Project A03 – The role of conformational dynamics for Y receptor activation
In order to limit adverse effects during treatment it is of primary pharmacological interest to develop therapeutics specifically binding to either Y1R or Y2R subtype, and bias downstream signaling (functional selectivity). Since YRs feature high conformational flexibility, we aim to elucidate the structural underpinnings of subtype specificity and functional selectivity using magnetic resonance spectroscopic methods suitable for resolving and characterizing conformational ensembles. For these experiments, we will stabilize the relevant receptor conformations using known subtype specific derivatives of endogenous peptide ligands. Accordingly, we will increase the population of conformations responsible for functional selectivity by binding of functionally biased ligands, transducer proteins or its mimetics. The results will be integrated with available high-resolution structures using computational methods, providing new leads for computer-aided drug discovery.
Characterizing the molecular interactions of Y1 and Y2 receptors with NPY
Project Leaders: Dr. Peter Schmidt and Prof. Dr. Andrea Sinz
In the proposed project, distance constraints of complexes between Y1 and Y2 receptors and NPY will be derived by NMR, using the paramagnetic relaxation enhancement (PRE) effect, as well as (photo-) chemical cross-linking combined with mass spectrometry (MS). The experimentally obtained constraints will be used to refine computational models of the NPY in the Y1 and the Y2 binding pocket. The ultimate goal is to characterize the binding modes and dynamics of peptides in interaction with Y receptors, which is a prerequisite for the development of highly selective drugs.
Contact
Dr. Peter Schmidt (Project Leader)
Leipzig University, Faculty of Medicine
Institute of Medical Physics and Biophysics
Härtelstraße 16 – 18, 04107 Leipzig
Phone +49 341 97 15742
E-Mail
Web biophysik.medizin.uni-leipzig.de/dr-peter-schmidt
Dr. Matthias Elgeti (Project Leader)
Leipzig University, Faculty of Medicine
Interdisciplinary Center for Bioinformatics (IZBI)
Härtelstraße 16 – 18, 04107 Leipzig
Phone +49 341 97 15774
E-Mail
Web elgetilab.github.io/
Jeannette Laugwith (PhD Student)
Leipzig University, Faculty of Medicine
Institute of Medical Physics and Biophysics
Härtelstraße 16 – 18, 04107 Leipzig
Resources
- Bruker Avance III 600 MHz NMR spectrometer
- Bruker Avance I 700 MHz NMR spectrometer
- New Avance Neo Console for 700 MHz NMR spectrometer and 2 solids probes
- LTQ-Orbitrap XLMassspectrometer incl. ESI and Nano-ESI
- Orbitrap Fusion Tribrid-Massspectrometer
- HPLC-System (Agilent 1200)
- Nano-HPLC-System (Ultimate 3000, Dionex)
- Orbitrap Q-Exactive Plus-Massspectrometer
- High Mass Q-TOF 2-Massspectrometer (MSVision)
- MALDI-TOF/TOF – Massspectrometer (Ultraflex III, Bruker Daltonik)
- FPLC-Systems (ÄKTA Prime, ÄKTA FPLC and ÄKTA Purev
Publications
Belyaeva J, Elgeti M. Exploring protein structural ensembles: Integration of sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling methods. Elife. 2024 Sep 16;13:e99770. doi: 10.7554/eLife.99770. PMID: 39283059; PMCID: PMC11405019.
Zhao J, Elgeti M, O’Brien ES, Sár CP, Ei Daibani A, Heng J, Sun X, White E, Che T, Hubbell WL, Kobilka BK, Chen C. Ligand efficacy modulates conformational dynamics of the µ-opioid receptor. Nature. 2024 May;629(8011):474-480. doi: 10.1038/s41586-024-07295-2 . Epub 2024 Apr 10. PMID: 38600384; PMCID: PMC11078757.
Schmidt P, Vogel A, Schwarze B, Seufert F, Licha K, Wycisk V, Kilian W, Hildebrand PW, Mitschang L. Towards Probing Conformational States of Y2 Receptor Using Hyperpolarized 129Xe NMR. Molecules. 2023; 28(3):1424.
Tänzler D, Kipping M, Lederer M, Günther WF, Arlt C, Hüttelmaier S, Merken-schlager A, Sinz A. Effects of theophylline on ADCY5 activation-From cellular studies to improved therapeutic options for ADCY5-related dyskinesia patients. PLoS One. 2023; 18:e0282593.
Wygas MM, Laugwitz JM, Schmidt P, Elgeti M, Kaiser A. Dynamics of the Second Extracellular Loop Control Transducer Coupling of Peptide-Activated GPCRs. Int J Mol Sci. 2023 Jul 30;24(15):12197. doi: 10.3390/ijms241512197. PMID: 37569573; PMCID: PMC10419011.
Wei AAJ, Iacobucci C, Schultze W, Ihling CH, Arlt C, Sinz A. Different Oligomeric States of the Tumor Suppressor p53 Show Identical Binding Behavior towards the S100β Homodimer. Chembiochem. 2022 Jun 3;23(11):e202100665. doi: 10.1002/cbic.202100665. Epub 2022 Apr 13. PMID: 35333001
Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions – A Method for All Seasons. Chemical Reviews Article ASAP. DOI: 10.1021/acs.chemrev.1c00786.
Krug U, Gloge A, Schmidt P, Becker-Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck-Sickinger AG, Glaubitz C, Huster D. The Conformational Equilibrium of the Neuropeptide Y2 Receptor in Bilayer Membranes. Angew Chem Int Ed Engl. 2020 Aug 13. doi: 10.1002/anie.202006075. Epub ahead of print. PMID: 32790043
Laugwitz JM, Haeri HH, Kaiser A, Krug U, Hinderberger D, Beck-Sickinger AG, Schmidt P. Probing the Y2 Receptor on Transmembrane, Intra- and Extra-Cellular Sites for EPR Measurements. molecules. 2020, 25(18), 4143.
Pacull EM, Sendker F, Bernhard F, Scheidt HA, Schmidt P, Huster D, Krug U. Integration of Cell-Free Expression and Solid-State NMR to Investigate the Dynamic Properties of Different Sites of the Growth Hormone Secretagogue Receptor. Front Pharmacol. 2020 Oct 29;11:562113. doi: 10.3389/fphar.2020.562113. PMID: 33324203; PMCID: PMC7723455.
Vogel A, Bosse M, Gauglitz M, Wistuba S, Schmidt P, Kaiser A, Gurevich VV, Beck-Sickinger AG, Hildebrand PW, Huster D. The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation. Molecules. 2020 Nov 24;25(23):5489. doi: 10.3390/molecules25235489. PMID: 33255213; PMCID: PMC7727705.
Bräuning B, Bertosin E, Praetorius F, Ihling C, Schatt A, Adler A, Richter C, Sinz A, Dietz H, Grolla M. Structure and mechanism of the two-component α-helical cytolytic toxin YaxAB. Nature Commun. 2018; 4:1806.
Iacobucci C, Götze M, Ihling CH, Arl C, Hage C, Schäfer M, Schmidt R, Piotrowski C, Sinz A. A Cross-linking/Mass Spectrometry Workflow Based on MS-Cleavable Cross-Linkers and the MeroX Software for Studying Protein Structures and Protein-Protein Interactions. Nature Protocols. 2018; 13:2864-89.
Schmidt P, Bender BJ, Kaiser A, Gulati K, Scheidt HA, Hamm HE, Meiler J, Beck-Sickinger AG, Huster D. Improved in Vitro Folding of the Y2 G Protein-Coupled Receptor into Bicelles. Front Mol Biosci. 2018; 4;100.
Yang Z, Han S, Keller M, Kaiser A, Bender BJ, Bosse M, Burkert K, Kögler LM, Wifling D, Bernhardt G, Plank N, Littmann T, Schmidt P, Yi C, Li B, Ye S, Zhang R, Xu B, Larhammar D, Stevens RC, Huster D, Meiler J, Zhao Q, Beck-Sickinger AG, Buschauer A, Wu B. Structural basis of ligand binding modes at the neuropeptide Y Y1 receptor. Nature. 2018; 556:520-4.
Hage C, Iacobucci C, Rehkamp A, Arlt C, Sinz A. The First Zero-Length Mass Spectrometry-Cleavable Cross-Linker for Protein Structure Analysis. Angew Chem Int Ed Engl. 2017; 56:14551-5.
Arlt C, Flegler V, Ihling CH, Schäfer M, Thondorf I, Sinz A. An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor. Angew Chem Int Ed Engl. 2017; 56:275-9.
Kaiser A, Mueller P, Zellmann T, Scheidt HA, Thomas L, Bosse M, Meier R, Meiler J, Huster D, Beck-Sickinger AG, Schmidt P. Unwinding of the C-Terminal Residues of Neuropeptide Y is critical for Y2 Receptor Binding and Activation. Angew Chemie Int Ed. 2015; 54:7446-9.
Schmidt P, Thomas L, Mueller P, Scheidt HA, Huster D. The G Protein-Coupled Neuropeptide Y Receptor Type 2 is Highly Dynamic in Lipid Membranes as Revealed by Solid-State NMR Spectroscopy. Chemistry Eur J. 2014; 20:4986-92.
Hofmann S, Frank R, Hey-Hawkins E, Beck-Sickinger AG, Schmidt P. Manipulating Y Receptor Selectivity of Short Neuropeptide Y Analogs by Introducing Carbaboranes. Neuropeptides. 2013; 47:59-66.
Kölbel K, Ihling, CH, Sinz A. Analysis of Peptide Secondary Structures by Photoactivatable Amino Acid Analogues. Angew Chem Int Ed Engl. 2012; 51:12602-5.
