TY - CONF AU - Sebák, Fanni AU - Szabó, Csenge Lilla AU - Ecsédi, Péter AU - Burkhard, LUY AU - Nyitray, László AU - Bodor, Andrea ED - Majdik, Cornelia TI - A rendezetlen fehérjék és az NMR spektroszkópia T2 - XXIX. Nemzetközi Vegyészkonferencia / 29th International Conference on Chemistry PB - Erdélyi Magyar Műszaki Tudományos Társaság (EMT) C1 - Kolozsvár T3 - Nemzetközi Vegyészkonferencia, ISSN 1843-6293 PY - 2023 SP - 1 PG - 1 UR - https://m2.mtmt.hu/api/publication/34236962 ID - 34236962 LA - English DB - MTMT ER - TY - JOUR AU - Sebák, Fanni AU - Ecsédi, Péter AU - Nyitray, László AU - Bodor, Andrea TI - Assignment of the disordered, proline-rich N-terminal domain of the tumour suppressor p53 protein using 1HN and 1Hα-detected NMR measurements JF - BIOMOLECULAR NMR ASSIGNMENTS J2 - BIOMOL NMR ASSIGM VL - 17 PY - 2023 IS - 2 SP - 309 EP - 314 PG - 6 SN - 1874-2718 DO - 10.1007/s12104-023-10160-4 UR - https://m2.mtmt.hu/api/publication/34213192 ID - 34213192 N1 - Analytical and BioNMR Laboratory, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest, 1117, Hungary Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary Export Date: 15 November 2023 Correspondence Address: Bodor, A.; Analytical and BioNMR Laboratory, Pázmány Péter sétány 1/a, Hungary; email: andrea.bodor@ttk.elte.hu AB - Protein p53 is mostly known for playing a key role in tumour suppression, and mutations in the p53 gene are amongst the most frequent genomic events accompanying oncogenic transformation. Continuous research is conducted to target disordered proteins/protein regions for cancer therapy, for which atomic level information is also necessary. The disordered N-terminal part of p53 contains the transactivation and the proline-rich domains—which besides being abundant in proline residues—contains repetitive Pro-Ala motifs. NMR assignment of such repetitive, proline-rich regions is challenging due to the lack of amide protons in the 1 H N -detected approaches, as well as due to the small chemical shift dispersion. In the present study we perform the full assignment of the p53 1–100 region by applying a combination of 1 H N - and 1 H α -detected NMR experiments. We also show the increased information content when using real-time homo- and heteronuclear decoupled acquisition schemes. On the other hand, we highlight the presence of minor proline species, and using Pro-selective experiments we determine the corresponding cis or trans conformation. Secondary chemical shifts for (C α –C β ) atoms indicate the disordered nature of this region, with expected helical tendency for the TAD1 region. As the role of the proline-rich domain is yet not well understood our results can contribute to further successful investigations. LA - English DB - MTMT ER - TY - JOUR AU - Méhes, Előd AU - Mones, Enys AU - Varga, Máté AU - Zsigmond, Áron AU - Biri-Kovács, Beáta AU - Nyitray, László AU - Barone, Vanessa AU - Krens, Gabriel AU - Heisenberg, Carl-Philipp AU - Vicsek, Tamás TI - 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation JF - COMMUNICATIONS BIOLOGY J2 - COMMUN BIOL VL - 6 PY - 2023 IS - 1 SN - 2399-3642 DO - 10.1038/s42003-023-05181-7 UR - https://m2.mtmt.hu/api/publication/34087969 ID - 34087969 N1 - Department of Biological Physics, ELTE Eötvös University, Budapest, Hungary Department of Genetics, ELTE Eötvös University, Budapest, Hungary Department of Biochemistry, ELTE Eötvös University, Budapest, Hungary Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, United States Institute of Science and Technology Austria, Klosterneuburg, Austria Export Date: 10 October 2023 Correspondence Address: Vicsek, T.; Department of Biological Physics, Hungary; email: vicsek@hal.elte.hu AB - Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering. LA - English DB - MTMT ER - TY - JOUR AU - Farkas, Sándor AU - Cioca, Daniel AU - Murányi, József AU - Hornyák, Péter AU - Brunyánszki, Attila AU - Szekér, Patrik AU - Boros, Eszter AU - Horváth, Patrik AU - Hujber, Zoltán AU - Rácz, Gábor Z. AU - Nagy, Noémi AU - Tóth, Rebeka AU - Nyitray, László AU - Péterfi, Zalán TI - Chlorotoxin binds to both matrix metalloproteinase 2 and neuropilin 1 JF - JOURNAL OF BIOLOGICAL CHEMISTRY J2 - J BIOL CHEM VL - 299 PY - 2023 IS - 9 PG - 16 SN - 0021-9258 DO - 10.1016/j.jbc.2023.104998 UR - https://m2.mtmt.hu/api/publication/34046199 ID - 34046199 LA - English DB - MTMT ER - TY - JOUR AU - Nagy-Fazekas, Dóra AU - Stráner, Pál AU - Ecsédi, Péter AU - Taricska, Nóra AU - Borbély, Adina Noémi AU - Nyitray, László AU - Perczel, András TI - A Novel Fusion Protein System for the Production of Nanobodies and the SARS-CoV-2 Spike RBD in a Bacterial System JF - BIOENGINEERING J2 - BIOENGINEERING-BASEL VL - 10 PY - 2023 IS - 3 SN - 2306-5354 DO - 10.3390/bioengineering10030389 UR - https://m2.mtmt.hu/api/publication/33715979 ID - 33715979 AB - Antibodies are key proteins of the immune system, and they are widely used for both research and theragnostic applications. Among them, camelid immunoglobulins (IgG) differ from the canonical human IgG molecules, as their light chains are completely missing; thus, they have only variable domains on their heavy chains (VHHs). A single VHH domain, often called a nanobody, has favorable structural, biophysical, and functional features compared to canonical antibodies. Therefore, robust and efficient production protocols relying on recombinant technologies are in high demand. Here, by utilizing ecotin, an Escherichia coli protein, as a fusion partner, we present a bacterial expression system that allows an easy, fast, and cost-effective way to prepare nanobodies. Ecotin was used here as a periplasmic translocator and a passive refolding chaperone, which allowed us to reach high-yield production of nanobodies. We also present a new, easily applicable prokaryotic expression and purification method of the receptor-binding domain (RBD) of the SARS-CoV-2 S protein for interaction assays. We demonstrate using ECD spectroscopy that the bacterially produced RBD is well-folded. The bacterially produced nanobody was shown to bind strongly to the recombinant RBD, with a Kd of 10 nM. The simple methods presented here could facilitate rapid interaction measurements in the event of the appearance of additional SARS-CoV-2 variants. LA - English DB - MTMT ER - TY - JOUR AU - Cousido-Siah, Alexandra AU - Carneiro, Laura AU - Kostmann, Camille AU - Ecsédi, Péter AU - Nyitray, László AU - Trave, Gilles AU - Gogl, Gergo TI - A scalable strategy to solve structures of PDZ domains and their complexes JF - ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY J2 - ACTA CRYSTALLOGR D STRUCT BIOL VL - 78 PY - 2022 IS - 4 SP - 509 EP - 516 PG - 8 SN - 2059-7983 DO - 10.1107/S2059798322001784 UR - https://m2.mtmt.hu/api/publication/32785740 ID - 32785740 N1 - Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Inst. de Genet. et de Biol. Molec. et Cell. (IGBMC) Inserm U1258/CNRS Umr 7104/Univ. de Strasbourg, 1 Rue Laurent Fries, BP 10142, Illkirch, 67404, France Department of Biochemistry, Elte Eotvos Lorand University, Budapest, 1117, Hungary Cited By :1 Export Date: 2 December 2022 Correspondence Address: Gogl, G.; Équipe Labellisée Ligue 2015, 1 Rue Laurent Fries, BP 10142, France; email: goglg@igbmc.fr LA - English DB - MTMT ER - TY - JOUR AU - Simon, Márton AU - Bartus, Éva AU - Mag, Beáta Zsófia AU - Boros, Eszter AU - Roszjár, Lea AU - Gógl, Gergő AU - Travé, Gilles AU - Martinek, Tamás AU - Nyitray, László TI - Promiscuity mapping of the S100 protein family using a high-throughput holdup assay JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 12 PY - 2022 IS - 1 PG - 11 SN - 2045-2322 DO - 10.1038/s41598-022-09574-2 UR - https://m2.mtmt.hu/api/publication/32777033 ID - 32777033 N1 - These authors contributed equally: Márton A. Simon and Éva Bartus LA - English DB - MTMT ER - TY - JOUR AU - Sebák, Fanni AU - Ecsédi, Péter AU - Bermel, Wolfgang AU - Burkhard, Luy AU - Nyitray, László AU - Bodor, Andrea TI - Selective 1Hα NMR methods to reveal functionally relevant proline cis/trans isomers in IDPs. Characterization of minor forms, effects of phosphorylation and, occurrence in proteome TS - Characterization of minor forms, effects of phosphorylation and, occurrence in proteome JF - ANGEWANDTE CHEMIE-INTERNATIONAL EDITION J2 - ANGEW CHEM INT EDIT VL - 61 PY - 2022 IS - 1 PG - 9 SN - 1433-7851 DO - 10.1002/anie.202108361 UR - https://m2.mtmt.hu/api/publication/32252567 ID - 32252567 N1 - Funding Agency and Grant Number: National Research, Development and Innovation OfficeNational Research, Development & Innovation Office (NRDIO) - Hungary [TKP2020-IKA-05, 2018-1.2.1-NKP-2018-00005]; NKFINational Research, Development & Innovation Office (NRDIO) - Hungary [K124900, K137940, K119359, EFOP-3.6.3-VEKOP-16-2017-00009]; Foundation for Hungarian Peptide and Protein Research; HGF program Information [43.35.02]; Virtmat Funding text: The ELTE Thematic Excellence Programme 2020 supported by National Research, Development and Innovation Office (TKP2020-IKA-05 and Project no. 2018-1.2.1-NKP-2018-00005); NKFI Grants K124900, K137940 to A.B., K119359 to L.N.; Szint+ Programme; EFOP-3.6.3-VEKOP-16-2017-00009 grant to F.S. and the Foundation for Hungarian Peptide and Protein Research are acknowledged. B.L. thanks the HGF program Information (43.35.02) and Virtmat for financial support. AB - It is important to identify proline cis/trans isomers that appear in several regulatory mechanisms of proteins, and to characterize minor species that are present due to the conformational heterogeneity in intrinsically disordered proteins (IDPs). To obtain residue level information on these mobile systems we introduce two H-1(alpha)-detected, proline selective, real-time homodecoupled NMR experiments and analyze the proline abundant transactivation domain of p53. The measurements are sensitive enough to identify minor conformers present in 4-15 % amounts; moreover, we show the consequences of CK2 phosphorylation on the cis/trans-proline equilibrium. Using our results and available literature data we perform a statistical analysis on how the amino acid type effects the cis/trans-proline distribution. The methods are applicable under physiological conditions, they can contribute to find key proline isomers in proteins, and statistical analysis results may help in amino acid sequence optimization for biotechnological purposes. LA - English DB - MTMT ER - TY - CHAP AU - Simon, Márton AU - Nyitray, László ED - Borg, Jean-Paul TI - Dynamic Control of Signaling by Phosphorylation of PDZ Binding Motifs T2 - PDZ Mediated Interactions VL - 2256 PB - Springer Boston CY - New York, New York SN - 9781071611654 T3 - Methods in Molecular Biology, ISSN 1064-3745 ; 2256. PY - 2021 SP - 179 EP - 192 PG - 14 DO - 10.1007/978-1-0716-1166-1_11 UR - https://m2.mtmt.hu/api/publication/33787387 ID - 33787387 N1 - Cited By :1 Export Date: 23 August 2021 Correspondence Address: Nyitray, L.; Department of Biochemistry, Hungary; email: nyitray@elte.hu Chemicals/CAS: protein serine threonine kinase; MAST2 protein, human; Microtubule-Associated Proteins; Protein-Serine-Threonine Kinases; Ribosomal Protein S6 Kinases, 90-kDa; RPS6KA1 protein, human Funding details: Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, NKFIH, K119359 Funding details: National Research, Development and Innovation Office, TKP2020-IKA-05 Funding text 1: We thank Dr. Gerg? G?gl for reading the manuscript. We also thank Vikt?ria Bilics for contributing in the FP measurement. This work was supported by the National Research, Development and Innovation Office (NKFIH) grants K119359 (to LN). MAS was supported through the New National Excellence Program of the Hungarian Ministry of Human Capacities. Project no. 2018-1.2.1-NKP-2018-00005 has been implemented with the support provided from the National Research, Development and Innovation Fund of Hungary, financed under the 2018-1.2.1-NKP funding scheme. This work was completed in the ELTE Thematic Excellence Programm 2020 Supperted by the Nation Research, Development and Innovation Office (TKP2020-IKA-05) Funding text 2: We thank Dr. Gergo˝ Gógl for reading the manuscript. We also thank Viktória Bilics for contributing in the FP measurement. This work was supported by the National Research, Development and Innovation Office (NKFIH) grants K119359 (to LN). MAS was supported through the New National Excellence Program of the Hungarian Ministry of Human Capacities. Project no. 2018-1.2.1-NKP-2018-00005 has been implemented with the support provided from the National Research, Development and Innovation Fund of Hungary, financed under the 2018-1.2.1-NKP funding scheme. This work was completed in the ELTE Thematic Excellence Programm 2020 Supperted by the Nation Research, Development and Innovation Office (TKP2020-IKA-05) AB - The dynamic regulation of protein-protein interactions (PPIs) involves phosphorylation of short liner motifs in disordered protein regions modulating binding affinities. The ribosomal-S6-kinase 1 is capable of binding to scaffold proteins containing PDZ domains through a PDZ-binding motif (PBM) located at the disordered C-terminus of the kinase. Phosphorylation of the PBM dramatically changes the interactome of RSK1 with PDZ domains exerting a fine-tuning mechanism to regulate PPIs. Here we present in detail highly effective biophysical (fluorescence polarization, isothermal calorimetry) and cellular (proteinfragment complementation) methods to study the effect of phosphorylation on RSK1-PDZ interactions that can be also applied to investigate phosphoregulation of other PPIs in signaling pathways. LA - English DB - MTMT ER - TY - JOUR AU - Ecsédi, Péter AU - Gógl, Gergő AU - Nyitray, László TI - Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes JF - FRONTIERS IN MOLECULAR BIOSCIENCES J2 - FRONT MOL BIOSCI VL - 8 PY - 2021 SN - 2296-889X DO - 10.3389/fmolb.2021.749052 UR - https://m2.mtmt.hu/api/publication/32476060 ID - 32476060 N1 - Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS, UMR 7104, Université de Strasbourg, Illkirch, France Export Date: 3 November 2021 Correspondence Address: Nyitray, L.; Department of Biochemistry, Hungary; email: laszlo.nyitray@ttk.elte.hu Funding details: Nemzeti Kutatási, Fejlesztési és Innovaciós Alap, NKFIA, K119359 Funding details: National Research, Development and Innovation Office AB - S100 proteins are small, dimeric, Ca2+-binding proteins of considerable interest due to their associations with cancer and rheumatic and neurodegenerative diseases. They control the functions of numerous proteins by forming protein–protein complexes with them. Several of these complexes were found to display “fuzzy” properties. Examining these highly flexible interactions, however, is a difficult task, especially from a structural biology point of view. Here, we summarize the available in vitro techniques that can be deployed to obtain structural information about these dynamic complexes. We also review the current state of knowledge about the structures of S100 complexes, focusing on their often-asymmetric nature. © Copyright © 2021 Ecsédi, Gógl and Nyitray. LA - English DB - MTMT ER -