Project B03 – Role of extracellular loop interactions in NPY receptor activation

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.


Marcel Wygas (PhD Student)

Leipzig University, Faculty of Life Sciences
Institute of Biochemistry
Brüderstrasse 34, D-04103 Leipzig


Signaling and nano-BRET binding assays


Groß VE, Gershkovich MM, Schöneberg TKaiser APrömel 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 VVBeck-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.

Ziffert I, Kaiser A, Babilon S, Mörl K, Beck-Sickinger AG. Unusually persistent Gαi-signaling of the neuropeptide Y2 receptor depletes cellular Gi/o pools and leads to a Gi-refractory state. Cell Commun Signal. 2020 Mar 30;18(1):49. doi: 10.1186/s12964-020-00537-6. PMID: 32223755.

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 Y1Nature. 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