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  1. Thesis ; Online: Accessing Protein – Ligand Interactions

    Kaderli, Janina

    Design and Characterisation of Promising Molecular Scaffolds on the Basis of 3D Pharmacophore Models

    2022  

    Keywords info:eu-repo/classification/ddc/540 ; Chemistry
    Language English
    Publisher ETH Zurich
    Publishing country ch
    Document type Thesis ; Online
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  2. Article ; Online: Nanoscale Hyperspectral Imaging of Amyloid Secondary Structures in Liquid.

    Lipiec, Ewelina / Kaderli, Janina / Kobierski, Jan / Riek, Roland / Skirlińska-Nosek, Katarzyna / Sofińska, Kamila / Szymoński, Marek / Zenobi, Renato

    Angewandte Chemie (International ed. in English)

    2021  Volume 60, Issue 9, Page(s) 4545–4550

    Abstract: Abnormal aggregation of amyloid-β is a very complex and heterogeneous process. Owing to methodological limitations, the aggregation pathway is still not fully understood. Herein a new approach is presented in which the secondary structure of single ... ...

    Abstract Abnormal aggregation of amyloid-β is a very complex and heterogeneous process. Owing to methodological limitations, the aggregation pathway is still not fully understood. Herein a new approach is presented in which the secondary structure of single amyloid-β aggregates is investigated with tip-enhanced Raman spectroscopy (TERS) in a liquid environment. Clearly resolved TERS signatures of the amide I and amide III bands enabled a detailed analysis of the molecular structure of single aggregates at each phase of the primary aggregation of amyloid-β and also of small species on the surface of fibrils attributed to secondary nucleation. Notably, a β-sheet rearrangement from antiparallel in protofibrils to parallel in fibrils is observed. This study allows better understanding of Alzheimer's disease etiology and the methodology can be applied in studies of other neurodegenerative disorders.
    MeSH term(s) Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Amyloid/chemistry ; Amyloid/metabolism ; Amyloid beta-Peptides/chemistry ; Humans ; Hyperspectral Imaging/methods ; Nanotechnology ; Protein Conformation, beta-Strand ; Spectrum Analysis, Raman
    Chemical Substances Amyloid ; Amyloid beta-Peptides
    Language English
    Publishing date 2021-01-07
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202010331
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  3. Article ; Online: NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24.

    Torres, Felix / Walser, Reto / Kaderli, Janina / Rossi, Emanuele / Bobby, Romel / Packer, Martin J / Sarda, Sunil / Walker, Graeme / Hitchin, James R / Milbradt, Alexander G / Orts, Julien

    Journal of medicinal chemistry

    2022  Volume 65, Issue 7, Page(s) 5565–5574

    Abstract: Structure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently ... ...

    Abstract Structure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently developed NMR molecular replacement (
    MeSH term(s) Crystallography, X-Ray ; Magnetic Resonance Spectroscopy ; Nuclear Proteins/metabolism ; Protein Binding ; Protein Domains ; Transcription Factors/metabolism
    Chemical Substances Nuclear Proteins ; Transcription Factors
    Language English
    Publishing date 2022-03-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.1c01703
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 151: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
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  4. Article ; Online: Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway.

    Lipiec, Ewelina / Perez-Guaita, David / Kaderli, Janina / Wood, Bayden R / Zenobi, Renato

    Angewandte Chemie (International ed. in English)

    2018  Volume 57, Issue 28, Page(s) 8519–8524

    Abstract: The aggregation pathways of neurodegenerative peptides determine the disease etiology, and their better understanding can lead to strategies for early disease treatment. Previous research has allowed modelling of hypothetic aggregation pathways. However, ...

    Abstract The aggregation pathways of neurodegenerative peptides determine the disease etiology, and their better understanding can lead to strategies for early disease treatment. Previous research has allowed modelling of hypothetic aggregation pathways. However, their direct experimental observation has been elusive owing to methodological limitations. Herein, we demonstrate that nanoscale chemical mapping by tip-enhanced Raman spectroscopy of single amyloid fibrils at various stages of aggregation captures the fibril formation process. We identify changes in TERS/Raman marker bands for Aβ
    MeSH term(s) Amyloid beta-Peptides/chemistry ; Nanotechnology ; Particle Size ; Protein Aggregates ; Protein Aggregation, Pathological ; Spectroscopy, Fourier Transform Infrared ; Spectrum Analysis, Raman ; Surface Properties
    Chemical Substances Amyloid beta-Peptides ; Protein Aggregates
    Language English
    Publishing date 2018-06-06
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.201803234
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  5. Article ; Online: Targeting the Main Protease (M

    Altincekic, Nadide / Jores, Nathalie / Löhr, Frank / Richter, Christian / Ehrhardt, Claus / Blommers, Marcel J J / Berg, Hannes / Öztürk, Sare / Gande, Santosh L / Linhard, Verena / Orts, Julien / Abi Saad, Marie Jose / Bütikofer, Matthias / Kaderli, Janina / Karlsson, B Göran / Brath, Ulrika / Hedenström, Mattias / Gröbner, Gerhard / Sauer, Uwe H /
    Perrakis, Anastassis / Langer, Julian / Banci, Lucia / Cantini, Francesca / Fragai, Marco / Grifagni, Deborah / Barthel, Tatjana / Wollenhaupt, Jan / Weiss, Manfred S / Robertson, Angus / Bax, Adriaan / Sreeramulu, Sridhar / Schwalbe, Harald

    ACS chemical biology

    2024  Volume 19, Issue 2, Page(s) 563–574

    Abstract: The main protease ... ...

    Abstract The main protease M
    MeSH term(s) Drug Discovery/methods ; SARS-CoV-2/metabolism ; Catalytic Domain ; Magnetic Resonance Spectroscopy ; Peptide Hydrolases/metabolism ; Protease Inhibitors/metabolism ; Antiviral Agents/pharmacology ; Molecular Docking Simulation
    Chemical Substances Peptide Hydrolases (EC 3.4.-) ; Protease Inhibitors ; Antiviral Agents
    Language English
    Publishing date 2024-01-17
    Publishing country United States
    Document type Journal Article
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.3c00720
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.

    Altincekic, Nadide / Korn, Sophie Marianne / Qureshi, Nusrat Shahin / Dujardin, Marie / Ninot-Pedrosa, Martí / Abele, Rupert / Abi Saad, Marie Jose / Alfano, Caterina / Almeida, Fabio C L / Alshamleh, Islam / de Amorim, Gisele Cardoso / Anderson, Thomas K / Anobom, Cristiane D / Anorma, Chelsea / Bains, Jasleen Kaur / Bax, Adriaan / Blackledge, Martin / Blechar, Julius / Böckmann, Anja /
    Brigandat, Louis / Bula, Anna / Bütikofer, Matthias / Camacho-Zarco, Aldo R / Carlomagno, Teresa / Caruso, Icaro Putinhon / Ceylan, Betül / Chaikuad, Apirat / Chu, Feixia / Cole, Laura / Crosby, Marquise G / de Jesus, Vanessa / Dhamotharan, Karthikeyan / Felli, Isabella C / Ferner, Jan / Fleischmann, Yanick / Fogeron, Marie-Laure / Fourkiotis, Nikolaos K / Fuks, Christin / Fürtig, Boris / Gallo, Angelo / Gande, Santosh L / Gerez, Juan Atilio / Ghosh, Dhiman / Gomes-Neto, Francisco / Gorbatyuk, Oksana / Guseva, Serafima / Hacker, Carolin / Häfner, Sabine / Hao, Bing / Hargittay, Bruno / Henzler-Wildman, K / Hoch, Jeffrey C / Hohmann, Katharina F / Hutchison, Marie T / Jaudzems, Kristaps / Jović, Katarina / Kaderli, Janina / Kalniņš, Gints / Kaņepe, Iveta / Kirchdoerfer, Robert N / Kirkpatrick, John / Knapp, Stefan / Krishnathas, Robin / Kutz, Felicitas / Zur Lage, Susanne / Lambertz, Roderick / Lang, Andras / Laurents, Douglas / Lecoq, Lauriane / Linhard, Verena / Löhr, Frank / Malki, Anas / Bessa, Luiza Mamigonian / Martin, Rachel W / Matzel, Tobias / Maurin, Damien / McNutt, Seth W / Mebus-Antunes, Nathane Cunha / Meier, Beat H / Meiser, Nathalie / Mompeán, Miguel / Monaca, Elisa / Montserret, Roland / Mariño Perez, Laura / Moser, Celine / Muhle-Goll, Claudia / Neves-Martins, Thais Cristtina / Ni, Xiamonin / Norton-Baker, Brenna / Pierattelli, Roberta / Pontoriero, Letizia / Pustovalova, Yulia / Ohlenschläger, Oliver / Orts, Julien / Da Poian, Andrea T / Pyper, Dennis J / Richter, Christian / Riek, Roland / Rienstra, Chad M / Robertson, Angus / Pinheiro, Anderson S / Sabbatella, Raffaele / Salvi, Nicola / Saxena, Krishna / Schulte, Linda / Schiavina, Marco / Schwalbe, Harald / Silber, Mara / Almeida, Marcius da Silva / Sprague-Piercy, Marc A / Spyroulias, Georgios A / Sreeramulu, Sridhar / Tants, Jan-Niklas / Tārs, Kaspars / Torres, Felix / Töws, Sabrina / Treviño, Miguel Á / Trucks, Sven / Tsika, Aikaterini C / Varga, Krisztina / Wang, Ying / Weber, Marco E / Weigand, Julia E / Wiedemann, Christoph / Wirmer-Bartoschek, Julia / Wirtz Martin, Maria Alexandra / Zehnder, Johannes / Hengesbach, Martin / Schlundt, Andreas

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 653148

    Abstract: The highly infectious disease COVID-19 caused by ... ...

    Abstract The highly infectious disease COVID-19 caused by the
    Language English
    Publishing date 2021-05-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.653148
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  7. Article ; Online: Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.

    Altincekic, Nadide / Korn, Sophie Marianne / Qureshi, Nusrat Shahin / Dujardin, Marie / Ninot-Pedrosa, Martí / Abele, Rupert / Abi Saad, Marie Jose / Alfano, Caterina / Almeida, Fabio C L / Alshamleh, Islam / de Amorim, Gisele Cardoso / Anderson, Thomas K / Anobom, Cristiane D / Anorma, Chelsea / Bains, Jasleen Kaur / Bax, Adriaan / Blackledge, Martin / Blechar, Julius / Böckmann, Anja /
    Brigandat, Louis / Bula, Anna / Bütikofer, Matthias / Camacho-Zarco, Aldo R / Carlomagno, Teresa / Caruso, Icaro Putinhon / Ceylan, Betül / Chaikuad, Apirat / Chu, Feixia / Cole, Laura / Crosby, Marquise G / de Jesus, Vanessa / Dhamotharan, Karthikeyan / Felli, Isabella C / Ferner, Jan / Fleischmann, Yanick / Fogeron, Marie-Laure / Fourkiotis, Nikolaos K / Fuks, Christin / Fürtig, Boris / Gallo, Angelo / Gande, Santosh L / Gerez, Juan Atilio / Ghosh, Dhiman / Gomes-Neto, Francisco / Gorbatyuk, Oksana / Guseva, Serafima / Hacker, Carolin / Häfner, Sabine / Hao, Bing / Hargittay, Bruno / Henzler-Wildman, K / Hoch, Jeffrey C / Hohmann, Katharina F / Hutchison, Marie T / Jaudzems, Kristaps / Jović, Katarina / Kaderli, Janina / Kalniņš, Gints / Kaņepe, Iveta / Kirchdoerfer, Robert N / Kirkpatrick, John / Knapp, Stefan / Krishnathas, Robin / Kutz, Felicitas / Zur Lage, Susanne / Lambertz, Roderick / Lang, Andras / Laurents, Douglas / Lecoq, Lauriane / Linhard, Verena / Löhr, Frank / Malki, Anas / Bessa, Luiza Mamigonian / Martin, Rachel W / Matzel, Tobias / Maurin, Damien / McNutt, Seth W / Mebus-Antunes, Nathane Cunha / Meier, Beat H / Meiser, Nathalie / Mompeán, Miguel / Monaca, Elisa / Montserret, Roland / Mariño Perez, Laura / Moser, Celine / Muhle-Goll, Claudia / Neves-Martins, Thais Cristtina / Ni, Xiamonin / Norton-Baker, Brenna / Pierattelli, Roberta / Pontoriero, Letizia / Pustovalova, Yulia / Ohlenschläger, Oliver / Orts, Julien / Da Poian, Andrea T / Pyper, Dennis J / Richter, Christian / Riek, Roland / Rienstra, Chad M / Robertson, Angus / Pinheiro, Anderson S / Sabbatella, Raffaele / Salvi, Nicola / Saxena, Krishna / Schulte, Linda / Schiavina, Marco / Schwalbe, Harald / Silber, Mara / Almeida, Marcius da Silva / Sprague-Piercy, Marc A / Spyroulias, Georgios A / Sreeramulu, Sridhar / Tants, Jan-Niklas / Tārs, Kaspars / Torres, Felix / Töws, Sabrina / Treviño, Miguel Á / Trucks, Sven / Tsika, Aikaterini C / Varga, Krisztina / Wang, Ying / Weber, Marco E / Weigand, Julia E / Wiedemann, Christoph / Wirmer-Bartoschek, Julia / Wirtz Martin, Maria Alexandra / Zehnder, Johannes / Hengesbach, Martin / Schlundt, Andreas

    8 ; 653148 ; Frontiers in molecular biosciences ; Switzerland

    2021  

    Abstract: The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium ... ...

    Abstract The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
    Keywords COVID-19 ; NMR spectroscopy ; SARS-CoV-2 ; accessory proteins ; cell-free protein synthesis ; intrinsically disordered region ; nonstructural proteins ; structural proteins
    Subject code 660
    Language English
    Publishing date 2021-05-10
    Publisher Frontiers
    Publishing country de
    Document type Article ; Online
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