Lipps, Georg
Lade...
E-Mail-Adresse
Geburtsdatum
Projekt
Organisationseinheiten
Berufsbeschreibung
Nachname
Lipps
Vorname
Georg
Name
Lipps, Georg
13 Ergebnisse
Suchergebnisse
Gerade angezeigt 1 - 10 von 13
Publikation Definition of the binding specificity of the T7 bacteriophage primase by analysis of a protein binding microarray using a thermodynamic model(Oxford University Press, 10.04.2024) Lipps, GeorgProtein binding microarrays (PBM), SELEX, RNAcompete and chromatin-immunoprecipitation have been intensively used to determine the specificity of nucleic acid binding proteins. While the specificity of proteins with pronounced sequence specificity is straightforward, the determination of the sequence specificity of proteins of modest sequence specificity is more difficult. In this work, an explorative data analysis workflow for nucleic acid binding data was developed that can be used by scientists that want to analyse their binding data. The workflow is based on a regressor realized in scikit-learn, the major machine learning module for the scripting language Python. The regressor is built on a thermodynamic model of nucleic acid binding and describes the sequence specificity with base- and position-specific energies. The regressor was used to determine the binding specificity of the T7 primase. For this, we reanalysed the binding data of the T7 primase obtained with a custom PBM. The binding specificity of the T7 primase agrees with the priming specificity (5′-GTC) and the template (5′-GGGTC) for the preferentially synthesized tetraribonucleotide primer (5′-pppACCC) but is more relaxed. The dominant contribution of two positions in the motif can be explained by the involvement of the initiating and elongating nucleotides for template binding.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Initial primer synthesis of a DNA primase monitored by real-time NMR spectroscopy(American Chemical Society, 27.03.2024) Wu, Pengzhi; Zehnder, Johannes; Schröder, Nina; Blümmel, Pascal E. W.; Salmon, Loïc; Damberger, Fred. F.; Lipps, Georg; Allain, Frédéric H.-T.; Wiegand, ThomasPrimases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein–DNA complex remains active in the solid-state NMR rotor and that time-resolved 31P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically(Oxford University Press, 09.06.2023) Schneider, Andy; Bergsch, Jan; Lipps, GeorgThe marine thermophilic archaeon Nanoarchaeum equitans possesses a monomeric primase encompassing the conserved domains of the small catalytic and the large regulatory subunits of archaeoeukaryotic heterodimeric primases in one protein chain. The recombinant protein primes on templates containing a triplet with a central thymidine, thus displaying a pronounced sequence specificity typically observed with bacterial type primases only. The N. equitans primase (NEQ395) is a highly active primase enzyme synthesizing short RNA primers. Termination occurs preferentially at about nine nucleotides, as determined by HPLC analysis and confirmed with mass spectrometry. Possibly, the compact monomeric primase NEQ395 represents the minimal archaeoeukaryotic primase and could serve as a functional and structural model of the heterodimeric archaeoeukaryotic primases, whose study is hindered by engagement in protein assemblies and rather low activity.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Efficient colonic drug delivery in domestic pigs employing a tablet formulation with dual control concept(Elsevier, 06/2023) Doggwiler, Viviane; Puorger, Chasper; Paredes, Valeria; Lanz, Michael; Nuss, Katja M.; Lipps, Georg; Imanidis, Georgios01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Tablet formulation with dual control concept for efficient colonic drug delivery(Elsevier, 25.01.2023) Doggwiler, Viviane; Lanz, Michael; Paredes, Valeria; Lipps, Georg; Imanidis, Georgios01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Stringent primer termination by an archaeo-eukaryotic DNA primase(Frontiers, 13.04.2021) Lipps, Georg; Bergsch, Jan; Devillier, Jean-Christophe; Jeschke, GunnarPriming of single stranded templates is essential for DNA replication. In recent years, significant progress was made in understanding how DNA primase fulfils this fundamental function, particularly with regard to the initiation. Equally intriguing is the unique property of archeao-eukaryotic primases to terminate primer formation at a well-defined unit length. The apparent ability to “count” the number of bases incorporated prior to primer release is not well understood, different mechanisms having been proposed for different species. We report a mechanistic investigation of primer termination by the pRN1 primase from Sulfolobus islandicus. Using an HPLC-based assay we determined structural features of the primer 5′-end that are required for consistent termination. Mutations within the unstructured linker connecting the catalytic domain to the template binding domain allowed us to assess the effect of altered linker length and flexibility on primer termination.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Stable and selective permeable hydrogel microcapsules for high-throughput cell cultivation and enzymatic analysis(Springer, 27.08.2020) Di Girolamo, Salvatore; Puorger, Chasper; Lipps, Georg01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Recent advances in understanding bacterial and archaeoeukaryotic primases(Elsevier, 12/2019) Lipps, GeorgDNA replication in all forms of life relies upon the initiation of synthesis on a single strand template by formation of a short oligonucleotide primer, which is subsequently elongated by DNA polymerases. Two structurally distinct classes of enzymes have evolved to perform this function, namely the bacterial DnaG-type primases and the Archaeal and Eukaryotic primases (AEP). Structural and mechanistic insights have provided a clear understanding of the role of the different domains of these enzymes in the context of the replisome and recent work sheds light upon primase-substrate interactions. We herein review the emerging picture of the primase mechanism on the basis of the structural knowledge obtained to date and propose future directions of this essential aspect of DNA replication.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Characterization of the housekeeping sortase from the human pathogen Propionibacterium acnes - first investigation of a class F sortase(Portland Press, 2019) Di Girolamo, Salvatore; Lipps, GeorgSortase enzymes play an important role in Gram-positive bacteria. They are responsible for the covalent attachment of proteins to the surface of the bacteria and perform this task via a highly sequence-specific transpeptidation reaction. Since these immobilized proteins are often involved in pathogenicity of Gram-positive bacteria, characterization of this type of enzyme is also of medical relevance. Different classes of sortases (A-F) have been found, which recognize characteristic recognition sequences present in substrate proteins. Up to date, sortase A from Staphylococcus aureus, a housekeeping class A sortase, is the most thoroughly studied representative of the sortase family of enzymes. Here we report the in-depth characterization of the class F sortase from Propionibacterium acnes, a class of sortases that has not been investigated before. As Sortase F is the only transpeptidase found in the P. acnes genome, it is the housekeeping sortase of this organism. Sortase F from P. acnes shows a behavior similar to sortases from class A in terms of pH dependence, recognition sequence and catalytic activity; furthermore, its activity is independent of bivalent ions, which contrasts to sortase A from S. aureus We demonstrate that sortase F is useful for protein engineering applications, by producing a site-specifically conjugated homogenous antibody-drug conjugate with a potency similar to that of a conjugate prepared with sortase A. Thus, the detailed characterization presented here will not only enable the development of anti-virulence agents targeting P. acnes but also provides a powerful alternative to sortase A for protein engineering applications. © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template(Cell Press, 27.12.2018) Boudet, Julien; Devillier, Jean-Christophe; Lipps, Georg01A - Beitrag in wissenschaftlicher Zeitschrift