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Volumn 339, Issue 2, 2004, Pages 471-479

Snorkeling preferences foster an amino acid composition bias in transmembrane helices

Author keywords

membrane; polarity; POPC, palmitoyloleoylphosphatidylcholine; protein; rotamer; side chain; SnD, snorkeling distance; SnP, snorkeling propensity; TM, transmembrane

Indexed keywords

ALANINE; AMINO ACID; ARGININE; ASPARAGINE; GLUTAMINE; GLYCINE; LYSINE; MEMBRANE PROTEIN; METHIONINE; PHENYLALANINE; THREONINE; TRYPTOPHAN; TYROSINE; VALINE;

EID: 2342544065     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.03.072     Document Type: Article
Times cited : (67)

References (55)
  • 1
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin E., von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7:1998;1029-1038
    • (1998) Protein Sci. , vol.7 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 2
    • 0031740601 scopus 로고    scopus 로고
    • Hydrophobic interactions of peptides with membrane interfaces
    • White S.H., Wimley W.C. Hydrophobic interactions of peptides with membrane interfaces. Biochim. Biophys. Acta. 1376:1998;339-352
    • (1998) Biochim. Biophys. Acta , vol.1376 , pp. 339-352
    • White, S.H.1    Wimley, W.C.2
  • 3
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: Physical principles
    • White S.H., Wimley W.C. Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. Struct. 28:1999;319-365
    • (1999) Annu. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 4
    • 0034734237 scopus 로고    scopus 로고
    • Unravelling the folding of bacteriorhodopsin
    • Booth P.J. Unravelling the folding of bacteriorhodopsin. Biochim. Biophys. Acta. 1460:2000;4-14
    • (2000) Biochim. Biophys. Acta , vol.1460 , pp. 4-14
    • Booth, P.J.1
  • 5
    • 0034734243 scopus 로고    scopus 로고
    • Structural determinants of purple membrane assembly
    • Krebs M.P., Isenbarger T.A. Structural determinants of purple membrane assembly. Biochim. Biophys. Acta. 1460:2000;15-26
    • (2000) Biochim. Biophys. Acta , vol.1460 , pp. 15-26
    • Krebs, M.P.1    Isenbarger, T.A.2
  • 6
    • 0033790343 scopus 로고    scopus 로고
    • Helical membrane protein folding, stability, and evolution
    • Popot J.L., Engelman D.M. Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem. 69:2000;881-922
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 881-922
    • Popot, J.L.1    Engelman, D.M.2
  • 8
    • 0037379072 scopus 로고    scopus 로고
    • How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles
    • DeGrado W.F., Gratkowski H., Lear J.D. How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci. 12:2003;647-665
    • (2003) Protein Sci. , vol.12 , pp. 647-665
    • Degrado, W.F.1    Gratkowski, H.2    Lear, J.D.3
  • 9
    • 2242431668 scopus 로고    scopus 로고
    • Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel
    • Bass R.B., Strop P., Barclay M., Rees D.C. Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel. Science. 298:2002;1582-1587
    • (2002) Science , vol.298 , pp. 1582-1587
    • Bass, R.B.1    Strop, P.2    Barclay, M.3    Rees, D.C.4
  • 11
    • 0037052565 scopus 로고    scopus 로고
    • The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism
    • Locher K.P., Lee A.T., Rees D.C. The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science. 296:2002;1091-1098
    • (2002) Science , vol.296 , pp. 1091-1098
    • Locher, K.P.1    Lee, A.T.2    Rees, D.C.3
  • 12
    • 0037057652 scopus 로고    scopus 로고
    • Crystal structure of bacterial multidrug efflux transporter AcrB
    • Murakami S., Nakashima R., Yamashita E., Yamaguchi A. Crystal structure of bacterial multidrug efflux transporter AcrB. Nature. 419:2002;587-593
    • (2002) Nature , vol.419 , pp. 587-593
    • Murakami, S.1    Nakashima, R.2    Yamashita, E.3    Yamaguchi, A.4
  • 13
    • 0037043709 scopus 로고    scopus 로고
    • Structural changes in the calcium pump accompanying the dissociation of calcium
    • Toyoshima C., Nomura H. Structural changes in the calcium pump accompanying the dissociation of calcium. Nature. 418:2002;605-611
    • (2002) Nature , vol.418 , pp. 605-611
    • Toyoshima, C.1    Nomura, H.2
  • 15
    • 0038670226 scopus 로고    scopus 로고
    • Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump
    • Yu E.W., McDermott G., Zgurskaya H.I., Nikaido H., Koshland D.E. Jr. Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump. Science. 300:2003;976-980
    • (2003) Science , vol.300 , pp. 976-980
    • Yu, E.W.1    McDermott, G.2    Zgurskaya, H.I.3    Nikaido, H.4    Koshland Jr., D.E.5
  • 16
    • 0033551432 scopus 로고    scopus 로고
    • Role of helix-helix interactions in assembly of the bacteriorhodopsin lattice
    • Isenbarger T.A., Krebs M.P. Role of helix-helix interactions in assembly of the bacteriorhodopsin lattice. Biochemistry. 38:1999;9023-9030
    • (1999) Biochemistry , vol.38 , pp. 9023-9030
    • Isenbarger, T.A.1    Krebs, M.P.2
  • 17
  • 19
    • 0035423934 scopus 로고    scopus 로고
    • Stabilizing membrane proteins
    • Bowie J.U. Stabilizing membrane proteins. Curr. Opin. Struct. Biol. 11:2001;397-402
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 397-402
    • Bowie, J.U.1
  • 20
    • 0035807810 scopus 로고    scopus 로고
    • Specificity in transmembrane helix-helix interactions can define a hierarchy of stability for sequence variants
    • Fleming K.G., Engelman D.M. Specificity in transmembrane helix-helix interactions can define a hierarchy of stability for sequence variants. Proc. Natl Acad. Sci. USA. 98:2001;14340-14344
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 14340-14344
    • Fleming, K.G.1    Engelman, D.M.2
  • 21
    • 0035797893 scopus 로고    scopus 로고
    • Thermodynamic stability of the bacteriorhodopsin lattice as measured by lipid dilution
    • Isenbarger T.A., Krebs M.P. Thermodynamic stability of the bacteriorhodopsin lattice as measured by lipid dilution. Biochemistry. 40:2001;11923-11931
    • (2001) Biochemistry , vol.40 , pp. 11923-11931
    • Isenbarger, T.A.1    Krebs, M.P.2
  • 23
    • 0036708468 scopus 로고    scopus 로고
    • Cooperativity and specificity of association of a designed transmembrane peptide
    • Gratkowski H., Dai Q.H., Wand A.J., DeGrado W.F., Lear J.D. Cooperativity and specificity of association of a designed transmembrane peptide. Biophys. J. 83:2002;1613-1619
    • (2002) Biophys. J. , vol.83 , pp. 1613-1619
    • Gratkowski, H.1    Dai, Q.H.2    Wand, A.J.3    Degrado, W.F.4    Lear, J.D.5
  • 24
    • 0037172965 scopus 로고    scopus 로고
    • Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein
    • Howard K.P., Lear J.D., DeGrado W.F. Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein. Proc. Natl Acad. Sci. USA. 99:2002;8568-8572
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 8568-8572
    • Howard, K.P.1    Lear, J.D.2    Degrado, W.F.3
  • 25
    • 0038010641 scopus 로고    scopus 로고
    • Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles
    • Lear J.D., Gratkowski H., Adamian L., Liang J., DeGrado W.F. Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry. 42:2003;6400-6407
    • (2003) Biochemistry , vol.42 , pp. 6400-6407
    • Lear, J.D.1    Gratkowski, H.2    Adamian, L.3    Liang, J.4    Degrado, W.F.5
  • 27
    • 0027499143 scopus 로고
    • Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins
    • Landolt-Marticorena C., Williams K.A., Deber C.M., Reithmeier R.A. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J. Mol. Biol. 229:1993;602-608
    • (1993) J. Mol. Biol. , vol.229 , pp. 602-608
    • Landolt-Marticorena, C.1    Williams, K.A.2    Deber, C.M.3    Reithmeier, R.A.4
  • 28
    • 0029738872 scopus 로고    scopus 로고
    • Experimentally determined hydrophobicity scale for proteins at membrane interfaces
    • Wimley W.C., White S.H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Struct. Biol. 3:1996;842-848
    • (1996) Nature Struct. Biol. , vol.3 , pp. 842-848
    • Wimley, W.C.1    White, S.H.2
  • 29
    • 0032406838 scopus 로고    scopus 로고
    • Statistical analysis of predicted transmembrane alpha-helices
    • Arkin I.T., Brunger A.T. Statistical analysis of predicted transmembrane alpha-helices. Biochim. Biophys. Acta. 1429:1998;113-128
    • (1998) Biochim. Biophys. Acta , vol.1429 , pp. 113-128
    • Arkin, I.T.1    Brunger, A.T.2
  • 30
    • 0031716791 scopus 로고    scopus 로고
    • Architecture of beta-barrel membrane proteins: Analysis of trimeric porins
    • Seshadri K., Garemyr R., Wallin E., von Heijne G., Elofsson A. Architecture of beta-barrel membrane proteins: analysis of trimeric porins. Protein Sci. 7:1998;2026-2032
    • (1998) Protein Sci. , vol.7 , pp. 2026-2032
    • Seshadri, K.1    Garemyr, R.2    Wallin, E.3    Von Heijne, G.4    Elofsson, A.5
  • 31
    • 0035795721 scopus 로고    scopus 로고
    • Amino acid distributions in integral membrane protein structures
    • Ulmschneider M.B., Sansom M.S. Amino acid distributions in integral membrane protein structures. Biochim. Biophys. Acta. 1512:2001;1-14
    • (2001) Biochim. Biophys. Acta , vol.1512 , pp. 1-14
    • Ulmschneider, M.B.1    Sansom, M.S.2
  • 32
    • 0027264995 scopus 로고
    • Predicting the topology of eukaryotic membrane proteins
    • Sipos L., von Heijne G. Predicting the topology of eukaryotic membrane proteins. Eur. J. Biochem. 213:1993;1333-1340
    • (1993) Eur. J. Biochem. , vol.213 , pp. 1333-1340
    • Sipos, L.1    Von Heijne, G.2
  • 33
    • 0028364507 scopus 로고
    • Membrane protein topology: Effects of delta mu H+ on the translocation of charged residues explain the "positive inside" rule
    • Andersson H., von Heijne G. Membrane protein topology: effects of delta mu H+ on the translocation of charged residues explain the "positive inside" rule. EMBO J. 13:1994;2267-2272
    • (1994) EMBO J. , vol.13 , pp. 2267-2272
    • Andersson, H.1    Von Heijne, G.2
  • 34
    • 0030791975 scopus 로고    scopus 로고
    • Anionic phospholipids are determinants of membrane protein topology
    • van Klompenburg W., Nilsson I., von Heijne G., de Kruijff B. Anionic phospholipids are determinants of membrane protein topology. EMBO J. 16:1997;4261-4266
    • (1997) EMBO J. , vol.16 , pp. 4261-4266
    • Van Klompenburg, W.1    Nilsson, I.2    Von Heijne, G.3    De Kruijff, B.4
  • 35
    • 0017151703 scopus 로고
    • Characterization of membrane proteins in detergent solutions
    • Tanford C., Reynolds J.A. Characterization of membrane proteins in detergent solutions. Biochim. Biophys. Acta. 457:1976;133-170
    • (1976) Biochim. Biophys. Acta , vol.457 , pp. 133-170
    • Tanford, C.1    Reynolds, J.A.2
  • 37
    • 0034030664 scopus 로고    scopus 로고
    • Structure and dynamics of K channel pore-lining helices: A comparative simulation study
    • Shrivastava I.H., Capener C.E., Forrest L.R., Sansom M.S. Structure and dynamics of K channel pore-lining helices: a comparative simulation study. Biophys. J. 78:2000;79-92
    • (2000) Biophys. J. , vol.78 , pp. 79-92
    • Shrivastava, I.H.1    Capener, C.E.2    Forrest, L.R.3    Sansom, M.S.4
  • 38
    • 0037062590 scopus 로고    scopus 로고
    • Lipid dependence of membrane anchoring properties and snorkeling behavior of aromatic and charged residues in transmembrane peptides
    • Strandberg E., Morein S., Rijkers D.T., Liskamp R.M., van der Wel P.C., Killian J.A. Lipid dependence of membrane anchoring properties and snorkeling behavior of aromatic and charged residues in transmembrane peptides. Biochemistry. 41:2002;7190-7198
    • (2002) Biochemistry , vol.41 , pp. 7190-7198
    • Strandberg, E.1    Morein, S.2    Rijkers, D.T.3    Liskamp, R.M.4    Van Der Wel, P.C.5    Killian, J.A.6
  • 39
    • 0028360934 scopus 로고
    • Interactions of synthetic peptide analogs of the class a amphipathic helix with lipids. Evidence for the snorkel hypothesis
    • Mishra V.K., Palgunachari M.N., Segrest J.P., Anantharamaiah G.M. Interactions of synthetic peptide analogs of the class A amphipathic helix with lipids. Evidence for the snorkel hypothesis. J. Biol. Chem. 269:1994;7185-7191
    • (1994) J. Biol. Chem. , vol.269 , pp. 7185-7191
    • Mishra, V.K.1    Palgunachari, M.N.2    Segrest, J.P.3    Anantharamaiah, G.M.4
  • 40
    • 0029761131 scopus 로고    scopus 로고
    • Interaction of model class A1, class A2, and class Y amphipathic helical peptides with membranes
    • Mishra V.K., Palgunachari M.N. Interaction of model class A1, class A2, and class Y amphipathic helical peptides with membranes. Biochemistry. 35:1996;11210-11220
    • (1996) Biochemistry , vol.35 , pp. 11210-11220
    • Mishra, V.K.1    Palgunachari, M.N.2
  • 41
    • 0033838443 scopus 로고    scopus 로고
    • Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferase
    • Buchko G.W., Rozek A., Kanda P., Kennedy M.A., Cushley R.J. Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferase. Protein. Sci. 9:2000;1548-1558
    • (2000) Protein. Sci. , vol.9 , pp. 1548-1558
    • Buchko, G.W.1    Rozek, A.2    Kanda, P.3    Kennedy, M.A.4    Cushley, R.J.5
  • 42
    • 0034711958 scopus 로고    scopus 로고
    • Statistical analysis of amino acid patterns in transmembrane helices: The GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions
    • Senes A., Gerstein M., Engelman D.M. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J. Mol. Biol. 296:2000;921-936
    • (2000) J. Mol. Biol. , vol.296 , pp. 921-936
    • Senes, A.1    Gerstein, M.2    Engelman, D.M.3
  • 43
    • 0026729232 scopus 로고
    • Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure
    • Wiener M.C., White S.H. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. Biophys. J. 61:1992;437-447
    • (1992) Biophys. J. , vol.61 , pp. 437-447
    • Wiener, M.C.1    White, S.H.2
  • 44
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side-chain prediction
    • Dunbrack R.L. Jr, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230:1993;543-574
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 46
    • 0032509124 scopus 로고    scopus 로고
    • Positively and negatively charged residues have different effects on the position in the membrane of a model transmembrane helix
    • Monne M., Nilsson I., Johansson M., Elmhed N., von Heijne G. Positively and negatively charged residues have different effects on the position in the membrane of a model transmembrane helix. J. Mol. Biol. 284:1998;1177-1183
    • (1998) J. Mol. Biol. , vol.284 , pp. 1177-1183
    • Monne, M.1    Nilsson, I.2    Johansson, M.3    Elmhed, N.4    Von Heijne, G.5
  • 47
    • 0032552880 scopus 로고    scopus 로고
    • The preference of tryptophan for membrane interfaces
    • Yau W.M., Wimley W.C., Gawrisch K., White S.H. The preference of tryptophan for membrane interfaces. Biochemistry. 37:1998;14713-14718
    • (1998) Biochemistry , vol.37 , pp. 14713-14718
    • Yau, W.M.1    Wimley, W.C.2    Gawrisch, K.3    White, S.H.4
  • 48
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 49
    • 0000484499 scopus 로고
    • Hydrophobic parameters of amino acid side-chains from the partitioning of N-acetyl-amino acid amides
    • Fauchere J.L., Pliska V. Hydrophobic parameters of amino acid side-chains from the partitioning of N-acetyl-amino acid amides. Eur. J. Med. Chem-Chim. Ther. 18:1983;369-375
    • (1983) Eur. J. Med. Chem-Chim. Ther. , vol.18 , pp. 369-375
    • Fauchere, J.L.1    Pliska, V.2
  • 50
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:1982;105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 51
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side-chains and backbone in a family of host-guest pentapeptides
    • Wimley W.C., Creamer T.P., White S.H. Solvation energies of amino acid side-chains and backbone in a family of host-guest pentapeptides. Biochemistry. 35:1996;5109-5124
    • (1996) Biochemistry , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 52
    • 0021691817 scopus 로고
    • Analysis of membrane and surface protein sequences with the hydrophobic moment plot
    • Eisenberg D., Schwarz E., Komaromy M., Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179:1984;125-142
    • (1984) J. Mol. Biol. , vol.179 , pp. 125-142
    • Eisenberg, D.1    Schwarz, E.2    Komaromy, M.3    Wall, R.4
  • 53
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman D.M., Steitz T.A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem. 15:1986;321-353
    • (1986) Annu. Rev. Biophys. Biophys. Chem. , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 54
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie J.U., Luthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164-170
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 55
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack R.L. Jr, Cohen F.E. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6:1997;1661-1681
    • (1997) Protein Sci. , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2


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