Publikacje

Nowacka M, Nowak E, Czarnocki-Cieciura M, Jackiewicz J, Skowronek K, Szczepanowski R, Wöhrl BM, Nowotny M.

Structures of substrate complexes of foamy viral protease-reverse transcriptase.

J Virol

Warminski  M, Kowalska  J, Nowak E, Kubacka  D, Tibble  R, Kasprzyk  R, Sikorski  PJ, Gross  JD, Nowotny  M, Jemielity J.

Structural Insights into the Interaction of Clinically Relevant Phosphorothioate mRNA Cap Analogs with Translation Initiation Factor 4E Reveal Stabilization via Electrostatic Thio-Effect.

ACS Chem Biol.

Cieśla M, Turowski TW, Nowotny M, Tollervey D, Boguta M.

The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase.

Nucleic Acids Res.

Koralewski R, Dymek B, Mazur M, Sklepkiewicz P, Olejniczak S, Czestkowski W, Matyszewski K, Andryianau G, Niedziejko P, Kowalski M, Gruza M, Borek B, Jedrzejczak K, Bartoszewicz A, Pluta E, Rymaszewska A, Kania M, Rejczak T, Piasecka S, Mlacki M, Mazurkiewicz M, Piotrowicz M, Salamon M, Zagozdzon A, Napiorkowska-Gromadzka A, Bartlomiejczak A, Mozga W, Dobrzański P, Dzwonek K, Golab J, Nowotny M, Olczak J, Golebiowski A.

Discovery of OATD-01, a First-in-Class Chitinase Inhibitor as Potential New Therapeutics for Idiopathic Pulmonary Fibrosis.

J Med Chem.

Hyjek-Składanowska M, Stasińska AR, Napiórkowska-Gromadzka A, Bartłomiejczak A, Seth PP, Chmielewski MK, Nowotny M.

Disulfide bridge cross-linking between protein and the RNA backbone as a tool to study RNase H1.

Bioorg Med Chem.

Kuciński J, Chamera S, Kmera A, Rowley MJ, Fujii S, Khurana P, Nowotny M, Wierzbicki AT.

Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana.

Plant Cell Physiol.

Malik D, Kobyłecki K, Krawczyk P, Poznański J, Jakielaszek A, Napiórkowska A, Dziembowski A, Tomecki R, Nowotny M.

Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine..

Nucleic Acids Res.

Kaus-Drobek M, Mücke N, Szczepanowski RH, Wedig T, Czarnocki-Cieciura M, Polakowska M, Herrmann H, Wysłouch-Cieszyńska A, Dadlez M.

Vimentin S-glutathionylation at Cys328 Inhibits Filament Elongation and Induces Severing of Mature Filaments in Vitro.

FEBS J.

Szewczyk M, Malik D, Borowski LS, Czarnomska SD, Kotrys AV, Klosowska-Kosicka K, Nowotny M, Szczesny RJ.

Human REXO2 Controls Short Mitochondrial RNAs Generated by mtRNA Processing and Decay Machinery to Prevent Accumulation of Double-Stranded RNA.

Nucleic Acids Res.

Hyjek-Składanowska M, Vickers T, Napiórkowska A, Anderson B, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M.

Origins of the increased affinity of phosphorothioate-modified therapeutic nucleic acids for proteins.

J Am Chem Soc.

Jaciuk M, Swuec P, Gaur V, Kasprzak JM, Renault L, Dobrychłop M, Nirwal S, Bujnicki JM, Costa A, Nowotny M.

A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair.

DNA Repair (Amst).

Nowotny M.

Crosslink and shield: protecting abasic sites from error-prone repair.

Nat Struct Mol Biol.

Gaur V, Ziajko W, Nirwal S, Szlachcic A, Gapińska M, Nowotny M

Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease.

Nucleic Acids Res.

Górecka KM, Krepl M, Szlachcic A, Poznański J, Šponer J, Nowotny M.

RuvC uses dynamic probing of the Holliday junction substrate to achieve sequence specificity and efficient resolution.

Nat Commun.

Hyjek M, Figiel M, Nowotny M.

RNases H: Structure and mechanism.

DNA Repair (Amst)

Figiel M, Krepl M, Park S, Poznański J, Skowronek K, Gołąb A, Ha T, Šponer J, Nowotny M.

Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase.

J Biol Chem

Wojtczak BA, Sikorski PJ, Fac-Dabrowska K, Nowicka A, Warminski M, Kubacka D, Nowak E, Nowotny M, Kowalska J, Jemielity J.

5′-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes.

J Am Chem Soc.

Razew M, Warkocki Z, Taube M, Kolondra A, Czarnocki-Cieciura M, Nowak E, Labedzka-Dmoch K, Kawinska A, Piatkowski J, Golik P, Kozak M, Dziembowski A, Nowotny M.

Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components.

Nat Commun.

Charbonnel C, Niazi AK, Elvira-Matelot E, Nowak E, Zytnicki M, de Bures A, Jobet E, Opsomer A, Shamandi N, Nowotny M, Carapito C, Reichheld J-P, Vaucheret H, Saez-Vasquez J.

The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain.

Nucleic Acids Res.

Rydzik AM, Warminski M, Sikorski PJ, Baranowski MR, Walczak S, Kowalska J, Zuberek J, Lukaszewicz M, Nowak E, W Claridge TD, Darzynkiewicz E, Nowotny M, Jemielity J.

mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.

Nucleic Acids Res.

Rydzik AM, Warminski M, Sikorski PJ, Baranowski MR, Walczak S, Kowalska J, Zuberek J, Lukaszewicz M, Nowak E, W Claridge TD, Darzynkiewicz E, Nowotny M, Jemielity J.

mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.

Nucleic Acids Res.

Figiel M, Nowotny M

Chapter Six - Structural Studies of RNases H2 as an Example of Crystal Structure Determination of Protein–Nucleic Acid Complexes

Methods in Enzymology

Figiel M, Krepl M, Poznanski J, Golab A, Šponer J, Nowotny M

Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase

Nucleic Acids Res.

Kalisiak K, Kuliński TM, Tomecki R, Cysewski D, Pietras Z, Chlebowski A, Kowalska K, Dziembowski A

A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans

Nucleic Acids Res

Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P

Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli

Nat Commun.

Nowotny M, Gaur V

Structure and mechanism of nucleases regulated by SLX4

Curr Opin Struct Biol

Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet J-F, Jagusztyn-Krynicka EK

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

Frontiers in Microbiology

Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK

Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231

BMC Microbiol.

Gaur V, Wyatt HDM, Komorowska W, Szczepanowski RH, de Sanctis D, Gorecka KM, West SC, Nowotny M

Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease

Cell Reports

Figiel M, Nowotny M.

Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition.

Nucleic Acids Res.

Mathys H, Basquin J, Ozgur S, Czarnocki-Cieciura M, Bonneau F, Aartse A, Dziembowski A, Nowotny M, Conti E, Filipowicz W.

Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression.

Mol Cell.

Miętus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M

Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding

Nucleic Acids Res

Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Nucleic Acids Res.

Tomecki R, Drazkowska K, Kucinski I, Stodus K, Szczesny RJ, Gruchota J, Owczarek EP, Kalisiak K, Dziembowski A

Multiple myeloma-associated hDIS3 mutations cause perturbations in cellular RNA metabolism and suggest hDIS3 PIN domain as a potential drug target

Nucleic Acids Res.

Nowak E, Miller JT, Bona MK, Studnicka J, Szczepanowski RH, Jurkowski J, Le Grice SFJ, Nowotny M

Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry

Nature Structural & Molecular Biology

Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM

Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation

Nat Commun

Górecka KM, Komorowska W, Nowotny M

Crystal structure of RuvC resolvase in complex with Holliday junction substrate

Nucleic Acids Res

Chon H, Sparks JL, Rychlik M, Nowotny M, Burgers PM, Crouch RJ, Cerritelli SM

RNase H2 roles in genome integrity revealed by unlinking its activities

Nucleic Acids Res

Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M

Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid

Nucleic Acids Res

Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM

Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger

Nucleic Acids Res

Figiel M, Chon H, Cerritelli SM, Cybulska M, Crouch RJ, Nowotny M

The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects

J Biol Chem

Rosta E, Nowotny M, Yang W, Hummer G

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations

J Am Chem Soc.

Jaciuk M, Nowak E, Skowronek K, Tańska A, Nowotny M

Structure of UvrA nucleotide excision repair protein in complex with modified DNA.

Nat Struct Mol Biol

Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch RJ, Nowotny M

Crystal structures of RNase H2 in complex with nucleic acid reveal the mechanism of RNA-DNA junction recognition and cleavage.

Mol Cell

Nowotny M, Yang W

Structural and functional modules in RNA interference

Curr Opin Struct Biol

Nowotny M

Retroviral integrase superfamily: the structural perspective.

EMBO Rep

Lee YT, Jacob J, Michowski W, Nowotny M, Kuznicki J, Chazin WJ.

Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain.

J Biol Chem.

Nowotny M, Spiechowicz M, Jastrzebska B, Filipek A, Kitagawa K, Kuznicki J

Calcium-regulated interaction of Sgt1 with S100A6 (calcyclin) and other S100 proteins

J Biol Chem.

Filipek A, Jastrzebska B, Nowotny M, Kuznicki J

CacyBP/SIP, a calcyclin and Siah-1-interacting protein, binds EF-hand proteins of the S100 family

J Biol Chem

Filipek A, Jastrzebska B, Nowotny M, Kwiatkowska K, Hetman M, Surmacz L, Wyroba E, Kuznicki J

Ca2+-dependent translocation of the calcyclin-binding protein in neurons and neuroblastoma NB-2a cells.

J Biol Chem

Filipek A, Jastrzebska B, Nowotny M, Kuznicki J

CacyBP/SIP, a calcyclin and Siah-1-interacting protein, binds EF-hand proteins of the S100 family

J Biol Chem

Nowotny M, Bhattacharya S, Filipek A, Krezel AM, Chazin W, Kuznicki J.

Characterization of the interaction of calcyclin (S100A6) and calcyclin-binding protein.

J Biol Chem.