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Volumn 76, Issue 1 I, 1999, Pages 40-49

Alamethicin helices in a bilayer and in solution: Molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

ALAMETHICIN; DIOLEOYLPHOSPHATIDYLCHOLINE; DIPALMITOYLPHOSPHATIDYLCHOLINE; METHANOL; WATER;

EID: 0032951553     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77176-6     Document Type: Article
Times cited : (200)

References (57)
  • 3
    • 0030024628 scopus 로고    scopus 로고
    • Membrane structure of voltage-gated channel-forming peptides by site-directed spin-labeling
    • Barranger-Mathys, M., and D. S. Cafiso. 1996. Membrane structure of voltage-gated channel-forming peptides by site-directed spin-labeling. Biochemistry. 35:498-505.
    • (1996) Biochemistry , vol.35 , pp. 498-505
    • Barranger-Mathys, M.1    Cafiso, D.S.2
  • 4
    • 0030733344 scopus 로고    scopus 로고
    • Structure and dynamics of an amphiphilic peptide in a lipid bilayer: A molecular dynamics study
    • Belohorcova, K., J. H. Davis, T. B. Woolf, and B. Roux. 1997. Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study. Biophys. J. 73:3039-3055.
    • (1997) Biophys. J. , vol.73 , pp. 3039-3055
    • Belohorcova, K.1    Davis, J.H.2    Woolf, T.B.3    Roux, B.4
  • 6
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • Berendsen, H. J. C., D. van der Spoel, and R. van Drunen. 1995. GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 95:43-56.
    • (1995) Comp. Phys. Comm. , vol.95 , pp. 43-56
    • Berendsen, H.J.C.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 7
    • 0030999097 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidycholine at full hydration, constant pressure and constant temperature
    • Berger, O., O. Edholm, and F. Jahnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidycholine 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
  • 8
    • 0031022167 scopus 로고    scopus 로고
    • Simulation studies of alamethicin-bilayer interactions
    • Biggin, P., J. Breed, H. S. Son, and M. S. P. Sansom. 1997. Simulation studies of alamethicin-bilayer interactions. Biophys. J. 72:627-636.
    • (1997) Biophys. J. , vol.72 , pp. 627-636
    • Biggin, P.1    Breed, J.2    Son, H.S.3    Sansom, M.S.P.4
  • 9
    • 0031892162 scopus 로고    scopus 로고
    • How many membrane proteins are there?
    • Boyd, D., C. Schierle, and J. Beckwith. 1998. How many membrane proteins are there? Protein Sci. 7:201-205.
    • (1998) Protein Sci. , vol.7 , pp. 201-205
    • Boyd, D.1    Schierle, C.2    Beckwith, J.3
  • 10
    • 0000882208 scopus 로고
    • Hypothesis about the function of membrane-buried proline residues in transport proteins
    • Brandl, C. J., and C. M. Deber. 1986. Hypothesis about the function of membrane-buried proline residues in transport proteins. Proc. Natl. Acad. Sci. USA. 83:917-921.
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 917-921
    • Brandl, C.J.1    Deber, C.M.2
  • 11
    • 0028226051 scopus 로고
    • Alamethicin - A peptide model for voltage gating and protein membrane interactions
    • Cafiso, D. S. 1994. Alamethicin - a peptide model for voltage gating and protein membrane interactions. Annu. Rev. Biophys. Biomol. Struct. 23:141-165.
    • (1994) Annu. Rev. Biophys. Biomol. Struct. , vol.23 , pp. 141-165
    • Cafiso, D.S.1
  • 12
    • 0029100456 scopus 로고
    • Hydrogen-bond stabilities in the isolated alamethicin helix - PH-dependent amide exchange measurements in methanol
    • Dempsey, C. E. 1995. Hydrogen-bond stabilities in the isolated alamethicin helix - pH-dependent amide exchange measurements in methanol. J. Am. Chem. Soc. 117:7526-7534.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 7526-7534
    • Dempsey, C.E.1
  • 13
    • 0029862704 scopus 로고    scopus 로고
    • Hydrogen-bond stabilities in membrane-reconstituted alamethicin from amide-resolved hydrogen-exchange measurements
    • Dempsey, C. E., and L. J. Handcock. 1996. Hydrogen-bond stabilities in membrane-reconstituted alamethicin from amide-resolved hydrogen-exchange measurements. Biophys. J. 70:1777-1788.
    • (1996) Biophys. J. , vol.70 , pp. 1777-1788
    • Dempsey, C.E.1    Handcock, L.J.2
  • 15
    • 0020360086 scopus 로고
    • A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5 Å resolution
    • Fox, R. O., and F. M. Richards. 1982. A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5 Å resolution. Nature. 300:325-330.
    • (1982) Nature , vol.300 , pp. 325-330
    • Fox, R.O.1    Richards, F.M.2
  • 17
    • 0025614191 scopus 로고
    • Restrained and unrestrained molecular dynamics simulations in the NVT ensemble of alamethicin
    • Fraternali, F. 1990. Restrained and unrestrained molecular dynamics simulations in the NVT ensemble of alamethicin. Biopolymers. 30: 1083-1099.
    • (1990) Biopolymers. , vol.30 , pp. 1083-1099
    • Fraternali, F.1
  • 18
    • 0029873933 scopus 로고    scopus 로고
    • Structure and orientation of the mammalian antibacterial peptide cecropin Pl within phospholipid membranes
    • Gazit, E., I. R. Miller, P. C. Biggin, M. S. P. Sansom, and Y. Shai. 1996. Structure and orientation of the mammalian antibacterial peptide cecropin Pl within phospholipid membranes. J. Mol. Biol. 258: 860-870.
    • (1996) J. Mol. Biol. , vol.258 , pp. 860-870
    • Gazit, E.1    Miller, I.R.2    Biggin, P.C.3    Sansom, M.S.P.4    Shai, Y.5
  • 19
    • 0030916534 scopus 로고    scopus 로고
    • Helix bending in alamethicin: Molecular dynamics simulations and amide hydrogen exchange in methanol
    • Gibbs, N., R. B. Sessions, P. B. Williams, and C. E. Dempsey. 1997. Helix bending in alamethicin: molecular dynamics simulations and amide hydrogen exchange in methanol. Biophys. J. 72:2490-2495.
    • (1997) Biophys. J. , vol.72 , pp. 2490-2495
    • Gibbs, N.1    Sessions, R.B.2    Williams, P.B.3    Dempsey, C.E.4
  • 21
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    • Hayward, S., and H. J. C. Berendsen. 1998. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins Struct. Funct. Genet. 30:144-154.
    • (1998) Proteins Struct. Funct. Genet. , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.C.2
  • 23
    • 0025889072 scopus 로고
    • Lipid-alamethicin interactions influence alamethicin orientation
    • Huang, H. W., and Y. Wu. 1991. Lipid-alamethicin interactions influence alamethicin orientation. Biophys. J. 60:1079-1087.
    • (1991) Biophys. J. , vol.60 , pp. 1079-1087
    • Huang, H.W.1    Wu, Y.2
  • 24
    • 0030953326 scopus 로고    scopus 로고
    • Computer simulation studies of biological membranes: Progress, promise and pitfalls
    • Jakobsson, E. 1997. Computer simulation studies of biological membranes: progress, promise and pitfalls. Trends Biochem. Sci. 22:339-344.
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 339-344
    • Jakobsson, E.1
  • 25
    • 0031835795 scopus 로고    scopus 로고
    • Structural features that modulate the transmembrane migration of a hydrophobic peptide in lipid vesicles
    • Jayasinghe, S., M. Barranger-Mathys, J. F. Ellena, C. Franklin, and D. S. Cafiso. 1998. Structural features that modulate the transmembrane migration of a hydrophobic peptide in lipid vesicles. Biophys. J. 74: 3023-3030.
    • (1998) Biophys. J. , vol.74 , pp. 3023-3030
    • Jayasinghe, S.1    Barranger-Mathys, M.2    Ellena, J.F.3    Franklin, C.4    Cafiso, D.S.5
  • 26
    • 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
  • 27
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 28
    • 0023907575 scopus 로고
    • Synthetic amphiphilic peptide models for protein ion channels
    • Lear, J. D., Z. R. Wasserman, and W. F. DeGrado. 1988. Synthetic amphiphilic peptide models for protein ion channels. Science. 240: 1177-1181.
    • (1988) Science , vol.240 , pp. 1177-1181
    • Lear, J.D.1    Wasserman, Z.R.2    DeGrado, W.F.3
  • 30
    • 33751158845 scopus 로고
    • Simulation of water transport through a lipid membrane
    • Marrink, S. J., and H. J. C. Berendsen. 1994. Simulation of water transport through a lipid membrane. J. Phys. Chem. 98:4155-4168.
    • (1994) J. Phys. Chem. , vol.98 , pp. 4155-4168
    • Marrink, S.J.1    Berendsen, H.J.C.2
  • 31
    • 0031880829 scopus 로고    scopus 로고
    • Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations
    • Marrink, S. J., O. Berger, D. P. Tieleman, and F. Jahnig. 1998. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophys. J. 74:931-943.
    • (1998) Biophys. J. , vol.74 , pp. 931-943
    • Marrink, S.J.1    Berger, O.2    Tieleman, D.P.3    Jahnig, F.4
  • 32
    • 0343118775 scopus 로고    scopus 로고
    • Molecular dynamics simulations of lipid bilayers
    • Merz, K. M. 1997. Molecular dynamics simulations of lipid bilayers. Curr. Opin. Struct. Biol. 7:511-517.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 511-517
    • Merz, K.M.1
  • 35
    • 0026848828 scopus 로고
    • Minimum energy conformations of proline-containing helices
    • Polinsky, A., M. Goodman, K. A. Williams, and C. M. Deber. 1992. Minimum energy conformations of proline-containing helices. Biopolymers. 32:399-406.
    • (1992) Biopolymers. , vol.32 , pp. 399-406
    • Polinsky, A.1    Goodman, M.2    Williams, K.A.3    Deber, C.M.4
  • 36
    • 0030735981 scopus 로고    scopus 로고
    • Influence of the membrane potential on the free energy of an intrinsic protein
    • Roux, B. 1997. Influence of the membrane potential on the free energy of an intrinsic protein. Biophys. J. 73:2980-2989.
    • (1997) Biophys. J. , vol.73 , pp. 2980-2989
    • Roux, B.1
  • 37
    • 0029813087 scopus 로고    scopus 로고
    • The pore domain of the nicotinic acetylcholine receptor: Molecular modelling and electrostatics
    • Sankararamakrishnan, R., C. Adcock, and M. S. P. Sansom. 1996. The pore domain of the nicotinic acetylcholine receptor: molecular modelling and electrostatics. Biophys. J. 71:1659-1671.
    • (1996) Biophys. J. , vol.71 , pp. 1659-1671
    • Sankararamakrishnan, R.1    Adcock, C.2    Sansom, M.S.P.3
  • 39
    • 0025935264 scopus 로고
    • The biophysics of peptide models of ion channels
    • Sansom, M. S. P. 1991. The biophysics of peptide models of ion channels. Prog. Biophys. Mol. Biol. 55:139-236.
    • (1991) Prog. Biophys. Mol. Biol. , vol.55 , pp. 139-236
    • Sansom, M.S.P.1
  • 40
    • 0026537558 scopus 로고
    • Proline residues in transmembrane helices of channel and transport proteins: A molecular modelling study
    • Sansom, M. S. P. 1992. Proline residues in transmembrane helices of channel and transport proteins: a molecular modelling study. Protein Eng. 5:53-60.
    • (1992) Protein Eng. , vol.5 , pp. 53-60
    • Sansom, M.S.P.1
  • 41
    • 0027817476 scopus 로고
    • Structure and function of channel-forming peptaibols
    • Sansom, M. S. P. 1993. Structure and function of channel-forming peptaibols. Q. Rev. Biophys. 26:365-421.
    • (1993) Q. Rev. Biophys. , vol.26 , pp. 365-421
    • Sansom, M.S.P.1
  • 42
    • 0031972614 scopus 로고    scopus 로고
    • Hydogen bonding in helical polypeptides from molecular dynamics simulations and amide exchange analysis: Alamethicin and melittin in methanol
    • Sessions, R. B., N. Gibbs, and C. E. Dempsey. 1998. Hydogen bonding in helical polypeptides from molecular dynamics simulations and amide exchange analysis: alamethicin and melittin in methanol. Biophys. J. 74:138-152.
    • (1998) Biophys. J. , vol.74 , pp. 138-152
    • Sessions, R.B.1    Gibbs, N.2    Dempsey, C.E.3
  • 43
    • 0030966534 scopus 로고    scopus 로고
    • Transmembrane helix structure, dynamics, and interactions: Multi-nanosecond molecular dynamics simulations
    • Shen, L., D. Bassolino, and T. Stouch. 1997. Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations. Biophys. J. 73:3-20.
    • (1997) Biophys. J. , vol.73 , pp. 3-20
    • Shen, L.1    Bassolino, D.2    Stouch, T.3
  • 45
    • 0000112789 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidycholine bilayer with different macroscopic boundary conditions and parameters
    • Tieleman, D. P., and H. J. C. Berendsen. 1996. Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidycholine bilayer with different macroscopic boundary conditions and parameters. J. Chem. Phys. 105:4871-4880.
    • (1996) J. Chem. Phys. , vol.105 , pp. 4871-4880
    • Tieleman, D.P.1    Berendsen, H.J.C.2
  • 46
    • 0031860932 scopus 로고    scopus 로고
    • A molecular dynamics study of the pores formed by E. Coli OmpF porin in a fully hydrated POPE bilayer
    • Tieleman, D. P., and H. J. C. Berendsen. 1998. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated POPE bilayer. Biophys. J. 74:2786-2801.
    • (1998) Biophys. J. , vol.74 , pp. 2786-2801
    • Tieleman, D.P.1    Berendsen, H.J.C.2
  • 47
    • 0031438285 scopus 로고    scopus 로고
    • A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems
    • Tieleman, D. P., S. J. Marrink, and H. J. C. Berendsen. 1997. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta. 1331:235-270.
    • (1997) Biochim. Biophys. Acta , vol.1331 , pp. 235-270
    • Tieleman, D.P.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 49
    • 0028921479 scopus 로고
    • Acetylcholine receptor channel imaged in the open state
    • Unwin, N. 1995. Acetylcholine receptor channel imaged in the open state. Nature. 373:37-43.
    • (1995) Nature , vol.373 , pp. 37-43
    • Unwin, N.1
  • 51
    • 0023248806 scopus 로고
    • Comparison of the conformation and orientation of alamethicin and melittin in lipid membranes
    • Vogel, H. 1987. Comparison of the conformation and orientation of alamethicin and melittin in lipid membranes. Biochemistry. 26:4562-4572.
    • (1987) Biochemistry , vol.26 , pp. 4562-4572
    • Vogel, H.1
  • 52
    • 0025782832 scopus 로고
    • Proline kinks in transmembrane α-helices
    • von Heijne, G. 1991. Proline kinks in transmembrane α-helices. J. Mol. Biol. 499-503.
    • (1991) J. Mol. Biol. , pp. 499-503
    • Von Heijne, G.1
  • 53
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archean, and eukaryotic organisms
    • Wallin, E., and G. von Heijne. 1998. Genome-wide analysis of integral membrane proteins from eubacterial, archean, and eukaryotic organisms. Protein Sci. 7:1029-1038.
    • (1998) Protein Sci. , vol.7 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 54
    • 0030731888 scopus 로고    scopus 로고
    • Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. I. Structure and dynamics
    • Woolf, T. B. 1997. Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. I. Structure and dynamics. Biophys. J. 73:2376-2392.
    • (1997) Biophys. J. , vol.73 , pp. 2376-2392
    • Woolf, T.B.1
  • 55
    • 0025801502 scopus 로고
    • Conserved positioning of proline residues in membrane-spanning helices of ion-channel proteins
    • Woolfson, D. N., R. J. Mortishire-Smith, and D. H. Williams. 1991. Conserved positioning of proline residues in membrane-spanning helices of ion-channel proteins. Biochem. Biophys. Res. Commun. 175:733-737.
    • (1991) Biochem. Biophys. Res. Commun. , vol.175 , pp. 733-737
    • Woolfson, D.N.1    Mortishire-Smith, R.J.2    Williams, D.H.3
  • 56
    • 0026754487 scopus 로고
    • Model ion channels: Gramicidin and alamethicin
    • Woolley, G. A., and B. A. Wallace. 1992. Model ion channels: gramicidin and alamethicin. J. Membr. Biol. 129:109-136.
    • (1992) J. Membr. Biol. , vol.129 , pp. 109-136
    • Woolley, G.A.1    Wallace, B.A.2
  • 57
    • 0025996871 scopus 로고
    • Proline in α-helix: Stability and conformation studied by dynamics simulation
    • Yun, R. H., A. Anderson, and J. Hermans. 1992. Proline in α-helix: stability and conformation studied by dynamics simulation. Proteins Struct. Funct. Genet. 10:219-228.
    • (1992) Proteins Struct. Funct. Genet. , vol.10 , pp. 219-228
    • Yun, R.H.1    Anderson, A.2    Hermans, J.3


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