Skip to main content

Recognition of Membrane Protein Structure from Amino Acid Sequence

  • Chapter
From Chemical Topology to Three-Dimensional Geometry

Part of the book series: Topics in Applied Chemistry ((TAPP))

  • 320 Accesses

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as 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 169.99
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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. G. D. Fasman, The role of electrostatic interactions in the structure of globular proteins, in: Prediction of Protein Structure and the Principles of Protein Conformations (G. D. Fasman, ed.), pp. 359–389, Plenum Press, New York (1989).

    Google Scholar 

  2. M. L. Jennings, Topography of membrane proteins, Annu. Rev. Biochem. 58, 999–1027 (1989).

    Article  CAS  Google Scholar 

  3. J. Kyte and R. F. Doolittle, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157, 105–132 (1982).

    Article  CAS  Google Scholar 

  4. D. M. Engelman, T. A. Steitz, and A. Goldman, Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins, Annu. Rev. Biophys. Biophys. Chem. 15, 321–353 (1986).

    Article  CAS  Google Scholar 

  5. J. L. Cornette, K. B. Cease, H. Margalit, J. L. Spouge, J. A. Berzofsky, and C. DeLisi, Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins, J. Mol. Biol. 195, 659–685 (1987).

    Article  CAS  Google Scholar 

  6. M. S. Weiss and G. E. Schulz, Structure of porin refined at 1.8 Å resolution, J. Mol. Biol. 227, 493–509 (1992).

    Article  CAS  Google Scholar 

  7. S. W. Cowan and J. P. Rosenbusch, Folding pattern diversity of integral membrane proteins, Science 264, 914–916 (1994).

    CAS  Google Scholar 

  8. T. M. Gray and B. W. Matthews, Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins, J. Mol. Biol. 175, 75–81 (1984).

    CAS  Google Scholar 

  9. D. M. Engelman, An implication of the structure of bacteriorhodopsin. Globular membrane proteins are stabilized by polar interactions, Biophys. J. 37, 187–188 (1982).

    CAS  Google Scholar 

  10. J. Deisenhofer, O. Epp, K. Miki, R. Huber, and H. Michel, Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3A resolution, Nature 318, 618–624 (1985).

    Article  Google Scholar 

  11. J. P. Allen, G. Feher, T. O. Yeates, H. Komiya, and D. C. Rees, Structure of the reaction center from Rhodobacter sphaeroides R-26: The protein subunits, Proc. Natl. Acad. Sci. USA 8, 6162–6166 (1987).

    Google Scholar 

  12. J. Deisenhofer and H. Michel, The photosynthetic reaction center from the purple bacterium Rhodop-seudomonas viridis. Science 245, 1463–1473 (1989).

    CAS  Google Scholar 

  13. R. Henderson, J. M. Baldwin, T. A. Ceska, F. Zemlin, E. Beckmann, and K. H. Downing, Model for the structure of bacteriorhodopsin based on high-resolution cryo-microscopy, J. Mol. Biol. 213, 899–929 (1990).

    CAS  Google Scholar 

  14. G. Blobel, Intracellular protein topogenesis, Proc. Natl. Acad. Sci. USA 77, 1496–1500 (1980).

    CAS  Google Scholar 

  15. W. L. Hubbell and C. Altenbach, Investigation of structure and dynamics in membrane proteins using site-directed spin labeling, Curr. Opin. Struct. Biol. 4, 566–573 (1994).

    Article  CAS  Google Scholar 

  16. J. Brunner and F. M. Richards, Analysis of membranes photolabeled with lipid analogues, J. Biol. Chem. 255, 3319–3329 (1980).

    CAS  Google Scholar 

  17. M. L. Jennings, M. P. Anderson, and R. Monaghan, Monoclonal antibodies against human erythrocyte band 3 protein, J. Biol. Chem. 261, 9002–9010 (1986).

    CAS  Google Scholar 

  18. C. Manoil and J. Beckwith, TnphoA: A transposon probe for protein export signals, Proc. Natl. Acad. Sci. USA 82, 8129–8133 (1985).

    CAS  Google Scholar 

  19. C. Manoil and J. Beckwith, A genetic approach to analyzing membrane protein topology, Science 233, 1403–1408 (1986).

    CAS  Google Scholar 

  20. J. A. Berzofsky, Intrinsic and extrinsic factors in protein antigenic structure, Science. 229, 932–940 (1985).

    CAS  Google Scholar 

  21. E. Bibi and H. R. Kaback, In vivo expression of the LacY gene in two segments leads to functional lac permease, Proc. Natl. Acad. Sci. USA 87, 4325–4329 (1990).

    CAS  Google Scholar 

  22. J. Soppa, J. Duschl, and D. Oesterhelt, Bacterioopsin, haloopsin, and sensory opsin I of the halobacterial isolate Halobactertum sp. strain SG1: Three new members of a growing family, J. Bacterial. 175, 2720–2726 (1993).

    CAS  Google Scholar 

  23. H. G. Khorana, Two light-transducing membrane proteins: Bacteriorhodopsin and the mammalian rhodopsin, Proc. Natl. Acad. Sci. USA 90, 1166–1171 (1993).

    CAS  Google Scholar 

  24. C. Sander and R. Schneider, Database of homology-derived structures and the structural meaning of sequence alignment, Proteins Struct. Fund. Genet. 9, 56–68 (1991).

    Article  CAS  Google Scholar 

  25. C. Sander and R. Schneider, The HSSP database of protein structure-sequence alignments, Nucleic Acids Res. 22, 3597–3599 (1994).

    CAS  Google Scholar 

  26. P. Bork, C. Ouzonis, C. Sander, R. Scharaf, R. Schneider, and E. Sonnhammer. What’s in a genome? Nature 358, 287 (1992).

    Article  CAS  Google Scholar 

  27. F. Jähning and O. Edolm, Can the structure of proteins be calculated? Z. Phys. B 78, 137–143 (1990).

    Google Scholar 

  28. L. Pauling and R. B. Corey, Configuration of polypeptide chains with favored orientations around single bonds: Two new pleated sheets, Proc. Natl. Acad. Sci. USA 37, 729–740 (1951).

    CAS  Google Scholar 

  29. L. Pauling, R. B. Corey, and H. R. Branson, The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain, Proc. Natl. Acad. Sci. USA 37, 205 (1951).

    CAS  Google Scholar 

  30. B. Rost and C. Sander, Prediction of protein secondary structure at better than 70% accuracy, J. Mol. Biol. 232, 584–599 (1993).

    Article  CAS  Google Scholar 

  31. B. Rost and C. Sander, Improved prediction of protein secondary structure by use of sequence profiles and neural networks, Proc. Natl. Acad. Sci. USA 90, 7558–7562 (1993).

    CAS  Google Scholar 

  32. B. Rost and C. Sander. Secondary structure prediction of all-helical proteins in two states. Protein Eng. 6, 831–836 (1993).

    Article  CAS  Google Scholar 

  33. B. Rost and C. Sander, Combining evolutionary information and neural networks to predict protein secondary structure. Proteins Struct. Funct. Genet. 20, 216–226 (1994).

    CAS  Google Scholar 

  34. W. R. Taylor, D. T. Jones, and N. M. Green. A method for α-helical integral membrane protein fold prediction, Proteins Struct. Funct. Genet. 18, 281–294 (1994).

    CAS  Google Scholar 

  35. P. Argos, J. K. M. Rao, and P. A. Hargrave, Structural prediction of membrane-bound proteins. Eur. J. Biochem. 128, 565–575 (1982).

    CAS  Google Scholar 

  36. M. Degli Esposti, M. Crimi, and G. Venturoli, A critical evaluation of the hydropathy profile of membrane proteins, Eur. J. Biochem. 190, 207–219 (1990).

    Article  CAS  Google Scholar 

  37. G. von Heijne, Membrane proteins—The amino acid composition of membrane-penetrating segments, Eur. J. Biochem. 120, 275–278 (1981).

    Article  Google Scholar 

  38. G. von Heijne, Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule, J. Mol. Biol. 225, 487–494 (1992).

    Google Scholar 

  39. B. Persson and P. Argos, Prediction of transmembrane segments in proteins utilising multiple sequence alignments, J. Mol. Biol. 237, 182–192 (1994).

    Article  CAS  Google Scholar 

  40. D. T. Jones, W. R. Taylor, and J. M. Thornton, A model approach to the prediction of all-helical membrane protein structure and topology, Biochemistry 33, 3038–3049 (1994).

    CAS  Google Scholar 

  41. R. Lohmann, G. Schneider, D. Behrens. and P. Wrede, A neural network model for the prediction of membrane-spanning amino acid sequences, Protein Science 3, 1597–1601 (1994).

    Article  CAS  Google Scholar 

  42. B. Rost, R. Casadio, P. Fariselli, and C. Sander, Transmembrane helices predicted at 95% accuracy, Protein Sci. 4, 521–533 (1995).

    CAS  Google Scholar 

  43. D. Eisenberg, E. Schwartz, M. Komaromy. and R. Wall, Analysis of membrane and surface protein sequences with the hydrophobic moment plot, J. Mol. Biol. 179, 125–142 (1984).

    Article  CAS  Google Scholar 

  44. D. Eisenberg, Three-dimensional structure of membrane surface proteins, Annu. Rev. Biochem. 53, 595–623 (1984).

    Article  CAS  Google Scholar 

  45. D. Juretić, B. K. Lee, N. Trínajsić, and R. W. Williams, Conformational preference functions for predicting helices in membrane proteins, Biopolymers 33, 255–273 (1993).

    Google Scholar 

  46. P. Y. Chou and G. D. Fasman, Conformational parameters for amino acids in helical, β-sheets and random coil regions calculated from proteins. Biochemistry 13, 211–222 (1974).

    CAS  Google Scholar 

  47. D. Juretić, Conformational preference functions and secondary structure prediction for membrane proteins, Acta Pharm. 43, 223–226 (1993).

    Google Scholar 

  48. D. Juretić, N. Trínajsić, and B. Lučić, Protein secondary structure conformations and associated hydrophobicity scales, J. Math. Chem. 14, 35–34 (1993).

    Google Scholar 

  49. D. Juretić and R. Pešić, A scale of β-preferences for structure-activity predictions in membrane proteins, Croat. Chem. Acta 68, 215–232 (1995).

    Google Scholar 

  50. D. Juretić, B. Lučić, and N. Trinajstić, Predicting membrane protein secondary structure: Preference functions method for finding optimal Conformational parameters, Croat. Chem. Acta 66, 201–208 (1993).

    Google Scholar 

  51. D. Juretić Secondary structure of membrane proteins: Prediction with conformational preference functions of soluble proteins, Croat. Chem. Acta 65, 921–932 (1992).

    Google Scholar 

  52. A. Bairoch and B. Boeckmann, SWISS-PROT protein sequence data bank: Current status. Nucleic Acids Res. 22, 3578–3580 (1994).

    CAS  Google Scholar 

  53. D. Juretić, and B. Lučić, and N. Trinajstić, Secondary structure prediction quality for naturally occurring amino acids in soluble proteins, J. Mol. Struct. (Teochem) 338, 43–50 (1995).

    Google Scholar 

  54. P. K. Ponnuswamy and M. M. Gromiha, Prediction of transmembrane helices from hydrophobic characteristics of proteins, Int. J. Peptide Protein Res. 42, 326–341 (1993).

    CAS  Google Scholar 

  55. D. G. Kneller, F. E. Cohen. and R. Langridge, Improvements in protein secondary structure prediction by an enhanced neural network, J. Mol Biol. 214, 171–182 (1990).

    Article  CAS  Google Scholar 

  56. D. Juretić and R. W. Williams, Protein secondary structure preferences, J. Math. Chem. 8, 229–242 (1991).

    Google Scholar 

  57. G. E. Arnold, A. K. Dunker, S. J. Johns, and R. J. Douthart, Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure, Proteins 12, 382–399 (1992).

    Article  CAS  Google Scholar 

  58. L. Zhong and W. C. Johnston, Jr., Environment affects amino acid preference for secondary structure, Proc. Natl. Acad. Sci. USA 89, 4462–4465 (1992).

    CAS  Google Scholar 

  59. S. M. Muskai and S. H. Kim, Predicting protein secondary structure content. A tandem neural network approach, J. Mol. Biol. 225, 713–727 (1992).

    Google Scholar 

  60. J.-F. Gibrat, J. Garnier, and B. Robson, Further developments of protein secondary structure predictions using information theory. New parameters and consideration of residue pairs, J. Mol. Biol. 198, 425–443 (1987).

    Article  CAS  Google Scholar 

  61. J.-F. Gibrat, B. Robson, and J. Garnier, Influence of the local amino acid sequence upon the zones of the torsional angles Φ and Ψ adopted by residues in proteins, Biochemistry 30, 1578–1586 (1991).

    Article  CAS  Google Scholar 

  62. G. von Heijne, The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology, EMBO J. 5, 3021–3027 (1986).

    Google Scholar 

  63. J. Edelman, Quadratic minimization of predictors for protein secondary structure: Application to membrane alpha-helices, J. Mol. Biol. 232, 165–191 (1993).

    Article  CAS  Google Scholar 

  64. W. Kühlbrandt, D. N. Wang, and Y. Fujiyoshi, Atomic model of plant light-harvesting complex by electron crystallography, Nature 367, 614–621 (1994).

    Google Scholar 

  65. G. McDermott, S. M. Prince, A. A. Freer, A. M. Hawthornthwaite-Lawless, M. Z. Papiz, R. J. Cogdell, and N. W. Isaacs, Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria, Nature 374, 517–521 (1995).

    Article  CAS  Google Scholar 

  66. S. C. King, C. L. Hansen, and T. H. Wilson, The interaction between aspartic acid 237 and lysine 358 in the lactose carrier of Escherichia coli, Biochim. Biophys. Acta 1062, 177–186 (1991).

    CAS  Google Scholar 

  67. J Calamia and C. Manoil, Lac permease of Escherichia coli: Topology and sequence elements promoting membrane insertion, Proc. Natl. Acad. Sci. USA 87, 4937–4941 (1990).

    CAS  Google Scholar 

  68. V. Chepuri and R. B. Gennis, The use of gene fusions to determine the topology of all of the subunits of cytochrome o terminal oxidase complex of Escherichia coli, J. Biol. Chem. 265, 12978–12986 (1990).

    CAS  Google Scholar 

  69. G. Gafvelin and G. von Heijne, Topological ‘frustration’ in multispanning E. coli inner membrane proteins, Cell 77, 401–412 (1994).

    Article  CAS  Google Scholar 

  70. S. S. Sturrock and J. F. Collins, MPsrch version 1.3, Biocomputing Research Unit, University of Edinburgh (1993).

    Google Scholar 

  71. T. F. Smith and M. S. Waterman, Identification ofcommon molecular subsequences, J. Mol. Biol. 147, 195–197 (1981).

    Article  CAS  Google Scholar 

  72. M. M. Müller, A. Vianney, J.-C. Lazzarony, R. E. Webster, and R. Portalier, Membrane topology of the Escherichia coli TolR protein required for cell envelope integrity, J. Bacteriol. 175, 6059–6061 (1993).

    Google Scholar 

  73. K. Eick-Helmerich and V. Braun, Import of biopolymers into Escherichia coli: Nucleotide sequences of the exbB and exbD genes are homologous to those of the tolQ and tolR genes, respectively, J. Bacteriol. 171, 5117–5126 (1989).

    CAS  Google Scholar 

  74. H. J. Sofia, V. Burland, D. L. Daniels, G. Plunkett, III, and F. R. Blattner, Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes, Nucleic Acids Res. 22, 2576–2586 (1994).

    CAS  Google Scholar 

  75. F. R. Blattner, V. Burland, G. Plunkett III, H. J. Sofia, and D. L. Daniels, Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 92.8 minutes, Nucleic Acids Res. 21, 5408–5417 (1993).

    CAS  Google Scholar 

  76. M. Melzer and L. Heide, Characterization of polyprenyldiphosphate: 4-hydroxybenzoate polyprenyl-transferase from Escherichia coli, Biochim. Biophys. Acta 1212, 93–102 (1994).

    CAS  Google Scholar 

  77. D. Juretić and B. Lučić, Predicting thesecondary structure of membranechannelproteins: The performance of preference functions compared to other statistical methods, HB93 Proceedings, Zagreb (1993).

    Google Scholar 

  78. D. Picot, P. J. Loll, and M. Garavito, The X-ray structure of the membrane protein prostaglandin H2 synthase-1, Nature 367, 243–249 (1994).

    Article  CAS  Google Scholar 

  79. F. E. Croxton and D. J. Cowden, Applied General Statistics, Prentice-Hall. Englewood Cliffs, New Jersey (1948).

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Kluwer Academic Publishers

About this chapter

Cite this chapter

Lučić, B., Trinajstić, N., Juretić, D. (2002). Recognition of Membrane Protein Structure from Amino Acid Sequence. In: Balaban, A.T. (eds) From Chemical Topology to Three-Dimensional Geometry. Topics in Applied Chemistry. Springer, Boston, MA. https://doi.org/10.1007/0-306-46907-3_5

Download citation

  • DOI: https://doi.org/10.1007/0-306-46907-3_5

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-306-45462-2

  • Online ISBN: 978-0-306-46907-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics