Structural similarities of micelle-bound peptide YY (PYY) and neuropeptide Y (NPY) are related to their affinity profiles at the Y receptors

Journal of Molecular Biology

Volumn 339, Issue 5, 2004, Pages 1153-1168

  Lerch, Mirjam ^a   Mayrhofer, Margot ^a   Zerbe, Oliver ^a,b  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

COSY, correlation spectroscopy; DPC, dodecylphosphocholine; dynamics; EMF, extended model free formalism; HPLC, high performance liquid chromatography; IPTG, isopropyl thiogalactopyranoside; membrane; NMR; peptide YY; structure

Indexed keywords

DODECYLPHOSPHORYLCHOLINE; NEUROPEPTIDE Y; PENTAPEPTIDE; PEPTIDE; PEPTIDE YY; RECEPTOR SUBTYPE; DRUG DERIVATIVE; HORMONE RECEPTOR; NEUROPEPTIDE Y RECEPTOR; PANCREAS POLYPEPTIDE; PEPTIDE YY RECEPTOR; PHOSPHORYLCHOLINE;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; COMPARATIVE STUDY; DIFFUSION; HYDROPHOBICITY; MEMBRANE MODEL; MICELLE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PARAMETER; PH MEASUREMENT; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; RECEPTOR BINDING; SEQUENCE HOMOLOGY; AMINO ACID SEQUENCE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; PH; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION; SWINE;

SUIDAE;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; HYDROGEN-ION CONCENTRATION; MICELLES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NEUROPEPTIDE Y; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PANCREATIC POLYPEPTIDE; PEPTIDE YY; PHOSPHORYLCHOLINE; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, GASTROINTESTINAL HORMONE; RECEPTORS, NEUROPEPTIDE Y; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP; SWINE;

EID: 3042621483     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.04.032     Document Type: Article

References (67)

1. Larhammar D. Evolution of neuropeptide Y, peptide YY and pancreatic polypeptide. Regul. Pept. 62:1996;1-11
2. Ekblad E., Sundler F. Distribution of pancreatic polypeptide and peptide YY. Peptides. 23:2002;251-261
3. Onaga T., Zabielski R., Kato S. Multiple regulation of peptide YY secretion in the digestive tract. Peptides. 23:2002;279-290
4. Schwartz T.W. Pancreatic polypeptide: a hormone under vagal control. Gastroenterology. 85:1983;1411-1425
5. Michel M.C., Beck-Sickinger A.G., Cox H., Doods H.N., Herzog H., Larhammar D., et al. XVI. International Union of Pharmacology recommendations for the nomenclature of neuropeptide Y, peptide YY, and pancreatic polypeptide receptors. Pharmacol. Rev. 50:1998;143-150
6. Keire D.A., Bowers C.W., Solomon T.E., Reeve J.R. Jr. Structure and receptor binding of PYY analogs. Peptides. 23:2002;305-321
7. Blundell T.L., Pitts J.E., Tickle I.J., Wood S.P., Wu C.-W. X-ray analysis (1.4 Å resolution) of avian pancreatic polypeptide: small globular protein hormone. Proc. Natl Acad. Sci. USA. 78:1981;4175-4179
8. 1H NMR assignments and solution structure of bovine pancreatic polypeptide. Biochemistry. 31:1992;1245-1253
9. 1H nuclear magnetic resonance and restrained molecular dynamics. Eur. J. Biochem. 209:1992;765-771
10. Monks S.A., Karagianis G., Howlett G.J., Norton R.S. Solution structure of human neuropeptide Y. J. Biomol. NMR. 8:1996;379-390
11. Bader R., Bettio A., Beck-Sickinger A.G., Zerbe O. Structure and dynamics of micelle-bound neuropeptide Y: comparison with unligated NPY and implications for receptor selection. J. Mol. Biol. 305:2001;307-329
12. Bettio A., Dinger M.C., Beck-Sickinger A.G. The neuropeptide Y monomer in solution is not folded in the pancreatic-polypeptide fold. Protein Sci. 11:2002;1834-1844
13. Keire D.A., Kobayashi M., Solomon T.E., Reeve J.R. Jr. Solution structure of monomeric peptide YY supports the functional significance of the PP-fold. Biochemistry. 39:2000;9935-9942
14. Kaiser E.T., Kezdy F.J. Secondary structures of proteins and peptides in amphiphilic environments. Proc. Natl Acad. Sci. USA. 80:1983;1137-1143
15. Kaiser E.T., Kezdy F.J. Amphiphilic secondary structure: design of peptide hormones. Science. 223:1984;249-255
16. Sargent D.F., Schwyzer R. Membrane lipid phase as catalyst for peptide-receptor interactions. Proc. Natl Acad. Sci. USA. 83:1986;5774-5778
17. Schwyzer R. In search of the "bio-active conformation" - is it induced by the target cell membrane? J. Mol. Recognit. 8:1995;3-8
18. Moroder L., Romano R., Guba W., Mierke D.F., Kessler H., Delporte C., et al. New evidence for a membrane-bound pathway in hormone receptor binding. Biochemistry. 32:1993;13551-13559
19. Lerch M., Gafner V., Bader R., Christen B., Folkers G., Zerbe O. Bovine pancreatic polypeptide (bPP) undergoes significant changes in conformation and dynamics upon binding to DPC micelles. J. Mol. Biol. 322:2002;1117-1133
20. Lauterwein J., Bösch C., Brown L.R., Wüthrich K. Physicochemical studies of the protein-lipid interactions in melittin-containing micelles. Biochim. Biophys. Acta. 556:1979;244-264
21. Bader R., Rytz G., Lerch M., Beck-Sickinger A.G., Zerbe O. Key motif to gain selectivity at the neuropeptide Y5-receptor: solution structure and dynamics of [Ala31,Pro32]-NPY. Biochemistry. 41:2002;8031-8042
22. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;Wiley, New York
23. Wishart D.S., Sykes B.D. Chemical shifts as a tool for structure determination. Methods Enzymol. 239:1994;363-392
24. Wüthrich K., Billeter M., Braun W. Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. J. Mol. Biol. 180:1984;715-740
25. HNα, in a globular protein. J. Mol. Biol. 180:1984;741-751
26. Güntert P., Mumenthaler C., Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program Dyana. J. Mol. Biol. 273:1997;283-298
27. Pearlman D.A., Case D.A., Caldwell J.W., Ross W.S., Cheatham T.E., DeBolt S., et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energectic properties of molecules. Comp. Phys. Commun. 91:1995;1-41
28. Kabsch W., Sander C. Dictionary of protein secondary strucutre: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637
29. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291
30. Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:1982;4546-4559
31. Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104:1982;4559-4570
32. Bader R., Lerch M., Zerbe O. NMR of membrane-associated peptides and proteins. Zerbe O. BioNMR in Drug Research. 2003;95-120 Wiley-VCH, Weinheim
33. Damberg P., Jarvet J., Gräslund A. Micellar systems as solvents in peptide and protein structure determination. Methods Enzymol. 339:2001;271-285
34. Cowley D.J., Hoflack J.M., Pelton J.T., Saudek V. Structure of neuropeptide Y dimer in solution. Eur. J. Biochem. 205:1992;1099-1106
35. Chang P.J., Noelken M.E., Kimmel J.R. Reversible dimerization of avian pancreatic polypeptide. Biochemistry. 19:1980;1844-1849
36. Wimley W.C., White S.H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Struct. Biol. 3:1996;842-848
37. Beck-Sickinger A.G., Wieland H.A., Wittneben H., Willim K.D., Rudolf K., Jung G. Complete L-alanine scan of neuropeptide Y reveals ligands binding to Y1 and Y2 receptors with distinguished conformations. Eur. J. Biochem. 225:1994;947-958
38. Minakata H., Taylor J.W., Walker M.W., Miller R.J., Kaiser E.T. Characterization of amphiphilic secondary structures in neuropeptide Y through the design, synthesis, and study of model peptides. J. Biol. Chem. 264:1989;7907-7913
39. Sankaramarkishnan R., Weinstein H. Positioning and stabilization of dynorphin peptides in membrane bilayers: the mechanistic role of aromatic and basic residues revealed from comparative MD simulations. J. Phys. Chem. 106:2002;206-218
40. Ben-Tal N., Honig B., Peitzsch R.M., Denisov G., McLaughlin S. Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results. Biophys. J. 71:1996;561-575
41. Bechinger B. Towards membrane protein design: pH-sensitive topology of histidine-containing polypeptides. J. Mol. Biol. 263:1996;768-775
42. Mozsolits H., Unabia S., Ahmad A., Morton C.J., Thomas W.G., Aguilar M.I. Electrostatic and hydrophobic forces tether the proximal region of the angiotensin II receptor (AT1A) carboxyl terminus to anionic lipids. Biochemistry. 41:2002;7830-7840
43. Heymann J.B., Zakharov S.D., Zhang Y.L., Cramer W.A. Characterization of electrostatic and nonelectrostatic components of protein-membrane binding interactions. Biochemistry. 35:1996;2717-2725
44. 13C. J. Biomol. NMR. 12:1998;109-121
45. 1H spectra of proteins via double-quantum filtering. Biochem. Biophys. Res. Commun. 117:1983;479-485
46. 1H spin system identification in macromolecules. J. Am. Chem. Soc. 110:1988;7870-7872
47. Macura S., Ernst R.R. Elucidation of cross-relaxation in liquids by two-dimensional NMR spectroscopy. Mol. Phys. 41:1980;95-117
48. Kumar A., Ernst R.R., Wüthrich K. A two-dimensional nuclear overhauser enhancement (2D NOE) experiment for the elucidation of complete proton,proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95:1980;1-6
49. Otting G. Zero-quantum suppression in NOESY and experiments with a z-filter. J. Magn. Reson. 86:1990;496-508
50. Szyperski T., Güntert P., Otting G., Wüthrich K. Determination of scalar coupling constants by inverse Fourier transfomation of in-phase multiplets. J. Magn. Reson. 99:1992;552-560
51. Gronenborn A.M., Bax A., Wingfield P.T., Clore G.M. A powerful method of sequential proton resonance assignment in proteins using relayed 15N-1H multiple quantum coherence spectroscopy. FEBS Letters. 243:1989;93-98
52. Meiboom S., Gill D. Modified spin-echo method for measuring spin-relaxation rates. Rev. Sci. Instrum. 29:1958;688-691
53. Vold R.L., Waugh J.S., Klein M.P., Phelps D.E. Measurement of spin relaxation rates in complex systems. J. Chem. Phys. 48:1968;3831-3832
54. Noggle J.H., Schirmer R.E. The Nuclear Overhauser Effect - Chemical Applications. 1971;Academic Press, New York
55. 15N NMR via proton-detected multiple-quantum coherences: studies of large peptides. J. Am. Chem. Soc. 106:1984;6104-6105
56. Güntert P., Billeter M., Ohlenschläger O., Brown L.R., Wüthrich K. Conformational analysis of protein and nucleic acid fragments with the new search algorithm FOUND. J. Biomol. NMR. 12:1998;543-548
57. Case D.A., Pearlman D.A., Caldwell J.W., Cheatham T.E. III, Ross W.S., Simmerling C.L., et al. AMBER 6. 1999;University of California, San Francisco
58. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 118:1995;2309
59. Berman H.M., Westbrook J., Feng Z., Gilliand G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242
60. Koradi R., Billeter M., Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:1996;51-55
61. 1H NMR spectroscopy. Biochemistry. 29:1990;7387-7401
62. Mandel A.M., Akke M., Palmer A.G. III. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 246:1995;144-163
63. 13C heteronuclear NMR spectroscopy. J. Am. Chem. Soc. 113:1991;4371-4380
64. 15N NMR relaxation. J. Am. Chem. Soc. 117:1995;12562-12566
65. McCrea K., Wisialowski T., Cabrele C., Church B., Beck-Sickinger A., Kraegen E., Herzog H. 2-36[K4,RYYSA(19-23)]PP a novel Y5-receptor preferring ligand with strong stimulatory effect on food intake. Regul. Pept. 87:2000;47-58
66. Small C.J., Morgan D.G., Meeran K., Heath M.M., Gunn I., Edwards C.M., et al. Peptide analogue studies of the hypothalamic neuropeptide Y receptor mediating pituitary adrenocorticotrophic hormone release. Proc. Natl Acad. Sci. USA. 94:1997;11686-11691
67. Bartels C., Xia T.-., Billeter M., Güntert P., Wüthrich K. The program XEASY for computer-supported spectral analysis of biological macromolecules. J. Biomol. NMR. 6:1995;1-10