Project B04 – Exploring topology and dynamics of molecular interactions at Y receptors in living cells via non-canonical amino acids
After discovering how natural neuropeptide ligands bind to the Y5 receptor (Y5R) in the first funding period, we aim now at dissecting the dynamic of the peptide binding process by applying molecular dynamic simulations and newly developed fluorescent conformational sensors. In the second place, we will apply our recently established crosslinking platform to investigate the molecular details of the interaction of the Y5R and the other Y receptors with arrestin. We expect to gain new information about basic mechanisms that determine the different behavior of even similar and phylogenetically tightly related GPCRs with respect to arrestin recruitment and internalization.
Mapping binding sites of NPY peptides on the Y5 receptor using genetically encoded crosslinkers
Very little is known about ligand binding to the Y5 receptor (Y5R) and its activation. We will use genetically encoded crosslinkers to map on the Y5R the binding paths of its three natural peptide ligands and identify inter-molecular pairs of vicinal amino acids. Spatial constraints will be derived, which will serve to build accurate computational models of the peptide-Y5R complexes. Analysing the models in the frame of existing data for other Y receptors will help identifying discriminants for selectivity and shed light on the evolution of the Y system.
Contact
Prof. Dr. Irene Coin (Project Leader)
Leipzig University, Faculty of Life Sciences
Institute of Biochemistry
Brüderstrasse 34, D-04103 Leipzig
Phone +49 341 97 36996
E-Mail
Web https://www.lw.uni-leipzig.de/coinlab/arbeitsgruppe
Ammar Al-kara (PhD Student)
Leipzig University, Faculty of Life Sciences
Institute of Biochemistry
Brüderstrasse 34, D-04103 Leipzig
Karolin Philipp (PhD Student)
Leipzig University, Faculty of Life Sciences
Institute of Biochemistry
Brüderstrasse 34, D-04103 Leipzig
Resources
Publications
Aydin Y, Böttke T, Lam JH, Ernicke S, Fortmann A, Tretbar M, Zarzycka B, Gurevich VV, Katritch V*, Coin I*. Structural details of a Class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells. Nat Commun. 2023; 14:1151.
Aydin Y, Coin I. Genetically encoded crosslinkers to address protein-protein interactions. Protein Sci. 2023; 32:e4637.
Ledwitch KV, Künze G, McKinney JR, Okwei E, Larochelle K, Pankewitz L, Ganguly S, Darling HL, Coin I, Meiler J. Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction. J Biomol NMR. 2023 Apr 4.
Rudolf S, Kaempf K, Vu O, Meiler J, Beck-Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y5 Receptor. Angew Chem Int Ed Engl. 2022 Jan 26;61(5):e202108738. doi: 10.1002/anie.202108738. PMID:34822209.
Aydin Y, Coin I*. Biochemical Insights into Structure and Function of Arrestins. FEBS J. 2021; 288: 2529-2549.
Böttke T, Ernicke S, Serfling R, Ihling C, Burda E, Gurevich VV, Sinz A, Coin I. Exploring GPCR-arrestin interfaces with genetically encoded crosslinkers. EMBO Rep. 2020 Nov 5;21(11):e50437. doi: 10.15252/embr.202050437. Epub 2020 Sep 14. PMID: 32929862; PMCID: PMC7645262.
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.
Seidel L, Zarzycka B, Katritch V, Coin I. Exploring pairwise chemical crosslinking to study peptide-receptor interactions. ChemBioChem, 2019; 20:1-11.
Coin I. Application of non-canonical crosslinking amino acids to study protein-protein interactions in live cells. Curr Opin Chem biol. 2018; 46:156-63.
Serfling R, Lorenz C, Etzel M, Schicht G, Böttke T, Mörl M, Coin I. Designer tRNAs for efficient incorporation of non-canonical amino acids by the pyrrolysine system in mammalian cells. Selected as breakthrough paper, journal cover. Nucleic Acids Res. 2018; 46:1-10.
Serfling R, Seidel L, Böttke T, Coin I. Optimizing the genetic incorporation of chemical probes into GPCRs for photo-crosslinking mapping and bioorthogonal chemistry in live mammalian cells. J Vis 2018; 134.
Seidel L, Zarzycka B, Zaidi SA, Katritch V, Coin I. Structural insight into the activation of a class B G-protein-coupled receptor by peptide hormones in live human cells. 2017; 6:27711.
Coin I, Katritch V, Sun T, Xiang Z, Siu FY, Beyermann M, Stevens RC, Wang L. Genetically encoded chemical probes reveal the binding path of Urocortin-I to CRF class B GPCR. 2013; 155:1258-69.
Xiang Z, Ren H, Hu YS, Coin I, Wei J, Cang H, Wang L. Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity. Nat Methods. 2013; 10:885-8.
Coin I, Perrin MH, Vale WW, Wang L. Photocrosslinkers incorporated into G-Protein-Coupled-Receptors in mammalian cells: a ligand comparison. Selected as Very-Important-Paper (VIP) by referees. Angew Chem Int Ed Engl. 2011; 50:8077-81.
Coin I, Beyermann M, Bienert M. Solid-phase peptide synthesis: from standard procedures to the synthesis of difficult sequences. Nat Protoc. 2007; 2:3247-56.
