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Wang Y, Kim J, Hilty C. Determination of protein-ligand binding modes using fast multi-dimensional NMR with hyperpolarization. Chem Sci 2020; 11:5935-5943. [PMID: 32874513 PMCID: PMC7441707 DOI: 10.1039/d0sc00266f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/05/2020] [Indexed: 11/21/2022] Open
Abstract
Elucidation of small molecule-protein interactions provides essential information for understanding biological processes such as cellular signaling, as well as for rational drug development. Here, multi-dimensional NMR with sensitivity enhancement by dissolution dynamic nuclear polarization (D-DNP) is shown to allow the determination of the binding epitope of folic acid when complexed with the target dihydrofolate reductase. Protein signals are selectively enhanced by polarization transfer from the hyperpolarized ligand. A pseudo three-dimensional data acquisition with ligand-side Hadamard encoding results in protein-side [13C, 1H] chemical shift correlations that contain intermolecular nuclear Overhauser effect (NOE) information. A scoring function based on this data is used to select pre-docked ligand poses. The top five poses are within 0.76 Å root-mean-square deviation from a reference structure for the encoded five protons, showing improvements compared with the poses selected by an energy-based scoring function without experimental inputs. The sensitivity enhancement provided by the D-DNP combined with multi-dimensional NMR increases the speed and potentially the selectivity of structure elucidation of ligand binding epitopes.
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Affiliation(s)
- Yunyi Wang
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Jihyun Kim
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Christian Hilty
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
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Kadavath H, Cabrales Fontela Y, Jaremko M, Jaremko Ł, Overkamp K, Biernat J, Mandelkow E, Zweckstetter M. Der Bindungsmodus eines Tau-Peptids mit Tubulin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Harindranath Kadavath
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Yunior Cabrales Fontela
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Mariusz Jaremko
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
| | - Łukasz Jaremko
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Kerstin Overkamp
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
| | - Jacek Biernat
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- CAESAR Forschungszentrum; Ludwig-Erhard-Allee 2 Bonn Deutschland
| | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- CAESAR Forschungszentrum; Ludwig-Erhard-Allee 2 Bonn Deutschland
| | - Markus Zweckstetter
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
- Klinik für Neurologie; Universitätsmedizin Göttingen; Waldweg 33 37073 Göttingen Deutschland
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Kadavath H, Cabrales Fontela Y, Jaremko M, Jaremko Ł, Overkamp K, Biernat J, Mandelkow E, Zweckstetter M. The Binding Mode of a Tau Peptide with Tubulin. Angew Chem Int Ed Engl 2018; 57:3246-3250. [PMID: 29314492 DOI: 10.1002/anie.201712089] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/15/2017] [Indexed: 11/09/2022]
Abstract
The microtubule-associated protein Tau promotes the polymerization of tubulin and modulates the function of microtubules. As a consequence of the dynamic nature of the Tau-tubulin interaction, the structural basis of this complex has remained largely elusive. By using NMR methods optimized for ligand-receptor interactions in combination with site-directed mutagenesis we demonstrate that the flanking domain downstream of the four microtubule-binding repeats of Tau binds competitively to a site on the α-tubulin surface. The binding process is complex, involves partial coupling of different interacting regions, and is modulated by phosphorylation at Y394 and S396. This study strengthens the hypothesis of an intimate relationship between Tau phosphorylation and tubulin binding and highlights the power of the INPHARMA NMR method to characterize the interaction of peptides derived from intrinsically disordered proteins with their molecular partners.
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Affiliation(s)
- Harindranath Kadavath
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Yunior Cabrales Fontela
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Mariusz Jaremko
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany
| | - Łukasz Jaremko
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Kerstin Overkamp
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany
| | - Jacek Biernat
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,CAESAR Research Center, Ludwig-Erhard-Allee 2, Bonn, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,CAESAR Research Center, Ludwig-Erhard-Allee 2, Bonn, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Klinik für Neurologie, Universitätsmedizin Göttingen, Waldweg 33, 37073, Göttingen, Germany
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