górna MW 2022 A cap 0-dependent mRNA capture method to analyze the yeast transcriptome. Nucleic Acids Res 5022e132
    7. Danazumi AU Iliyasu Gital S Idris S Bs Dibba L Balogun EO Górna MW 2022 Immunoinformatic design of a putative multi-epitope vaccine candidate against Trypanosoma brucei gambiense. Comput Struct Biotechnol J 205574-5585
    8. Merski M Macedo-Ribeiro S Wieczorek RM Górna MW 2022 The Repeating, Modular Architecture of the HtrA Proteases. Biomolecules 126793
    9. Katsuya-Gaviria K Paris G Dendooven T Bandyra KJ 2022 Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism. RNA Biol 191419-436
    10. Klimecka MM Antosiewicz A# Izert MA# Szybowska PE Twardowski PK Delaunay C Górna MW 2021 A Uniform Benchmark for Testing SsrA-Derived Degrons in the Escherichia coli ClpXP Degradation Pathway. Molecules 26195936
    11. Izert MA Szybowska PE Górna MW Merski M 2021 The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins Front Bioinform 1696368
    12. Izert MA Klimecka MM Górna MW 2021 Applications of Bacterial Degrons and Degraders - Toward Targeted Protein Degradation in Bacteria. Front Mol Biosci 8669762
    13. Blanco N Stafford K Lavoie MC Brandenburg A Górna MW Merski M 2021 A Simple Model for the Total Number of SARS-CoV-2 Infections on a National Level. Epidemiol Infect 149e80
    14. Brunner JS Vogel A Lercher A Caldera M Korosec A Pühringer M Hofmann M Hajto A Kieler M Garrido LQ Kerndl M Kuttke M Mesteri I Górna MW Kulik M Dominiak PM Brandon AE Estevez E Egan CL Gruber F Schweiger M Menche J Bergthaler A Weichhart T Klavins K Febbraio MA Sharif O Schabbauer G 2020 The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages. Nat Metab 2121427-1442
    15. Merski M Skrzeczkowski J Roth JK Górna MW 2020 A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins. Molecules 25225326
    16. Jarnot P Ziemska-Legiecka J Dobson L Merski M Mier P Andrade-Navarro MA Hancock JM Dosztányi Z Paladin L Necci M Piovesan D Tosatto SCE Promponas VJ Grynberg M Gruca A 2020 PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. Nucleic Acids Res 48W1W77–84
    17. Merski M# Młynarczyk K# Ludwiczak J Skrzeczkowski J Dunin-Horkawicz S Górna MW 2020 Self-analysis of repeat proteins reveals evolutionarily conserved patterns. BMC Bioinformatics 211179
    18. Kutner J# Shabalin IG# Matelska D Handing KB Gasiorowska O Sroka P Gorna MW Ginalski K Wozniak K Minor W 2018 Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. Biochemistry 576963-977

    #Equal contribution

    DEPOSITIONS

    Small molecule crystal structures

    Malinska M, Gorna M, Merski M (2019). Zn-TCEP metal-organic salt = [Zn(H2O)5][Zn2C18H24O12P2]·7H2O

    catena-[Penta-aqua-zinc(ii) bis(μ-3,3',3''-phosphinetriyltripropionato)-di-zinc(ii) heptahydrate]

    CCDC ICSD entry 1964322 | CSD entry DEHFUR01 | doi:10.5517/ccdc.csd.cc23y17c

    RNA sequencing data

    A cap-dependent mRNA capture method to analyze the transcriptome (2022) ENA: PRJEB49214 | GEO: GSE210198.

    Mass spectrometry data

    PRIDE

    Maria Górna – publication list

    1. Kramer S Karolak NK Odenwald J Gabiatti B Castañeda Londoño PA Zavřelová A Freire ER Almeida KS Braune S Moreira C Eder A Goos C Field M Carrington M Holetz F Górna MW Zoltner M 2023 A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res 51147520-7540
    2. Danazumi AU Ishmam IT# Idris S# Izert MA Balogun EO Górna MW 2023 Targeted Protein Degradation Might Present a Novel Therapeutic Approach in the Fight Against African Trypanosomiasis. Eur J Pharm Sci 186106451
    3. Pinto SM Subbannayya Y Kim H Hagen L Górna MW Nieminen AI Bjørås M Espevik T Kainov D Kandasamy RK 2023 MultiOMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience 261105895
    4. Aminu S Danazumi AU Alhafiz ZA Gorna MW Ibrahim MA 2023 β-Sitosterol could serve as a dual inhibitor of Trypanosoma congolense sialidase and phospholipase A2: in vitro kinetic analyses and molecular dynamic simulations. Mol Divers 2741645-1660
    5. Budniak UA Karolak NK Kulik M Młynarczyk K Górna MW Dominiak PM 2022 The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method. J Phys Chem B 126459152-9167
    6. Nowacka M# Latoch P# Izert MA Karolak NK Tomecki R Koper M Tudek A Starosta AL Górna MW 2022 A cap 0-dependent mRNA capture method to analyze the yeast transcriptome. Nucleic Acids Res 5022e132
    7. Danazumi AU Iliyasu Gital S Idris S Bs Dibba L Balogun EO Górna MW 2022 Immunoinformatic design of a putative multi-epitope vaccine candidate against Trypanosoma brucei gambiense. Comput Struct Biotechnol J 205574-5585
    8. Merski M Macedo-Ribeiro S Wieczorek RM Górna MW 2022 The Repeating, Modular Architecture of the HtrA Proteases. Biomolecules 126793
    9. Klimecka MM Antosiewicz A# Izert MA# Szybowska PE Twardowski PK Delaunay C Górna MW 2021 A Uniform Benchmark for Testing SsrA-Derived Degrons in the Escherichia coli ClpXP Degradation Pathway. Molecules 26195936
    10. Izert MA Szybowska PE Górna MW Merski M 2021 The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins Front Bioinform 1696368
    11. Izert MA Klimecka MM Górna MW 2021 Applications of Bacterial Degrons and Degraders - Toward Targeted Protein Degradation in Bacteria. Front Mol Biosci 8669762
    12. Blanco N Stafford K Lavoie MC Brandenburg A Górna MW Merski M 2021 A Simple Model for the Total Number of SARS-CoV-2 Infections on a National Level. Epidemiol Infect 149e80
    13. Brunner JS Vogel A Lercher A Caldera M Korosec A Pühringer M Hofmann M Hajto A Kieler M Garrido LQ Kerndl M Kuttke M Mesteri I Górna MW Kulik M Dominiak PM Brandon AE Estevez E Egan CL Gruber F Schweiger M Menche J Bergthaler A Weichhart T Klavins K Febbraio MA Sharif O Schabbauer G 2020 The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages. Nat Metab 2121427-1442
    14. Merski M Skrzeczkowski J Roth JK Górna MW 2020 A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins. Molecules 25225326
    15. Merski M# Młynarczyk K# Ludwiczak J Skrzeczkowski J Dunin-Horkawicz S Górna MW 2020 Self-analysis of repeat proteins reveals evolutionarily conserved patterns. BMC Bioinformatics 211179
    16. Kutner J# Shabalin IG# Matelska D Handing K Gasiorowska O Sroka P Gorna MW Ginalski K Wozniak K Minor W 2018 Structural, biochemical, and evolutionary characterization of glyoxylate/hydroxypyruvate reductases shows their division into two distinct subfamilies. Biochemistry 576963-977
    17. Byrgazov K Kastner R Gorna M Hoermann G Koenig M Lucini CB Ulreich R Benesch M Strenger V Lackner H Schwinger W Sovinz P Haas OA van den Heuvel-Eibrink M Niemeyer CM Hantschel O Valent P Superti-Furga G Urban C Dworzak MN Lion T 2017 NDEL1-PDGFRB fusion gene in a myeloid malignancy with eosinophilia associated with resistance to tyrosine kinase inhibitors. Leukemia 311237-240
    18. Dikoglu E Alfaiz A Gorna M Bertola D Chae JH Cho TJ Derbent M Alanay Y Guran T Kim OH Llerenar JC Jr Yamamoto G Superti-Furga G Reymond A Xenarios I Stevenson B Campos-Xavier B Bonafé L Superti-Furga A Unger S 2015 Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome. Am J Med Genet A 16771501-9
    19. Dölker N# Górna MW# Sutto L Torralba AS Superti-Furga G Gervasio FL 2014 The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion. PLoS Comput Biol 1010e1003863
    20. Bonafé L# Liang J# Gorna MW# Zhang Q Ha-Vinh R Campos-Xavier AB Unger S Beckmann JS Le Béchec A Stevenson B Giedion A Liu X Superti-Furga G Wang W Spahr A Superti-Furga A 2014 MMP13 mutations are the cause of recessive metaphyseal dysplasia, Spahr type. Am J Med Genet A 164A51175-9
    21. Vladimer GI Górna MW Superti-Furga G 2014 IFITs: Emerging Roles as Key Anti-Viral Proteins. Front Immunol 594
    22. Unger S# Górna MW# Le Béchec A Do Vale-Pereira S Bedeschi MF Geiberger S Grigelioniene G Horemuzova E Lalatta F Lausch E Magnani C Nampoothiri S Nishimura G Petrella D Rojas-Ringeling F Utsunomiya A Zabel B Pradervand S Harshman K Campos-Xavier B Bonafé L Superti-Furga G Stevenson B Superti-Furga A 2013 FAM111A mutations result in hypoparathyroidism and impaired skeletal development. Am J Hum Genet 926990-5
    23. Abbas YM Pichlmair A# Górna MW# Superti-Furga G Nagar B 2013 Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins. Nature 494743560-4
    24. Bandyra KJ Said N Pfeiffer V Górna MW Vogel J Luisi BF 2012 The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell 476943-53
    25. Górna MW Carpousis AJ Luisi BF 2012 From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome. Q Rev Biophys 452105-45
    26. Pichlmair A Lassnig C Eberle CA Górna MW Baumann CL Burkard TR Bürckstümmer T Stefanovic A Krieger S Bennett KL Rülicke T Weber F Colinge J Müller M Superti-Furga G 2011 IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA. Nat Immunol 127624-30
    27. Goncalves A Bürckstümmer T Dixit E Scheicher R Górna MW Karayel E Sugar C Stukalov A Berg T Kralovics R Planyavsky M Bennett KL Colinge J Superti-Furga G 2011 Functional dissection of the TBK1 molecular network. PLoS One 69e23971
    28. Górna MW Pietras Z Tsai YC Callaghan AJ Hernández H Robinson CV Luisi BF 2010 The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA 163553-62
    29. Worrall JA# Górna M# Crump NT Phillips LG Tuck AC Price AJ Bavro VN Luisi BF 2008 Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. J Mol Biol 3824870-83
    30. Worrall JA Górna M Pei XY Spring DR Nicholson RL Luisi BF 2007 Design and chance in the self-assembly of macromolecules. Biochem Soc Trans 35Pt 3502-7

    #Equal contribution

    H-Index

    (Scopus)
    13

    Citations

    (excl. autocitations)
    1300+