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Xu B, Vasile S, Østergaard S, Paulsson JF, Pruner J, Åqvist J, Wulff BS, Gutiérrez-de-Terán H, Larhammar D. Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y 2 Receptor. Mol Pharmacol 2018; 93:323-334. [PMID: 29367257 DOI: 10.1124/mol.117.110627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/19/2018] [Indexed: 11/22/2022] Open
Abstract
Understanding the agonist-receptor interactions in the neuropeptide Y (NPY)/peptide YY (PYY) signaling system is fundamental for the design of novel modulators of appetite regulation. We report here the results of a multidisciplinary approach to elucidate the binding mode of the native peptide agonist PYY to the human Y2 receptor, based on computational modeling, peptide chemistry and in vitro pharmacological analyses. The preserved binding orientation proposed for full-length PYY and five analogs, truncated at the amino terminus, explains our pharmacological results where truncations of the N-terminal proline helix showed little effect on peptide affinity. This was followed by receptor mutagenesis to investigate the roles of several receptor positions suggested by the modeling. As a complement, PYY-(3-36) analogs were synthesized with modifications at different positions in the common PYY/NPY C-terminal fragment (32TRQRY36-amide). The results were assessed and interpreted by molecular dynamics and Free Energy Perturbation (FEP) simulations of selected mutants, providing a detailed map of the interactions of the PYY/NPY C-terminal fragment with the transmembrane cavity of the Y2 receptor. The amidated C-terminus would be stabilized by polar interactions with Gln2886.55 and Tyr2195.39, while Gln1303.32 contributes to interactions with Q34 in the peptide and T32 is close to the tip of TM7 in the receptor. This leaves the core, α-helix of the peptide exposed to make potential interactions with the extracellular loops. This model agrees with most experimental data available for the Y2 system and can be used as a basis for optimization of Y2 receptor agonists.
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Affiliation(s)
- Bo Xu
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Silvana Vasile
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Søren Østergaard
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Johan F Paulsson
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Jasna Pruner
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Johan Åqvist
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Birgitte S Wulff
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Hugo Gutiérrez-de-Terán
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Dan Larhammar
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
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Hegefeld WA, Kuczera K, Jas GS. Structural dynamics of neuropeptide hPYY. Biopolymers 2011; 95:487-502. [PMID: 21360523 DOI: 10.1002/bip.21608] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/04/2011] [Accepted: 02/05/2011] [Indexed: 01/07/2023]
Abstract
We have employed a combination of experiment and simulation to characterize the ensemble of structures sampled by human Peptide YY (hPYY), an important member of the neuropeptide Y family. Experimental structural characterization carried out with far UV circular dichroism spectroscopy and Fourier Transform-Infrared measurements confirmed that the major feature of the secondary structure of hPYY is the α-helix, encompassing about half the peptide residues, with smaller contributions from turn and β-sheet like structures. The peptide undergoes thermal denaturation characterized by a melting temperature of 48°C with an enthalpy change of -24.5 kcal/mol and entropy change of -76.2 cal/(mol K). In our computational studies, based on a 4-μsec MD trajectory generated with the AMBER03 potential, we found excellent agreement of the predicted features with experimental data, including a stable C-terminal helix, a central turn and conservation of about 80% of measured long-range NOE contacts. The main structural fluctuations involved partial helix unwinding and large-scale motions of the N-terminal. Our joint experimental/computational approach leads to several insights into the biological function of PYY. We conclude that the C-terminal helix is crucial for the structural integrity of PYY. The structures and motions found in the simulations suggest microscopic explanations for observed changes in biological activity of the peptide upon mutation and truncation. We also performed microsecond-length MD and replica-exchange simulations of hPYY with the OPLS-AA force field, for which computed structures did not agree well with experimental data, predicting significant loss of helicity and NOE contacts.
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Bader R, Zerbe O. Are Hormones from the Neuropeptide Y Family Recognized by Their Receptors from the Membrane-Bound State? Chembiochem 2005; 6:1520-34. [PMID: 16038001 DOI: 10.1002/cbic.200400439] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Hormones and many other neurotransmitters, growth factors, odorant molecules, and light all present stimuli for a class of membrane-anchored receptors called G protein-coupled receptors (GPCRs). The GPCRs are the largest family of cell-surface receptors involved in signal transduction. About 1% of all known genes of Drosophila and more than 5% of the genes of Caenorhabditis elegans encode GPCRs. In addition, more than 50% of current therapeutic agents on the market target these receptors. When the enormous biological and pharmaceutical importance of these receptors is considered, it is surprising how little is known about the mechanism with which these receptors recognize their natural ligands. In this review we present a structural approach, utilizing techniques of high-resolution NMR spectroscopy, to address the question of whether peptides from the neuropeptide Y family of neurohormones are recognized directly from solution or from the membrane-bound state. In our studies we discovered that the structures of the membrane-bound species are better correlated to the pharmacological properties of these peptides than the solution structures are. These findings are supported by the observation that many biophysical properties of these peptides seem to be optimized for membrane binding. We finally present a scenario of possible events during receptor recognition.
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Affiliation(s)
- Reto Bader
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Keire DA, Mannon P, Kobayashi M, Walsh JH, Solomon TE, Reeve JR. Primary structures of PYY, [Pro(34)]PYY, and PYY-(3-36) confer different conformations and receptor selectivity. Am J Physiol Gastrointest Liver Physiol 2000; 279:G126-31. [PMID: 10898754 DOI: 10.1152/ajpgi.2000.279.1.g126] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We synthesized PYY-(1-36) (nonselective between Y(1) and Y(2) receptor subtype agonists), [Pro(34)]PYY (selective for Y(1)), and PYY-(3-36) (selective for Y(2)) to determine whether solution conformation plays a role in receptor subtype selectivity. The three peptides exhibited the expected specificities in displacing labeled PYY-(1-36) from cells transfected with Y(1) receptors (dissociation constants = 0.42, 0.21, and 1,050 nM, respectively) and from cells transfected with Y(2) receptors (dissociation constants = 0.03, 710, and 0.11 nM, respectively) for PYY-(1-36), [Pro(34)]PYY, and PYY-(3-36). Sedimentation equilibrium analyses revealed that the three PYY analogs were 80-90% monomer at the concentrations used for the subsequent circular dichroism (CD) and (1)H-nuclear magnetic resonance (NMR) studies. CD analysis measured helicities for PYY-(1-36), [Pro(34)]PYY, and PYY-(3-36) of 42%, 31%, and 24%, suggesting distinct differences in secondary structure. The backbone (1)H-NMR resonances of the three peptides further substantiated marked conformational differences. These patterns support the hypothesis that Y(1) and Y(2) receptor subtype binding affinities depend on the secondary and tertiary solution state structures of PYY and its analogs.
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Affiliation(s)
- D A Keire
- The Beckman Research Institute of the City of Hope, Duarte, California 91010-0269, USA
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Li XA, Sutcliffe MJ, Schwartz TW, Dobson CM. Sequence-specific 1H NMR assignments and solution structure of bovine pancreatic polypeptide. Biochemistry 1992; 31:1245-53. [PMID: 1734969 DOI: 10.1021/bi00119a038] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sequence-specific 1H NMR assignments for the 36 residue bovine pancreatic polypeptide (bPP) have been completed. The secondary and tertiary structure of bPP in solution has been determined from experimental NMR data. It is shown that bPP has a very well-defined C-terminal alpha-helix involving residues 15-32. Although regular secondary structure cannot be clearly defined in the N-terminal region, residues 4-8 maintain a rather ordered conformation in solution. This is attributed primarily to the hydrophobic interactions between this region and the C-terminal helix. The two segments of the structure are joined by a turn which is poorly defined. The four end residues both at the N-terminus and the C-terminus are highly disordered in solution. The overall fold of the bPP molecule is very closely similar to that found in the crystal structure of avian pancreatic polypeptide (aPP). The RMS deviation for backbone atoms of residues 4-8 and 15-32 between the bPP mean structure and the aPP crystal structure is 0.65 A, although there is only 39% identity of the residues. Furthermore, the average conformations of some (mostly from the alpha-helix) side chains of bPP in solution are closely similar to those of aPP in the crystal structure. A large number of side chains of bPP, however, show significant conformational averaging in solution.
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Affiliation(s)
- X A Li
- Oxford Centre for Molecular Sciences, University of Oxford, U.K
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