Alpha-periodicity analysis of small multidrug resistance (SMR) efflux transporters

Biochemistry and Cell Biology

Volumn 76, Issue 5, 1998, Pages 791-797

  Edwards, Robert A ^a   Turner, Raymond J ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

Amphipathicity; Hydrophopathy; Modeling; Multidrug resistance; Periodicity; QAC; SMR; Transporter

Indexed keywords

CARRIER PROTEIN; MULTIDRUG RESISTANCE PROTEIN; QUATERNARY AMMONIUM DERIVATIVE;

AMINO ACID SUBSTITUTION; CONFERENCE PAPER; DRUG TRANSPORT; ENZYME CONFORMATION; ENZYME POLYMORPHISM; HYDROPHILICITY; MULTIDRUG RESISTANCE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTON TRANSPORT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 0032460712     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o98-101     Document Type: Conference Paper

References (34)

1. Baldwin, J.M., Schertler, G.F.X., and Unger, V.M. 1997. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J. Mol. Biol. 272: 144-164.
2. Bishop, R.E. 1997. Chacterization of the enterobacterial frd-efp gene interval: implication for the origin of antibiotic resistance and virulence. Ph.D. thesis, University of Alberta, Edmonton, Alta., Canada.
3. Castello, P.R., Gonzalez Flecha, F.L., Caride, A.J., Fernandez, H.N., Delfino, J.M., and Fossi, J.P. 1997. The membrane topology of the amino-terminal domain of the red cell calcium pump. Protein Sci. 6: 1708-1717.
4. Cole, S.T. 1987. Nucleotide sequence and comparative analysis of the frd operon encoding the fumarate reductase of Proteus vulgaris: extensive sequence divergence of the membrane anchors and absence of a frd-linked ampC cephalosporinase gene. Eur. J. Biochem 167: 481-488.
5. Cornette, J.L. Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A., and DeLisi, C. 1987. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol. 112: 535-542.
6. degli Esposti, M., Crimi, M., and Venturoli, G. 1990. A critical evaluation of the hydropathy profile of membrane proteins. Eur. J. Biochem. 190: 207-219.
7. Donnelly, D., and Cogdell, R.J. 1993. Predicting the point at which transmembrane helices protrude from the bilayer: a model of the antenna complexes from photosynthetic bacteria. Protein Eng. 6: 629-635.
8. Donnelly, D., Overington, J.P., Ruffle, S.V., Nugent, J.H.A., and Blundell, T.L. 1993. Modeling α-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. Protein Sci. 2: 55-70.
9. Eisenberg, D. 1984. Three-dimensional structure of membrane and surface proteins. Annu. Rev. Biochem. 53: 595-623.
10. Eisenberg, D., Weiss, R.M., and Terwilliger, T.C. 1984. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. U.S.A. 81: 140-144.
11. Fasman, G.D., and Gilbert, W.A. 1990. The prediction of transmembrane protein sequences and their conformation: an evaluation. Trends Biochem. Sci. 15: 89-92.
12. Greener, T., Govezensky, D., and Zamir, A. 1993. A novel multi-copy suppressor of groEL mutation includes two nested open reading frames transcribed from different promoters. EMBO J. 12: 889-896.
13. Grinius, L.L., and Goldberg, E.B. 1994. Bacterial multidrug resistance is due to a single membrane protein which functions as a drug pump. J. Biol. Chem. 269: 29998-30004.
14. Hägerhäll, C., and Hederstedt, L. 1996. A structural model for the membrane-integral domain of succinate:quinone oxidoreductases. FEBS Lett. 389: 25-31.
15. Higgins, D.G., Thompson, J.D., and Gibson, T.J. 1996. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266: 383-402.
16. Komiya, H., Yeates, T.O., Rees, D.C., Allen, J.P., and Feher, G. 1988. Structure of the reaction center from Rhodobacter sphaeroides R-26: symmetry relations and sequence comparisons between different species. Proc. Natl. Acad. Sci. U.S.A. 85: 9012-9016.
17. Lebendiker, M., and Schuldiner, S. 1996. Identification of residues in the translocation pathway of EmrE, a multidrug antiporter from Escherichia coli. J. Biol. Chem. 271: 21193-21199.
18. Lewis, K. 1994. Multidrug resistance pumps in bacteria: variations in a theme. Trends Biochem. Sci. 19: 119-123.
19. Littlejohn, T.G., DiBerardino, D., Messerotti, L.J., Spiers, S.J., and Skurray, R.A. 1991. Structure and evolution of a family of genes encoding antiseptic and disinfectant resistance in Staphylococcus aureus. Gene, 101: 59-66.
20. Paulsen, I.T., Littlejohn, T.G., Rådström, P., Sundström, L., Sköld, O., Swedberg, G., and Skurray, R.A. 1993. The 3′ conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants. Antimicrob. Agents Chemother. 37: 761-768.
21. Paulsen, I.T., Brown, M.H., Dunstan, S.J., and Skurray, R.A. 1995. Molecular characterization of the staphylococcal multidrug resistance export protein QacC. J. Bacteriol. 177: 2827-2833.
22. Paulsen, I.T., Skurray, R.A., Tam, R., Saier, M.H., Turner, R.J., Weiner, J.H., Goldberg, E.B., and Grinius, L.L. 1996. The SMR family: a novel family of multidrug efflux proteins involved with the efflux of lipophilic drugs. Mol. Microbiol. 19: 1167-1175.
23. Purewal, A.S. 1991. Nucleotide sequence of the ethidium efflux gene from Escherichia coli. FEMS Microbiol. Lett. 82: 229-232.
24. Rees, D.C., DeAntonio, L., and Eisenberg, D. 1989. Hydrophobic organization of membrane proteins. Science (Washington, D.C.), 245: 510-513.
25. Schiffer, M., and Edmundson, A.B. 1967. Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys. J. 7: 121-135.
26. Schuldiner, S., Lebendiker, M., and Yerushalmi, H. 1997. EmrE, the smallest ion-coupled transporter, provides a unique paradigm for structure-function studies. J. Exp. Biol. 200: 335-341.
27. Schwaiger, M., Lebendiker, M., Yerushalmi, H., Coles, M., Gröger, A., Schwarz, C., Schuldiner, S., and Kessler, H. 1998. NMR investigation of the multidrug transporter EmrE, an integral membrane protein. Eur. J. Biochem. 254: 610-619.
28. Sipos, L., and von Heijne, G. 1993. Predicting the topology of eukaryotic membrane proteins. Eur. J. Biochem. 213: 1333-1340.
29. Taylor, W.R., Jones, D.T., and Green, N.M. 1994. A method for alpha-helical integral membrane protein fold prediction. Proteins Struct. Funct. Genet. 18: 281-294.
30. Turner, R.J., and Weiner, J.H. 1993. Evaluation of transmembrane helix prediction methods using the recently defined NMR structures of the coat proteins from bacteriophages M13 and Pf1. Biochim. Biophys. Acta, 1202: 161-168.
31. 0ATP synthase using variational and hydrophobic moment analyses. Biochim. Biophys. Acta, 1140: 199-207.
32. von Heijne, G. 1992. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225: 487-494.
33. + and is soluble in organic solvents. J. Biol. Chem. 270: 6856-6863.
34. Yerushalmi, H., Lebendiker, M., and Schuldiner, S. 1996. Negative dominance studies demonstrate the oligomeric structure of EmrE, a multidrug antiporter from Escherichia coli2E J. Biol. Chem. 271: 31044-31048.