메뉴 건너뛰기




Volumn 93, Issue 12, 2007, Pages 4278-4288

The dynamic orientation of membrane-bound peptides: Bridging simulations and experiments

Author keywords

[No Author keywords available]

Indexed keywords

LYSINE; PEPTIDE; TRYPTOPHAN;

EID: 37349011230     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.113043     Document Type: Article
Times cited : (61)

References (59)
  • 2
    • 0015514472 scopus 로고
    • The fluid mosaic model of the structure of cell membranes
    • Singer, S. J., and G. L. Nicolson. 1972. The fluid mosaic model of the structure of cell membranes. Science. 175:720-731.
    • (1972) Science , vol.175 , pp. 720-731
    • Singer, S.J.1    Nicolson, G.L.2
  • 3
    • 33748715411 scopus 로고    scopus 로고
    • Isotope-edited IR spectroscopy for the study of membrane proteins
    • Arkin, I. T. 2006. Isotope-edited IR spectroscopy for the study of membrane proteins. Curr. Opin. Chem. Biol. 10:394-401.
    • (2006) Curr. Opin. Chem. Biol , vol.10 , pp. 394-401
    • Arkin, I.T.1
  • 4
    • 0035942298 scopus 로고    scopus 로고
    • Sensitivity of single membrane-spanning α-helical peptides to hydrophobic mismatch with a lipid bilayer: Effects on backbone structure, orientation, and extent of membrane incorporation
    • de Planque, M. R., E. Goormaghtigh, D. V. Greathouse, R. E. Koeppe 2nd, J. A. Kruijtzer, R. M. Liskamp, B. de Kruijff, and J. A. Killian. 2001. Sensitivity of single membrane-spanning α-helical peptides to hydrophobic mismatch with a lipid bilayer: effects on backbone structure, orientation, and extent of membrane incorporation. Biochemistry. 40:5000-5010.
    • (2001) Biochemistry , vol.40 , pp. 5000-5010
    • de Planque, M.R.1    Goormaghtigh, E.2    Greathouse, D.V.3    Koeppe 2nd, R.E.4    Kruijtzer, J.A.5    Liskamp, R.M.6    de Kruijff, B.7    Killian, J.A.8
  • 5
    • 0034186215 scopus 로고    scopus 로고
    • A solid-state NMR index of helical membrane protein structure and topology
    • Marassi, F. M., and S. J. Opella. 2000. A solid-state NMR index of helical membrane protein structure and topology. J. Magn. Reson. 144:150-155.
    • (2000) J. Magn. Reson , vol.144 , pp. 150-155
    • Marassi, F.M.1    Opella, S.J.2
  • 7
    • 0036708458 scopus 로고    scopus 로고
    • 2H NMR. Biophys. J. 83:1479-1488.
    • 2H NMR. Biophys. J. 83:1479-1488.
  • 8
    • 7044224836 scopus 로고    scopus 로고
    • The alignment, structure and dynamics of membrane-associated polypeptides by solid-state NMR spectroscopy
    • Bechinger, B., C. Aisenbrey, and P. Bertani. 2004. The alignment, structure and dynamics of membrane-associated polypeptides by solid-state NMR spectroscopy. Biochim. Biophys. Acta. 1666:190-204.
    • (2004) Biochim. Biophys. Acta , vol.1666 , pp. 190-204
    • Bechinger, B.1    Aisenbrey, C.2    Bertani, P.3
  • 9
    • 0021474573 scopus 로고
    • Mattress model of lipid-protein interactions in membranes
    • Mouritsen, O. G., and M. Bloom. 1984. Mattress model of lipid-protein interactions in membranes. Biophys. J. 46:141-153.
    • (1984) Biophys. J , vol.46 , pp. 141-153
    • Mouritsen, O.G.1    Bloom, M.2
  • 10
    • 0001065811 scopus 로고
    • Theory of protein-lipid and protein-protein interactions in bilayer membranes
    • Owicki, J. C., and H. M. McConnell. 1979. Theory of protein-lipid and protein-protein interactions in bilayer membranes. Proc. Natl. Acad. Sci. USA. 76:4750-4754.
    • (1979) Proc. Natl. Acad. Sci. USA , vol.76 , pp. 4750-4754
    • Owicki, J.C.1    McConnell, H.M.2
  • 12
    • 0030819982 scopus 로고    scopus 로고
    • Site-directed dichroism as a method for obtaining rotational and orientational constraints for oriented polymers
    • Arkin, I. T., K. R. MacKenzie, and A. T. Brunger. 1997. Site-directed dichroism as a method for obtaining rotational and orientational constraints for oriented polymers. J. Am. Chem. Soc. 119:8973-8980.
    • (1997) J. Am. Chem. Soc , vol.119 , pp. 8973-8980
    • Arkin, I.T.1    MacKenzie, K.R.2    Brunger, A.T.3
  • 14
    • 11244346029 scopus 로고    scopus 로고
    • Molecular dynamics simulation of transmembrane polypeptide orientational fluctuations
    • Goodyear, D. J., S. Sharpe, C. W. Grant, and M. R. Morrow. 2005. Molecular dynamics simulation of transmembrane polypeptide orientational fluctuations. Biophys. J. 88:105-117.
    • (2005) Biophys. J , vol.88 , pp. 105-117
    • Goodyear, D.J.1    Sharpe, S.2    Grant, C.W.3    Morrow, M.R.4
  • 15
    • 21444450972 scopus 로고    scopus 로고
    • Magic angle spinning and static oriented sample NMR studies of the relaxation in the rotating frame of membrane peptides
    • Art. No 194908
    • Fares, C., J. Qian, and J. H. Davis. 2005. Magic angle spinning and static oriented sample NMR studies of the relaxation in the rotating frame of membrane peptides. J. Chem. Phys. 122: Art. No 194908.
    • (2005) J. Chem. Phys , pp. 122
    • Fares, C.1    Qian, J.2    Davis, J.H.3
  • 16
    • 0028970552 scopus 로고
    • 1H nuclear magnetic resonance of a transmembrane peptide
    • 1H nuclear magnetic resonance of a transmembrane peptide. Biophys. J. 69:1917-1932.
    • (1995) Biophys. J , vol.69 , pp. 1917-1932
    • Davis, J.H.1    Auger, M.2    Hodges, R.S.3
  • 18
    • 0036286655 scopus 로고    scopus 로고
    • Computer simulation studies of model biological membranes
    • Saiz, L., and M. L. Klein. 2002. Computer simulation studies of model biological membranes. Acc. Chem. Res. 35:482-489.
    • (2002) Acc. Chem. Res , vol.35 , pp. 482-489
    • Saiz, L.1    Klein, M.L.2
  • 19
    • 0035812426 scopus 로고    scopus 로고
    • Simulation of the spontaneous aggregation of phospholipids into bilayers
    • Marrink, S. J., E. Lindahl, O. Edholm, and A. E. Mark. 2001. Simulation of the spontaneous aggregation of phospholipids into bilayers. J. Am. Chem. Soc. 123:8638-8639.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 8638-8639
    • Marrink, S.J.1    Lindahl, E.2    Edholm, O.3    Mark, A.E.4
  • 20
    • 10344247720 scopus 로고    scopus 로고
    • MD simulations of spontaneous membrane protein/detergent micelle formation
    • Bond, P. J., J. M. Cuthbertson, S. S. Deol, and M. S. Sansom. 2004. MD simulations of spontaneous membrane protein/detergent micelle formation. J. Am. Chem. Soc. 126:15948-15949.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 15948-15949
    • Bond, P.J.1    Cuthbertson, J.M.2    Deol, S.S.3    Sansom, M.S.4
  • 21
    • 33846842302 scopus 로고    scopus 로고
    • Self-assembling of peptide/membrane complexes by atomistic molecular dynamics simulations
    • Esteban-Martin, S., and J. Salgado. 2007. Self-assembling of peptide/membrane complexes by atomistic molecular dynamics simulations. Biophys. J. 92:903-912.
    • (2007) Biophys. J , vol.92 , pp. 903-912
    • Esteban-Martin, S.1    Salgado, J.2
  • 22
    • 10044296377 scopus 로고    scopus 로고
    • Molecular view of hexagonal phase formation in phospholipid membranes
    • Marrink, S. J., and A. E. Mark. 2004. Molecular view of hexagonal phase formation in phospholipid membranes. Biophys. J. 87:3894-3900.
    • (2004) Biophys. J , vol.87 , pp. 3894-3900
    • Marrink, S.J.1    Mark, A.E.2
  • 24
    • 1942455271 scopus 로고    scopus 로고
    • Molecular dynamics simulations of hydrophilic pores in lipid bilayers
    • Leontiadou, H., A. E. Mark, and S. J. Marrink. 2004. Molecular dynamics simulations of hydrophilic pores in lipid bilayers. Biophys. J. 86:2156-2164.
    • (2004) Biophys. J , vol.86 , pp. 2156-2164
    • Leontiadou, H.1    Mark, A.E.2    Marrink, S.J.3
  • 25
    • 18744403982 scopus 로고    scopus 로고
    • Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations
    • Im, W. 2005. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 102:6771-6776.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6771-6776
    • Im, W.1
  • 26
    • 18844362955 scopus 로고    scopus 로고
    • Folding is not required for bilayer insertion: Replica exchange simulations of an a-helical peptide with an explicit lipid bilayer
    • Nymeyer, H., T. B. Woolf, and A. E. Garcia. 2005. Folding is not required for bilayer insertion: replica exchange simulations of an a-helical peptide with an explicit lipid bilayer. Proteins. 59:783-790.
    • (2005) Proteins , vol.59 , pp. 783-790
    • Nymeyer, H.1    Woolf, T.B.2    Garcia, A.E.3
  • 27
    • 21244431672 scopus 로고    scopus 로고
    • Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins
    • Venturoli, M., B. Smit, and M. M. Sperotto. 2005. Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins. Biophys. J. 88:1778-1798.
    • (2005) Biophys. J , vol.88 , pp. 1778-1798
    • Venturoli, M.1    Smit, B.2    Sperotto, M.M.3
  • 28
    • 33646198955 scopus 로고    scopus 로고
    • Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: A systematic investigation of hydrophobic mismatch
    • Kandasamy, S. K., and R. G. Larson. 2006. Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch. Biophys. J. 90:2326-2343.
    • (2006) Biophys. J , vol.90 , pp. 2326-2343
    • Kandasamy, S.K.1    Larson, R.G.2
  • 29
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and assembly of membrane proteins via simulation
    • Bond, P. J., and M. S. Sansom. 2006. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 128:2697-2704.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.2
  • 30
    • 0001006658 scopus 로고
    • Interaction of a synthetic amphiphilic polypeptide and lipids in a bilayer structure
    • Davis, J. H., D. M. Clare, R. S. Hodges, and M. Bloom. 1983. Interaction of a synthetic amphiphilic polypeptide and lipids in a bilayer structure. Biochemistry. 22:5298-5305.
    • (1983) Biochemistry , vol.22 , pp. 5298-5305
    • Davis, J.H.1    Clare, D.M.2    Hodges, R.S.3    Bloom, M.4
  • 34
    • 28244458040 scopus 로고    scopus 로고
    • Self-association of transmembrane a-helices in model membranes: Importance of helix orientation and role of hydrophobic mismatch
    • Sparr, E., W. L. Ash, P. V. Nazarov, D. T. Rijkers, M. A. Hemminga, D. P. Tieleman, and J. A. Killian. 2005. Self-association of transmembrane a-helices in model membranes: importance of helix orientation and role of hydrophobic mismatch. J. Biol. Chem. 280:39324-39331.
    • (2005) J. Biol. Chem , vol.280 , pp. 39324-39331
    • Sparr, E.1    Ash, W.L.2    Nazarov, P.V.3    Rijkers, D.T.4    Hemminga, M.A.5    Tieleman, D.P.6    Killian, J.A.7
  • 35
    • 33746647787 scopus 로고    scopus 로고
    • Peptides in lipid bilayers: The power of simple models
    • Killian, J. A., and T. K. Nyholm. 2006. Peptides in lipid bilayers: the power of simple models. Curr. Opin. Struct. Biol. 16:473-479.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 473-479
    • Killian, J.A.1    Nyholm, T.K.2
  • 36
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
    • (2001) J. Mol. Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 37
    • 0030999097 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
    • Berger, O., O. Edholm, and F. Jahnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72:2002-2013.
    • (1997) Biophys. J , vol.72 , pp. 2002-2013
    • Berger, O.1    Edholm, O.2    Jahnig, F.3
  • 38
    • 0001585978 scopus 로고    scopus 로고
    • Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
    • Feenstra, K. A., B. Hess, and H. J. C. Berendsen. 1999. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. 20:786-798.
    • (1999) J. Comput. Chem , vol.20 , pp. 786-798
    • Feenstra, K.A.1    Hess, B.2    Berendsen, H.J.C.3
  • 41
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede, T., J. Kopp, N. Guex, and M. C. Peitsch. 2003. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31:3381-3385.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 42
    • 0028258175 scopus 로고
    • Molecular dynamics simulation of a phospholipid membrane
    • Egberts, E., S. J. Marrink, and H. J. C. Berendsen. 1994. Molecular dynamics simulation of a phospholipid membrane. Eur. Biophys. J. 22:423-436.
    • (1994) Eur. Biophys. J , vol.22 , pp. 423-436
    • Egberts, E.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 43
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 44
    • 20444366208 scopus 로고    scopus 로고
    • Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch
    • Park, S. H., and S. J. Opella. 2005. Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch. J. Mol. Biol. 350:310-318.
    • (2005) J. Mol. Biol , vol.350 , pp. 310-318
    • Park, S.H.1    Opella, S.J.2
  • 45
    • 4444343863 scopus 로고    scopus 로고
    • Lipid bilayer topology of the transmembrane α-helix of M13 major coat protein and bilayer polarity profile by site-directed fluorescence spectroscopy
    • Koehorst, R. B., R. B. Spruijt, F. J. Vergeldt, and M. A. Hemminga. 2004. Lipid bilayer topology of the transmembrane α-helix of M13 major coat protein and bilayer polarity profile by site-directed fluorescence spectroscopy. Biophys. J. 87:1445-1455.
    • (2004) Biophys. J , vol.87 , pp. 1445-1455
    • Koehorst, R.B.1    Spruijt, R.B.2    Vergeldt, F.J.3    Hemminga, M.A.4
  • 46
    • 15244348542 scopus 로고    scopus 로고
    • The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment
    • Duong-Ly, K. C., V. Nanda, W. F. Degrado, and K. P. Howard. 2005. The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Sci. 14:856-861.
    • (2005) Protein Sci , vol.14 , pp. 856-861
    • Duong-Ly, K.C.1    Nanda, V.2    Degrado, W.F.3    Howard, K.P.4
  • 47
    • 33846595904 scopus 로고
    • High resolution heteronuclear dipolar solid-state NMR spectroscopy
    • Wu, C. H., A. Ramamoorthy, and S. J. Opella. 1994. High resolution heteronuclear dipolar solid-state NMR spectroscopy. J. Magn. Reson. 109:270-272.
    • (1994) J. Magn. Reson , vol.109 , pp. 270-272
    • Wu, C.H.1    Ramamoorthy, A.2    Opella, S.J.3
  • 48
    • 0034186215 scopus 로고    scopus 로고
    • A solid-state NMR index of helical membrane protein structure and topology
    • Marassi, F. M., and S. J. Opella. 2000. A solid-state NMR index of helical membrane protein structure and topology. J. Magn. Res. 144:150-155.
    • (2000) J. Magn. Res , vol.144 , pp. 150-155
    • Marassi, F.M.1    Opella, S.J.2
  • 50
    • 33846562986 scopus 로고    scopus 로고
    • Structure, topology, and tilt of cell-signaling peptides containing nuclear localization sequences in membrane bilayers determined by solid-state NMR and molecular dynamics simulation studies
    • Ramamoorthy, A., S. K. Kandasamy, D. K. Lee, S. Kidambi, and R. G. Larson. 2007. Structure, topology, and tilt of cell-signaling peptides containing nuclear localization sequences in membrane bilayers determined by solid-state NMR and molecular dynamics simulation studies. Biochemistry. 30:965-975.
    • (2007) Biochemistry , vol.30 , pp. 965-975
    • Ramamoorthy, A.1    Kandasamy, S.K.2    Lee, D.K.3    Kidambi, S.4    Larson, R.G.5
  • 52
    • 0242659352 scopus 로고    scopus 로고
    • Protein-lipid interactions studied with designed transmembrane peptides: Role of hydrophobic matching and interfacial anchoring
    • de Planque, M. R., and J. A. Killian. 2003. Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol. Membr. Biol. 20:271-284.
    • (2003) Mol. Membr. Biol , vol.20 , pp. 271-284
    • de Planque, M.R.1    Killian, J.A.2
  • 53
    • 33748493587 scopus 로고    scopus 로고
    • Indole localization in lipid membranes revealed by molecular simulation
    • Norman, K. E., and H. Nymeyer. 2006. Indole localization in lipid membranes revealed by molecular simulation. Biophys. J. 91:2046-2054.
    • (2006) Biophys. J , vol.91 , pp. 2046-2054
    • Norman, K.E.1    Nymeyer, H.2
  • 54
    • 22344440794 scopus 로고    scopus 로고
    • Electrostatic contributions to indole-lipid interactions
    • Gaede, H. C., W. M. Yau, and K. Gawrisch. 2005. Electrostatic contributions to indole-lipid interactions. J. Phys. Chem. B. 109:13014-13023.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 13014-13023
    • Gaede, H.C.1    Yau, W.M.2    Gawrisch, K.3
  • 56
    • 0031740601 scopus 로고    scopus 로고
    • Hydrophobic interactions of peptides with membrane interfaces
    • White, S. H., and W. C. Wimley. 1998. Hydrophobic interactions of peptides with membrane interfaces. Biochim. Biophys. Acta. 1376:339-352.
    • (1998) Biochim. Biophys. Acta , vol.1376 , pp. 339-352
    • White, S.H.1    Wimley, W.C.2
  • 59
    • 85031444858 scopus 로고    scopus 로고
    • Suat Özdirekcan, Catherine Etchebest, J. Antoinette Killian, and Patrick F. J. Fuchs. On the orientation of a designed transmembrane peptide: towards the right tilt angle? J. Am. Chem. Soc. In press.
    • Suat Özdirekcan, Catherine Etchebest, J. Antoinette Killian, and Patrick F. J. Fuchs. On the orientation of a designed transmembrane peptide: towards the right tilt angle? J. Am. Chem. Soc. In press.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.