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

    Dawidziak DM, Dzadz DA, Kuska MI, Kanavalli M, Klimecka MM, Merski M, Bandyra KJ, Górna MW. Human FASTK preferentially binds single-stranded and G-rich RNA. bioRxiv 2024.07.16.603671; doi: 10.1101/2024.07.16.603671

    Izert-Nowakowska MA, Klimecka MM, Antosiewicz A, Wróblewski K, Bandyra KJ, Góral TK, Kmiecik S, Serwa RA, Górna MW. Towards Targeted Protein Degradation - depletion of the essential GroEL protein in Escherichia coli using CLIPPERs. bioRxiv 2024.02.29.582761; doi: 10.1101/2024.02.29.582761

    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

    Górna MW, Merski M. Discovery and Analysis of Repeats and Low-Complexity Architectures in Proteins and Conservation of their Evolutionary Relationships Using Self-Homology Dot Plots. Methods in Molecular Biology series, vol. "Protein SuperSecondary Structure", accepted.

    Go!RNA lab publications

    1. Bandyra KJ Fröhlich KS Vogel J Rodnina M Goyal A Luisi BF 2024 Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance. Nucleic Acids Res
    2. 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
    3. 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
    4. 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
    5. 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
    6. 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
    7. 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
    8. 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
    9. Merski M Macedo-Ribeiro S Wieczorek RM Górna MW 2022 The Repeating, Modular Architecture of the HtrA Proteases. Biomolecules 126793
    10. 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
    11. 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
    12. 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
    13. Izert MA Klimecka MM Górna MW 2021 Applications of Bacterial Degrons and Degraders - Toward Targeted Protein Degradation in Bacteria. Front Mol Biosci 8669762
    14. 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
    15. 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
    16. Merski M Skrzeczkowski J Roth JK Górna MW 2020 A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins. Molecules 25225326
    17. 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
    18. 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
    19. 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

    Protein structures

    Wroblewski K, Izert-Nowakowska MA, Goral TK, Klimecka MM, Kmiecik S, Gorna MW.

    GroEL with bound GroTAC peptide. PDB 8S32 | EMDB EMD-19687

    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

    Small Angle X-ray Scattering data

    Fas-activated serine/threonine kinase/phosphoprotein FASTK (76-549). SASBDB: SASDVV2

    Fas-activated serine/threonine kinase/phosphoprotein FASTK (169-549). SASBDB: SASDVW2

    RNA sequencing data

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

    Mass spectrometry data

    PRIDE: PXD045730