Skip to main content

Membrane Protein Fragments Reveal Both Secondary and Tertiary Structure of Membrane Proteins

  • Protocol
  • First Online:
Membrane Protein Structure Determination

Part of the book series: Methods in Molecular Biology ((MIMB,volume 654))

Abstract

Structural data on membrane proteins, while crucial to understanding cellular function, are scarce due to difficulties in applying to membrane proteins the common techniques of structural biology. Fragments of membrane proteins have been shown to reflect, in many cases, the secondary structure of the parent protein with fidelity and are more amenable to study. This chapter provides many examples of how the study of membrane protein fragments has provided new insight into the structure of the parent membrane protein.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html

  2. Katragadda M, Alderfer JL, Yeagle PL (2000) Solution structure of the loops of bacteriorhodopsin closely resemble the crystal structure. Biochim Biophys Acta 1466:1–6

    Article  PubMed  CAS  Google Scholar 

  3. Katragadda M, Alderfer JL, Yeagle PL (2001) Assembly of a polytopic membrane protein structure from the solution structures of overlapping peptide fragments of bacteriorhodopsin. Biophys J 81:1029–1036

    Article  PubMed  CAS  Google Scholar 

  4. Yeagle PL, Albert AD (2002) Use of nuclear magnetic resonance to study the three-dimensional structure of rhodopsin. Methods Enzymol 343:223–231

    Article  PubMed  Google Scholar 

  5. Yeagle PL, Albert AD (2007) G-protein coupled receptor structure. Biochim Biophys Acta 1768:808–824

    Article  PubMed  CAS  Google Scholar 

  6. Konig B, Arendt A, McDowell JH, Kahlert M, Hargrave PA, Hofmann KP (1989) Three cytoplasmic loops of rhodopsin interact with transducin. Proc Natl Acad Sci U S A 86:6878–6882

    Article  PubMed  CAS  Google Scholar 

  7. Yeagle PL, Alderfer JL, Albert AD (1995) Structure of the carboxyl terminal domain of bovine rhodopsin. Nat Struct Biol 2:832–834

    Article  PubMed  CAS  Google Scholar 

  8. Berlose J, Convert O, Brunissen A, Chassaing G, Lavielle S (1994) Three dimensional structure of the highly conserved seventh transmembrane domain of G-protein-coupled receptors. FEBS Lett 225:827–843

    CAS  Google Scholar 

  9. Lazarova T, Brewin KA, Stoeber K, Robinson CR (2004) Characterization of peptides corresponding to the seven transmembrane domains of human adenosine A2a receptor. Biochemistry 43:12945–12954

    Article  PubMed  CAS  Google Scholar 

  10. Arshava B, Taran I, Xie H, Becker JM, Naider F (2002) High resolution NMR analysis of the seven transmembrane domains of a heptahelical receptor in organic–aqueous medium. Biopolymers 64:161–176

    Article  PubMed  CAS  Google Scholar 

  11. Katragadda M, Chopra A, Bennett M, Alderfer JL, Yeagle PL, Albert AD (2001) Structures of the transmembrane helices of the G-protein coupled receptor, rhodopsin. J Pept Res 58:79–89

    Article  PubMed  CAS  Google Scholar 

  12. Haris PI (1988) Synthetic peptide fragments as probes for structure determination of potassium ion-channel proteins. Biosci Rep 18:299–312

    Article  Google Scholar 

  13. Gargaro AR, Bloomberg GB, Dempsey CE, Murray M, Tanner MJ (1994) The solution structures of the first and second transmembrane-spanning segments of band 3. Eur J Biochem 221:445–454

    Article  PubMed  CAS  Google Scholar 

  14. Aggeli A, Bannister ML, Bell M et al (1998) Conformation and ion-channeling activity of a 27-residue peptide modeled on the single-transmembrane segment of the IsK (minK) protein. Biochemistry 37:8121–8131

    Article  PubMed  CAS  Google Scholar 

  15. Duarte AM, de Jong ER, Wechselberger R, van Mierlo CP, Hemminga MA (2007) Segment TM7 from the cytoplasmic hemi-channel from VO-H+-V-ATPase includes a flexible region that has a potential role in proton translocation. Biochim Biophys Acta 1768:2263–2270

    Article  PubMed  CAS  Google Scholar 

  16. Duarte AM, Wolfs CJ, van Nuland NA et al (2007) Structure and localization of an essential transmembrane segment of the proton translocation channel of yeast H+-V-ATPase. Biochim Biophys Acta 1768:218–227

    Article  PubMed  CAS  Google Scholar 

  17. Ding J, Rainey JK, Xu C, Sykes BD, Fliegel L (2006) Structural and functional characterization of transmembrane segment VII of the Na+/H+ exchanger isoform 1. J Biol Chem 281:29817–29829

    Article  PubMed  CAS  Google Scholar 

  18. Bennett M, D'Rozario R, Sansom M, Yeagle PL (2006) Asymmetric stability among the transmembrane helices of lactose permease. Biochemistry 45:8088–8095

    Article  PubMed  CAS  Google Scholar 

  19. Morein S, Trouard TP, Hauksson JB, Rilfors L, Arvidson G, Lindblom G (1996) Two-dimensional 1H-NMR of transmembrane peptides from Escherichia coli phosphatidylglycerophosphate synthase in micelles. Eur J Biochem 241:489–497

    Article  PubMed  CAS  Google Scholar 

  20. Bondarenko V, Xu Y, Tang P (2007) Structure of the first transmembrane domain of the neuronal acetylcholine receptor beta2 subunit. Biophys J 92:1616–1622

    Article  PubMed  CAS  Google Scholar 

  21. MacKenzie KR, Prestegard JH, Engelman DM (1997) A transmembrane helix dimer: structure and implications. Science 276:131–133

    Article  PubMed  CAS  Google Scholar 

  22. Scheidt HA, Vogel A, Eckhoff A, Koenig BW, Huster D (2007) Solid-state NMR characterization of the putative membrane anchor of TWD1 from Arabidopsis thaliana. Eur Biophys J 36:393–404

    Article  PubMed  CAS  Google Scholar 

  23. Mousson F, Beswick V, Coic YM, Huynh-Dinh T, Sanson A, Neumann JM (2001) Investigating the conformational coupling between the transmembrane and cytoplasmic domains of a single-spanning membrane protein. A 1H-NMR study. FEBS Lett 505:431–435

    Article  PubMed  CAS  Google Scholar 

  24. Teriete P, Franzin CM, Choi J, Marassi FM (2007) Structure of the Na, K-ATPase regulatory protein FXYD1 in micelles. Biochemistry 46:6774–6783

    Article  PubMed  CAS  Google Scholar 

  25. Dmitriev O, Jones PC, Jiang W, Fillingame RH (1999) Structure of the membrane domain of subunit b of the Escherichia coli F0F1 ATP synthase. J Biol Chem 274:15598–15604

    Article  PubMed  CAS  Google Scholar 

  26. Pellegrini M, Mierke DF (1999) Molecular complex of cholecystokinin-8 and N-terminus of the cholecystokinin A receptor by NMR spectroscopy. Biochemistry 38:14775–14783

    Article  PubMed  CAS  Google Scholar 

  27. Giragossian C, Mierke DF (2003) Determination of ligand–receptor interactions of cholecystokinin by nuclear magnetic resonance. Life Sci 73:705–713

    Article  PubMed  CAS  Google Scholar 

  28. Giragossian C, Schaschke N, Moroder L, Mierke DF (2004) Conformational and molecular modeling studies of beta-cyclodextrin–heptagastrin and the third extracellular loop of the cholecystokinin 2 receptor. Biochemistry 43:2724–2731

    Article  PubMed  CAS  Google Scholar 

  29. Giragossian C, Sugg EE, Szewczyk JR, Mierke DF (2003) Intermolecular interactions between peptidic and nonpeptidic agonists and the third extracellular loop of the cholecystokinin 1 receptor. J Med Chem 46:3476–3482

    Article  PubMed  CAS  Google Scholar 

  30. Giragossian C, Mierke DF (2002) Intermolecular interactions between cholecystokinin-8 and the third extracellular loop of the cholecystokinin-2 receptor. Biochemistry 41:4560–4566

    Article  PubMed  CAS  Google Scholar 

  31. Giragossian C, Mierke DF (2001) Intermolecular interactions between cholecystokinin-8 and the third extracellular loop of the cholecystokinin A receptor. Biochemistry 40:3804–3809

    Article  PubMed  CAS  Google Scholar 

  32. Piserchio A, Bisello A, Rosenblatt M, Chorev M, Mierke DF (2000) Characterization of parathyroid hormone/receptor interactions: structure of the first extracellular loop. Biochemistry 39:8153–8160

    Article  PubMed  CAS  Google Scholar 

  33. Ulfers AL, Piserchio A, Mierke DF (2002) Extracellular domains of the neurokinin-1 receptor: structural characterization and interactions with substance P. Biopolymers 66:339–349

    Article  PubMed  CAS  Google Scholar 

  34. Demene H, Granier S, Muller D et al (2003) Active peptidic mimics of the second intracellular loop of the V(1A) vasopressin receptor are structurally related to the second intracellular rhodopsin loop: a combined 1H NMR and biochemical study. Biochemistry 42:8204–8213

    Article  PubMed  CAS  Google Scholar 

  35. Yeagle PL, Alderfer JL, Albert AD (1997) The first and second cytoplasmic loops of the G-protein receptor, rhodopsin, independently form β-turns. Biochemistry 36:3864–3869

    Article  PubMed  CAS  Google Scholar 

  36. Mierke DF, Royo M, Pelligrini M, Sun H, Chorev M (1996) Third cytoplasmic loop of the PTH/PTHrP receptor. J Am Chem Soc 118:8998–9004

    Article  CAS  Google Scholar 

  37. Pellegrini M, Royo M, Chorev M, Mierke DF (1996) Conformational characterization of a peptide mimetic of the third cytoplasmic loop of the G-protein coupled parathyroid hormone/parathyroid hormone related protein receptor. Biopolymers 40:653–666

    Article  PubMed  CAS  Google Scholar 

  38. Ruan KH, So SP, Wu J, Li D, Huang A, Kung J (2001) Solution structure of the second extracellular loop of human thromboxane A2 receptor. Biochemistry 40:275–280

    Article  PubMed  CAS  Google Scholar 

  39. Wu J, So SP, Ruan KH (2003) Solution structure of the third extracellular loop of human thromboxane A2 receptor. Arch Biochem Biophys 414:287–293

    Article  PubMed  CAS  Google Scholar 

  40. Franzoni L, Nicastro G, Pertinhez TA et al (1999) Structure of two fragments of the third cytoplasmic loop of the rat angiotensin II AT1A receptor. Implications with respect to receptor activation and G-protein selection and coupling. J Biol Chem 274:227–235

    Article  PubMed  CAS  Google Scholar 

  41. Nicastro G, Peri F, Franzoni L, de Chiara C, Sartor G, Spisni A (2003) Conformational features of a synthetic model of the first extracellular loop of the angiotensin II AT1A receptor. J Pept Sci 9:229–243

    Article  PubMed  CAS  Google Scholar 

  42. Jung H, Windhaber R, Palm D, Schnackerz KD (1995) NMR and circular dichroism studies of synthetic peptides derived from the third intracellular loop of the beta-adrenoceptor. FEBS Lett 358:133–136

    Article  PubMed  CAS  Google Scholar 

  43. Katragadda M, Maciejewski MW, Yeagle PL (2004) Structural studies of the putative helix 8 in the human beta(2) adrenergic receptor: an NMR study. Biochim Biophys Acta 1663:74–81

    Article  PubMed  CAS  Google Scholar 

  44. Chung DA, Zuiderweg ER, Fowler CB, Soyer OS, Mosberg HI, Neubig RR (2002) NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: evidence for a novel cytoplasmic helix. Biochemistry 41:3596–3604

    Article  PubMed  CAS  Google Scholar 

  45. Choi G, Guo J, Makriyannis A (2005) The conformation of the cytoplasmic helix 8 of the CB1 cannabinoid receptor using NMR and circular dichroism. Biochim Biophys Acta 1668:1–9

    Article  PubMed  CAS  Google Scholar 

  46. Choi G, Landin J, Xie XQ (2002) The cytoplasmic helix of cannabinoid receptor CB2, a conformational study by circular dichroism and (1)H NMR spectroscopy in aqueous and membrane-like environments. J Pept Res 60:169–177

    Article  PubMed  CAS  Google Scholar 

  47. Jung H, Windhaber R, Palm D, Schnackerz KD (1996) Conformation of a beta-adrenoceptor-derived signal transducing peptide as inferred by circular dichroism and 1H NMR spectroscopy. Biochemistry 35:6399–6405

    Article  PubMed  CAS  Google Scholar 

  48. Yeagle PL, Alderfer JL, Albert AD (1996) Structure determination of the fourth cytoplasmic loop and carboxyl terminal domain of bovine rhodopsin. Mol Vis 2. http://www.molvis.org/molvis/v2/p12/

  49. Wallace BA, Janes RW (1999) Tryptophans in membrane proteins. Adv Exp Med Biology 467:789–799

    Article  CAS  Google Scholar 

  50. Yeagle PL, Danis C, Choi G, Alderfer JL, Albert AD (2000) Three dimensional structure of the seventh transmembrane helical domain of the G-protein receptor, rhodopsin. Mol Vis. http://www.molvis.org/molvis/v6/a17/

  51. Arshava B, Liu SF, Jiang H, Breslav M, Becker JM, Naider F (1998) Structure of segments of a G protein-coupled receptor: CD and NMR analysis of the Saccharomyces cerevisiae tridecapeptide pheromone receptor. Biopolymers 46:343–357

    Article  PubMed  CAS  Google Scholar 

  52. Xie HB, Ding FX, Schreiber D et al (2000) Synthesis and biophysical analysis of transmembrane domains of a Saccharomyces cerevisiae G protein-coupled receptor. Biochemistry 39:15462–15474

    Article  PubMed  CAS  Google Scholar 

  53. Estephan R, Englander J, Arshava B, Samples KL, Becker JM, Naider F (2005) Biosynthesis and NMR analysis of a 73-residue domain of a Saccharomyces cerevisiae G protein-coupled receptor. Biochemistry 44:11795–11810

    Article  PubMed  CAS  Google Scholar 

  54. Naider F, Khare S, Arshava B, Severino B, Russo J, Becker JM (2005) Synthetic peptides as probes for conformational preferences of domains of membrane receptors. Biopolymers 80:199–213

    Article  PubMed  CAS  Google Scholar 

  55. Cohen LS, Arshava B, Estephan R et al (2008) Expression and biophysical analysis of two double-transmembrane domain-containing fragments from a yeast G protein-coupled receptor. Biopolymers 90:117–130

    Article  PubMed  CAS  Google Scholar 

  56. Zheng H, Zhao J, Sheng W, Xie XQ (2006) A transmembrane helix-bundle from G-protein coupled receptor CB2: biosynthesis, purification, and NMR characterization. Biopolymers 83:46–61

    Article  PubMed  CAS  Google Scholar 

  57. Ma D, Liu Z, Li L, Tang P, Xu Y (2005) Structure and dynamics of the second and third transmembrane domains of human glycine receptor. Biochemistry 44:8790–8800

    Article  PubMed  CAS  Google Scholar 

  58. Girvin ME, Rastogi VK, Abildgaard F, Markley JL, Fillingame RH (1998) Solution structure of the transmembrane H+-transporting subunit c of the F1F0 ATP synthase. Biochemistry 37:8817–8824

    Article  PubMed  CAS  Google Scholar 

  59. Bocharov EV, Mineev KS, Volynsky PE et al (2008) Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state. J Biol Chem 283:6950–6956

    Article  PubMed  CAS  Google Scholar 

  60. Bocharov EV, Pustovalova YE, Pavlov KV et al (2007) Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger. J Biol Chem 282:16256–16266

    Article  PubMed  CAS  Google Scholar 

  61. Call ME, Schnell JR, Xu C, Lutz RA, Chou JJ, Wucherpfennig KW (2006) The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 127:355–368

    Article  PubMed  CAS  Google Scholar 

  62. Venkatraman J, Nagana Gowda GA, Balaram P (2002) Structural analysis of synthetic peptide fragments from EmrE, a multidrug resistance protein, in a membrane-mimetic environment. Biochemistry 41:6631–6639

    Article  PubMed  CAS  Google Scholar 

  63. Murail S, Robert JC, Coic YM et al (2008) Secondary and tertiary structures of the transmembrane domains of the translocator protein TSPO determined by NMR. Stabilization of the TSPO tertiary fold upon ligand binding. Biochim Biophys Acta 1778:1375–1381

    Article  PubMed  CAS  Google Scholar 

  64. Jamin N, Neumann J-M, Ostuni MA, Thi Kim Ngoc Vu, Yao ZX, Murail S, Robert J-C, Giatzakis C, Papadopoulos V, Lacapere J-J (2005) Characterization of the cholesterol recognition amino acid consensus sequence of the peripheral-type benzodiazepine receptor. Mol Endocrinol 19(3):588–594

    Article  PubMed  CAS  Google Scholar 

  65. Neumoin A, Arshava B, Becker J, Zerbe O, Naider F (2007) NMR studies in dodecylphosphocholine of a fragment containing the seventh transmembrane helix of a G-protein-coupled receptor from Saccharomyces cerevisiae. Biophys J 93:467–482

    Article  PubMed  CAS  Google Scholar 

  66. Yeagle PL, Alderfer JL, Albert AD (1995) Structure of the third cytoplasmic loop of bovine rhodopsin. Biochemistry 34:14621–14625

    Article  PubMed  CAS  Google Scholar 

  67. Dorey M, Hargrave PA, McDowell JH et al (1999) Effects of phosphorylation on the structure of the G-protein receptor, rhodopsin. Biochim Biophys Acta 1416:217–224

    Article  PubMed  CAS  Google Scholar 

  68. Yeagle PL, Alderfer JL, Albert AD (1997) Three dimensional structure of the cytoplasmic face of the G protein receptor rhodopsin. Biochemistry 36:9649–9654

    Article  PubMed  CAS  Google Scholar 

  69. Albert AD, Yeagle PL (2000) NMR analysis of the three dimensional structure of rhodopsin domains. Methods Enzymol 315:107–115

    Article  PubMed  CAS  Google Scholar 

  70. Chopra A, Yeagle PL, Alderfer JA, Albert A (2000) Solution structure of the sixth transmembrane helix of the G-protein coupled receptor, rhodopsin. Biochim Biophys Acta 1463:1–5

    Article  PubMed  CAS  Google Scholar 

  71. Yeagle PL, Salloum A, Chopra A et al (2000) Structures of the intradiskal loops and amino terminus of the G-protein receptor, rhodopsin. J Pept Res 55:455–465

    Article  PubMed  CAS  Google Scholar 

  72. Bennett M, Yeagle JA, Maciejewski M, Ocampo J, Yeagle PL (2004) Stability of loops in the structure of lactose permease. Biochemistry 43:12829–12837

    Article  PubMed  CAS  Google Scholar 

  73. Sale K, Faulon JL, Gray GA, Schoeniger JS, Young MM (2004) Optimal bundling of transmembrane helices using sparse distance constraints. Protein Sci 13:2613–2627

    Article  PubMed  CAS  Google Scholar 

  74. Sorgen PL, Hu Y, Guan L, Kaback HR, Girvin ME (2002) An approach to membrane protein structure without crystals. Proc Natl Acad Sci U S A 99:14037–14040

    Article  PubMed  CAS  Google Scholar 

  75. Yeagle PL, Choi G, Albert AD (2001) Studies on the structure of the G-protein coupled receptor rhodopsin including the putative G-protein binding site in unactivated and activated forms. Biochemistry 40:11932–11937

    Article  PubMed  CAS  Google Scholar 

  76. Choi G, Landin J, Galan JF, Birge RR, Albert AD, Yeagle PL (2002) Structural studies of metarhodopsin II, the activated form of the G-protein coupled receptor, rhodopsin. Biochemistry 41:7318–7324

    Article  PubMed  CAS  Google Scholar 

  77. Oxenoid K, Kim HJ, Jacob J, Sonnichsen FD, Sanders CR (2004) NMR assignments for a helical 40 kDa membrane protein. J Am Chem Soc 126:5048–5049

    Article  PubMed  CAS  Google Scholar 

  78. Musial-Siwek M, Kendall DA, Yeagle PL (2008) Solution NMR of signal peptidase, a membrane protein. Biochim Biophys Acta 1778:937–944

    Article  PubMed  CAS  Google Scholar 

  79. Humphrey W, Dalke A, Schulten K (1996) VMD – visual molecular dynamics. J Mol Graph 14:33–38

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Philip L. Yeagle .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Yeagle, P.L., Albert, A.D. (2010). Membrane Protein Fragments Reveal Both Secondary and Tertiary Structure of Membrane Proteins. In: Lacapère, JJ. (eds) Membrane Protein Structure Determination. Methods in Molecular Biology, vol 654. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-762-4_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-762-4_15

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-761-7

  • Online ISBN: 978-1-60761-762-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics