Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
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).
M. L. Jennings, Topography of membrane proteins, Annu. Rev. Biochem. 58, 999–1027 (1989).
J. Kyte and R. F. Doolittle, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157, 105–132 (1982).
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).
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).
M. S. Weiss and G. E. Schulz, Structure of porin refined at 1.8 Å resolution, J. Mol. Biol. 227, 493–509 (1992).
S. W. Cowan and J. P. Rosenbusch, Folding pattern diversity of integral membrane proteins, Science 264, 914–916 (1994).
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).
D. M. Engelman, An implication of the structure of bacteriorhodopsin. Globular membrane proteins are stabilized by polar interactions, Biophys. J. 37, 187–188 (1982).
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).
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).
J. Deisenhofer and H. Michel, The photosynthetic reaction center from the purple bacterium Rhodop-seudomonas viridis. Science 245, 1463–1473 (1989).
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).
G. Blobel, Intracellular protein topogenesis, Proc. Natl. Acad. Sci. USA 77, 1496–1500 (1980).
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).
J. Brunner and F. M. Richards, Analysis of membranes photolabeled with lipid analogues, J. Biol. Chem. 255, 3319–3329 (1980).
M. L. Jennings, M. P. Anderson, and R. Monaghan, Monoclonal antibodies against human erythrocyte band 3 protein, J. Biol. Chem. 261, 9002–9010 (1986).
C. Manoil and J. Beckwith, TnphoA: A transposon probe for protein export signals, Proc. Natl. Acad. Sci. USA 82, 8129–8133 (1985).
C. Manoil and J. Beckwith, A genetic approach to analyzing membrane protein topology, Science 233, 1403–1408 (1986).
J. A. Berzofsky, Intrinsic and extrinsic factors in protein antigenic structure, Science. 229, 932–940 (1985).
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).
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).
H. G. Khorana, Two light-transducing membrane proteins: Bacteriorhodopsin and the mammalian rhodopsin, Proc. Natl. Acad. Sci. USA 90, 1166–1171 (1993).
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).
C. Sander and R. Schneider, The HSSP database of protein structure-sequence alignments, Nucleic Acids Res. 22, 3597–3599 (1994).
P. Bork, C. Ouzonis, C. Sander, R. Scharaf, R. Schneider, and E. Sonnhammer. What’s in a genome? Nature 358, 287 (1992).
F. Jähning and O. Edolm, Can the structure of proteins be calculated? Z. Phys. B 78, 137–143 (1990).
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).
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).
B. Rost and C. Sander, Prediction of protein secondary structure at better than 70% accuracy, J. Mol. Biol. 232, 584–599 (1993).
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).
B. Rost and C. Sander. Secondary structure prediction of all-helical proteins in two states. Protein Eng. 6, 831–836 (1993).
B. Rost and C. Sander, Combining evolutionary information and neural networks to predict protein secondary structure. Proteins Struct. Funct. Genet. 20, 216–226 (1994).
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).
P. Argos, J. K. M. Rao, and P. A. Hargrave, Structural prediction of membrane-bound proteins. Eur. J. Biochem. 128, 565–575 (1982).
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).
G. von Heijne, Membrane proteins—The amino acid composition of membrane-penetrating segments, Eur. J. Biochem. 120, 275–278 (1981).
G. von Heijne, Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule, J. Mol. Biol. 225, 487–494 (1992).
B. Persson and P. Argos, Prediction of transmembrane segments in proteins utilising multiple sequence alignments, J. Mol. Biol. 237, 182–192 (1994).
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).
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).
B. Rost, R. Casadio, P. Fariselli, and C. Sander, Transmembrane helices predicted at 95% accuracy, Protein Sci. 4, 521–533 (1995).
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).
D. Eisenberg, Three-dimensional structure of membrane surface proteins, Annu. Rev. Biochem. 53, 595–623 (1984).
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).
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).
D. Juretić, Conformational preference functions and secondary structure prediction for membrane proteins, Acta Pharm. 43, 223–226 (1993).
D. Juretić, N. Trínajsić, and B. Lučić, Protein secondary structure conformations and associated hydrophobicity scales, J. Math. Chem. 14, 35–34 (1993).
D. Juretić and R. Pešić, A scale of β-preferences for structure-activity predictions in membrane proteins, Croat. Chem. Acta 68, 215–232 (1995).
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).
D. Juretić Secondary structure of membrane proteins: Prediction with conformational preference functions of soluble proteins, Croat. Chem. Acta 65, 921–932 (1992).
A. Bairoch and B. Boeckmann, SWISS-PROT protein sequence data bank: Current status. Nucleic Acids Res. 22, 3578–3580 (1994).
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).
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).
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).
D. Juretić and R. W. Williams, Protein secondary structure preferences, J. Math. Chem. 8, 229–242 (1991).
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).
L. Zhong and W. C. Johnston, Jr., Environment affects amino acid preference for secondary structure, Proc. Natl. Acad. Sci. USA 89, 4462–4465 (1992).
S. M. Muskai and S. H. Kim, Predicting protein secondary structure content. A tandem neural network approach, J. Mol. Biol. 225, 713–727 (1992).
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).
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).
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).
J. Edelman, Quadratic minimization of predictors for protein secondary structure: Application to membrane alpha-helices, J. Mol. Biol. 232, 165–191 (1993).
W. Kühlbrandt, D. N. Wang, and Y. Fujiyoshi, Atomic model of plant light-harvesting complex by electron crystallography, Nature 367, 614–621 (1994).
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).
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).
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).
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).
G. Gafvelin and G. von Heijne, Topological ‘frustration’ in multispanning E. coli inner membrane proteins, Cell 77, 401–412 (1994).
S. S. Sturrock and J. F. Collins, MPsrch version 1.3, Biocomputing Research Unit, University of Edinburgh (1993).
T. F. Smith and M. S. Waterman, Identification ofcommon molecular subsequences, J. Mol. Biol. 147, 195–197 (1981).
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).
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).
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).
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).
M. Melzer and L. Heide, Characterization of polyprenyldiphosphate: 4-hydroxybenzoate polyprenyl-transferase from Escherichia coli, Biochim. Biophys. Acta 1212, 93–102 (1994).
D. Juretić and B. Lučić, Predicting thesecondary structure of membranechannelproteins: The performance of preference functions compared to other statistical methods, HB93 Proceedings, Zagreb (1993).
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).
F. E. Croxton and D. J. Cowden, Applied General Statistics, Prentice-Hall. Englewood Cliffs, New Jersey (1948).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights 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