Project B03 – Transient contacts for ligand recognition and modulation of receptor activation by Y1R and Y2R N termini
The structures and functions of Y1R’s and Y2R’s N termini are still largely elusive despite recent cryo-electron microscopy studies on human Y1R and Y2R in complex with neuropeptide Y. Previous experiments from projects A03 and B03 (Sinz/Schmidt; Kaiser) strongly suggest an involvement of Y2R’s N-terminus during the ligand binding process and in the stabilization of defined signaling states of the receptor. We hypothesize that the N-terminus of Y2R might act as an intrinsically disordered region that forms transient interactions with ligands during the receptor recognition process, thereby affecting binding selectivity and specific receptor functions. We will use an integrative approach, combining state-of-the-art techniques in structural mass spectrometry and functional readouts, to correlate the dynamic contributions of Y1R’s and Y2R’s N termini with receptor-specific functions.
Role of extracellular loop interactions in NPY receptor activation
Project Leader: Dr. Anette Kaiser
We postulate a bitopic binding pose for many peptide-activated GPCRs: The extracellular loops of the GPCR interact via a large binding surface with the main portion of the often α-helical peptide ligand. At the same time, the terminus of the peptide unwinds and dips deeper into the common transmembrane cradle of rhodopsin-like GPCRs. Leveraging the Y1 and Y2 receptors as examples, we will engage in an iterative loop of computational design and experimental verification to delineate the impact of each binding pocket on affinity, selectivity, and activation. Further, we want to explore the evolutionary origins of the bitopic binding pockets by studying an ancient receptor homologue out of Caenorhabditis elegans.
Contact
Dr. Anette Kaiser (Project Leader)
Leipzig University, Faculty of Medicine
Clinic for Anesthesiology and Intensive Care
Liebigstrasse 19, ZFG, 04103 Leipzig
Phone +49 341 97 10598
E-Mail
Web uniklinikum-leipzig.de/arbeitgruppe_kaiser
Web akaiserlab.org/
Prof. Dr. Andrea Sinz (Project Leader)
Martin Luther University Halle-Wittenberg
Faculty of Natural Sciences I, Institute of Pharmacy
Kurt-Mothes-Str. 3a, D-06108 Halle/Saale
Phone +49 345 55 25170
E-Mail
Web http://agsinz.pharmazie.uni-halle.de/
Marcel Wygas (PhD Student)
Leipzig University, Faculty of Life Sciences
Institute of Biochemistry
Brüderstrasse 34, D-04103 Leipzig
Resources
- Signaling and nano-BRET binding assays
Publications
Ianni AD, Ihling CH, Vranka T, Matoušek V, Sinz A, Iacobucci C. Evaluating Imide-Based Mass Spectrometry-Cleavable Cross-Linkers for Structural Proteomics Studies. JACS Au. 2024 Jul 16;4(8):2936-2943. doi: 10.1021/jacsau.4c00282. PMID: 39211594; PMCID: PMC11350583.
Reinhardt F, Kaiser A, Prömel S, Stadler PF. Evolution of Neuropeptide Y/RFamide-like receptors in Nematodes. Heliyon. 2024; 10:14 e34473. doi.org/10.1016/j.heliyon.2024.e34473.
Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A. A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline. Anal Chem. 2024 May 2. doi: 10.1021/acs.analchem.4c00829. Epub ahead of print. PMID: 38696819.
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.
Groß VE, Gershkovich MM, Schöneberg T, Kaiser A, Prömel S. NanoBRET in C. elegans illuminates functional receptor interactions in real time. BMC Mol Cell Biol. 2022 Jan 31;23(1):8. doi: 10.1186/s12860-022-00405-w . PMID: 35100990 .
Tang T, Tan Q, Han S, Diemar A, Löbner K, Wang H, Schüß C, Behr V, Mörl K, Wang M, Chu X, Yi C, Keller M, Kofoed J, Reedtz-Runge S, Kaiser A, Beck-Sickinger AG, Zhao Q, Wu B. Receptor-specific recognition of NPY peptides revealed by structures of NPY receptors. Sci Adv. 2022 May 6;8(18):eabm1232. doi: 10.1126/sciadv.abm1232. Epub 2022 May 4. PMID: 35507650; PMCID: PMC9067930.
Gershkovich MM, Groß VE, Vu O, Schoeder CT, Meiler J, Prömel S, Kaiser A. Structural Perspective on Ancient Neuropeptide Y-like System reveals Hallmark Features for Peptide Recognition and Receptor Activation. J Mol Biol. 2021 Apr 16;433(13):166992. doi: 10.1016/j.jmb.2021.166992. Epub ahead of print. PMID: 33865871.
Tang T, Hartig C, Chen Q, Zhao W, Kaiser A, Zhang X, Zhang H, Qu H, Yi C, Ma L, Han S, Zhao Q, Beck-Sickinger AG, Wu B. Structural basis for ligand recognition of the neuropeptide Y Y2 receptor. Nat Commun. 2021 Feb 2;12(1):737. doi: 10.1038/s41467-021-21030-9. PMID: 33531491; PMCID: PMC7854658.
Kaiser A, Coin I. Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules. 2020 Oct 15;25(20):4724. doi: 10.3390/molecules25204724. PMID: 33076289; PMCID: PMC7587574.
Kaiser A, Wanka L, Ziffert I, Beck-Sickinger AG. Biased agonists at the human Y1 receptor lead to prolonged membrane residency and extended receptor G protein interaction. Cell Mol Life Sci. 2020 Jan 9. doi: 10.1007/s00018-019-03432-7. Online ahead of print. PMID: 31919571.
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. 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 Sep 10;25(18):4143. doi: 10.3390/molecules25184143. PMID: 32927734; PMCID: PMC7571237.
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.
Ziffert I, Kaiser A, Hoppenz P, Mörl K, Beck-Sickinger AG. Shuttling of Peptide-Drug Conjugates by G Protein-Coupled Receptors Is Significantly Improved by Pulsed Application. ChemMedChem. 2020 Jul 22. doi: 10.1002/cmdc.202000490. Online ahead of print. PMID: 32700391.
Gershkovich MM, Groß VE, Kaiser A, Prömel S. Pharmacological and functional similarities of the human neuropeptide Y system in C. elegans challenges phylogenetic views on the FLP/NPR system. Cell Commun Signal. 2019 Sep 18;17(1):123. doi: 10.1186/s12964-019-0436-1. PMID: 31533726 Free PMC article.
Bech EM, Kaiser A, Bellmann-Sickert K, Nielsen SS, Sørensen KK, Elster L, Hatzakis N, Pedersen SL, Beck-Sickinger AG, Jensen KJ. Half-Life Extending Modifications of Peptide YY3-36 Direct Receptor-Mediated Internalization. Mol Pharm. 2019 Aug 5;16(8):3665-3677. doi: 10.1021/acs.molpharmaceut.9b00554. Epub 2019 Jul 25. PMID: 31310716
Bender BJ, Vortmeier G, Ernicke S, Bosse M, Kaiser A, Els-Heindl S, Krug U, Beck-Sickinger A, Meiler J, Huster D. Structural Model of Ghrelin Bound to its G Protein-Coupled Receptor. Structure. 2019 Mar 5;27(3):537-544.e4. doi: 10.1016/j.str.2018.12.004. Epub 2019 Jan 24. PMID: 30686667
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. Nature. 2018; 556:520-4.
Kaiser A, Hempel C, Wanka L, Schubert M, Hamm HE, Beck-Sickinger AG. G Protein Preassembly Rescues Efficacy of W6.48 Toggle Mutations in Neuropeptide Y2 Mol Pharmacol. 2018; 93:387-401.
Wanka L, Babilon S, Kaiser A, Mörl K, Beck-Sickinger AG. Different mode of arrestin-3 binding at the human Y1 and Y2 receptor. Cell Signal. 2018 Oct;50:58-71. doi: 10.1016/j.cellsig.2018.06.010. Epub 2018 Jun 23. PMID: 29944985
Burkert K, Zellmann T, Meier R, Kaiser A, Stichel J, Meiler J, Mittapalli GK, Roberts E, Beck-Sickinger AG. A Deep Hydrophobic Binding Cavity is the Main Interaction for Different Y2R Antagonists. ChemMedChem. 2017; 12:75-85.
Schrottke S, Kaiser A, Vortmeier G, Els-Heindl S, Worm D, Bosse M, Schmidt P, Scheidt HA, Beck-Sickinger AG, Huster D. Expression, Functional Characterization, and Solid-State NMR Investigation of the G Protein-Coupled GHS Receptor in Bilayer Membranes. Sci Rep. 2017 Apr 7;7:46128. doi: 10.1038/srep46128. PMID: 28387359 Free PMC article.
Burkert K, Zellmann T, Meier R, Kaiser A, Stichel J, Meiler J, Mittapalli GK, Roberts E, Beck-Sickinger AG. A Deep Hydrophobic Binding Cavity is the Main Interaction for Different Y2 R Antagonists. ChemMedChem. 2017 Jan 5;12(1):75-85. doi: 10.1002/cmdc.201600433. Epub 2016 Nov 30. PMID: 27874262
Kaiser A, Müller 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 Chem Int Ed Engl. 2015; 54:7446-9.
Schönauer R, Kaiser A, Holze C, Babilon S, Köbberling J, Riedl B, Beck-Sickinger AG. Fluorescently labeled adrenomedullin allows real-time monitoring of adrenomedullin receptor trafficking in living cells. J Pept Sci. 2015 Dec;21(12):905-12. doi: 10.1002/psc.2833. PMID: 26767744
Kaiser A, Müller 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 Chem Int Ed Engl. 2015 Jun 15;54(25):7446-9. doi: 10.1002/anie.201411688. Epub 2015 Apr 29. PMID: 25924821 Free PMC article.
Mäde V, Bellmann-Sickert K, Kaiser A, Meiler J, Beck-Sickinger AG. Position and length of fatty acids strongly affect receptor selectivity pattern of human pancreatic polypeptide analogues. ChemMedChem. 2014; 9:2463-74.
Witte K, Kaiser A, Schmidt P, Splith V, Thomas L, Berndt S, Huster D, Beck-Sickinger AG. Oxidative in vitro folding of a cysteine deficient variant of the G protein-coupled neuropeptide Y receptor type 2 improves stability at high concentration. Biol Chem. 2013 Aug;394(8):1045-56. doi: 10.1515/hsz-2013-0120. PMID: 23732681
