메뉴 건너뛰기




Volumn 33, Issue 1, 2004, Pages 16-28

Implicit solvent model estimates of the stability of model structures of the alamethicin channel

Author keywords

Continuum solvent models; Membrane curvature; Molecular dynamics; Peptide membrane interactions; Poisson equation

Indexed keywords

ALAMETHICIN; MEMBRANE PROTEIN; SOLVENT; WATER;

EID: 1042267271     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-003-0345-4     Document Type: Article
Times cited : (26)

References (49)
  • 1
    • 0021107942 scopus 로고
    • Structure of alamethicin in solution: Nuclear magnetic resonance relaxation studies
    • Banerjee U, Chan SI (1983) Structure of alamethicin in solution: nuclear magnetic resonance relaxation studies. Biochemistry 22:3709-3713
    • (1983) Biochemistry , vol.22 , pp. 3709-3713
    • Banerjee, U.1    Chan, S.I.2
  • 2
    • 0028244098 scopus 로고
    • Collisions between helical peptides in membranes monitored using electron paramagnetic resonance: Evidence that alamethicin is monomeric in the absence of a membrane potential
    • Barranger-Mathys M, Cafiso DS (1994) Collisions between helical peptides in membranes monitored using electron paramagnetic resonance: evidence that alamethicin is monomeric in the absence of a membrane potential. Biophys J 67:172-176
    • (1994) Biophys J , vol.67 , pp. 172-176
    • Barranger-Mathys, M.1    Cafiso, D.S.2
  • 3
    • 0016311447 scopus 로고
    • A molecular model of membrane excitability
    • Baumann G, Mueller P (1974) A molecular model of membrane excitability. J Supramol Struct 2:538-557
    • (1974) J Supramol Struct , vol.2 , pp. 538-557
    • Baumann, G.1    Mueller, P.2
  • 4
    • 0029938187 scopus 로고    scopus 로고
    • Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes
    • Ben-Shaul A, Ben-Tal N, Honig B (1996) Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes. Biophys J 71:130-137
    • (1996) Biophys J , vol.71 , pp. 130-137
    • Ben-Shaul, A.1    Ben-Tal, N.2    Honig, B.3
  • 5
    • 0029768644 scopus 로고    scopus 로고
    • Helix-helix interactions in lipid bilayers
    • Ben-Tal N, Honig B (1996) Helix-helix interactions in lipid bilayers. Biophys J 71:3046-3050
    • (1996) Biophys J , vol.71 , pp. 3046-3050
    • Ben-Tal, N.1    Honig, B.2
  • 6
    • 0029669955 scopus 로고    scopus 로고
    • Free-energy determinants of alpha-helix insertion into lipid bilayers
    • Ben-Tal N, Ben-Shaul A, Nicholls A, Honig B (1996) Free-energy determinants of alpha-helix insertion into lipid bilayers. Biophys J 70:1803-1812
    • (1996) Biophys J , vol.70 , pp. 1803-1812
    • Ben-Tal, N.1    Ben-Shaul, A.2    Nicholls, A.3    Honig, B.4
  • 8
    • 0011613265 scopus 로고    scopus 로고
    • Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane
    • Bernèche S, Nina M, Roux B (1998) Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J 75:1603-1618
    • (1998) Biophys J , vol.75 , pp. 1603-1618
    • Bernèche, S.1    Nina, M.2    Roux, B.3
  • 9
    • 0016183539 scopus 로고
    • Statistical analysis of alamethicin channels in black lipid membranes
    • Boheim G (1974) Statistical analysis of alamethicin channels in black lipid membranes. J Membr Biol 19:277-303
    • (1974) J Membr Biol , vol.19 , pp. 277-303
    • Boheim, G.1
  • 10
    • 0037018915 scopus 로고    scopus 로고
    • Stability of an ion channel in lipid bilayers: Implicit solvent model calculations with gramicidin
    • Bransburg-Zabary S, Kessel A, Gutman M, Ben-Tal N (2002) Stability of an ion channel in lipid bilayers: implicit solvent model calculations with gramicidin. Biochemistry 41:6946-6954
    • (2002) Biochemistry , vol.41 , pp. 6946-6954
    • Bransburg-Zabary, S.1    Kessel, A.2    Gutman, M.3    Ben-Tal, N.4
  • 11
    • 0029863372 scopus 로고    scopus 로고
    • Molecular dynamics simulations of water within models of ion channels
    • Breed J, Sankararamakrishnan R, Kerr ID, Sansom MS (1996) Molecular dynamics simulations of water within models of ion channels. Biophys J 70:1643-1661
    • (1996) Biophys J , vol.70 , pp. 1643-1661
    • Breed, J.1    Sankararamakrishnan, R.2    Kerr, I.D.3    Sansom, M.S.4
  • 12
  • 13
    • 0030807799 scopus 로고    scopus 로고
    • Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues
    • Breed J, Kerr ID, Molle G, Duclohier H, Sansom MS (1997b) Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues. Biochim Biophys Acta 1330:103-109
    • (1997) Biochim Biophys Acta , vol.1330 , pp. 103-109
    • Breed, J.1    Kerr, I.D.2    Molle, G.3    Duclohier, H.4    Sansom, M.S.5
  • 14
    • 0032053619 scopus 로고    scopus 로고
    • Simulations of protein folding and unfolding
    • Brooks CL 3rd (1998) Simulations of protein folding and unfolding. Curr Opin Struct Biol 8:222-226
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 222-226
    • Brooks III, C.L.1
  • 15
    • 0028226051 scopus 로고
    • Alamethicin: A peptide model for voltage gating and protein-membrane interactions
    • Cafiso D (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.1
  • 16
    • 0023769808 scopus 로고
    • Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system
    • Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT (1988) Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins 4:31-47
    • (1988) Proteins , vol.4 , pp. 31-47
    • Dauber-Osguthorpe, P.1    Roberts, V.A.2    Osguthorpe, D.J.3    Wolff, J.4    Genest, M.5    Hagler, A.T.6
  • 17
    • 0019464222 scopus 로고
    • The spontaneous insertion of proteins into and across membranes: The helical hairpin hypothesis
    • Engelman DM, Steitz TA (1981) The spontaneous insertion of proteins into and across membranes: the helical hairpin hypothesis. Cell 23:411-422
    • (1981) Cell , vol.23 , pp. 411-422
    • Engelman, D.M.1    Steitz, T.A.2
  • 20
    • 0027362726 scopus 로고
    • A molecular model for lipid-protein interaction in membranes: The role of hydrophobic mismatch
    • Fattal DR, Ben-Shaul A (1993) A molecular model for lipid-protein interaction in membranes: the role of hydrophobic mismatch. Biophys J 65:1795-1809
    • (1993) Biophys J , vol.65 , pp. 1795-1809
    • Fattal, D.R.1    Ben-Shaul, A.2
  • 21
    • 0020360086 scopus 로고
    • A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5-A resolution
    • Fox RO Jr, Richards FM (1982) A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5-A resolution. Nature 300:325-330
    • (1982) Nature , vol.300 , pp. 325-330
    • Fox Jr., R.O.1    Richards, F.M.2
  • 22
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson MK, Sharp KA, Honig B (1987) Calculating the electrostatic potential of molecules in solution: method and error assessment. J Comput Chem 9:327-335
    • (1987) J Comput Chem , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.3
  • 23
    • 0016848186 scopus 로고
    • Potential-dependent conductances in lipid membranes containing alamethicin
    • Gordon LG, Haydon DA (1975) Potential-dependent conductances in lipid membranes containing alamethicin. Philos Trans R Soc Lond B Biol Sci 270:433-447
    • (1975) Philos Trans R Soc Lond B Biol Sci , vol.270 , pp. 433-447
    • Gordon, L.G.1    Haydon, D.A.2
  • 24
    • 0035252920 scopus 로고    scopus 로고
    • Protein design based on folding models
    • Guerois R, Serrano L (2001) Protein design based on folding models. Curr Opin Struct Biol 11:101-106
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 101-106
    • Guerois, R.1    Serrano, L.2
  • 26
    • 0024558250 scopus 로고
    • The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices
    • Jacobs RE, White SH (1989) The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices. Biochemistry 28:3421-3437
    • (1989) Biochemistry , vol.28 , pp. 3421-3437
    • Jacobs, R.E.1    White, S.H.2
  • 27
    • 0028070549 scopus 로고
    • Parallel helix bundles and ion channels: Molecular modeling via simulated annealing and restrained molecular dynamics
    • Kerr ID, Sankararamakrishnan R, Smart OS, Sansom MS (1994) Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics. Biophys J 67:1501-1515
    • (1994) Biophys J , vol.67 , pp. 1501-1515
    • Kerr, I.D.1    Sankararamakrishnan, R.2    Smart, O.S.3    Sansom, M.S.4
  • 28
    • 35448950945 scopus 로고    scopus 로고
    • Free energy determinants of peptide association with lipid bilayers
    • Simon S, McIntosh T (eds). Academic Press, San Diego
    • Kessel A, Ben-Tal N (2002) Free energy determinants of peptide association with lipid bilayers. In: Simon S, McIntosh T (eds) Current topics in membranes, vol 52: peptide-lipid interactions. Academic Press, San Diego, pp 205-253
    • (2002) Current Topics in Membranes, Vol 52: Peptide-lipid Interactions , vol.52 , pp. 205-253
    • Kessel, A.1    Ben-Tal, N.2
  • 29
    • 0034118188 scopus 로고    scopus 로고
    • Continuum solvent model calculations of alamethicin-membrane interactions: Thermodynamic aspects
    • Kessel A, Cafiso DS, Ben-Tal N (2000a) Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects. Biophys J 78:571-583
    • (2000) Biophys J , vol.78 , pp. 571-583
    • Kessel, A.1    Cafiso, D.S.2    Ben-Tal, N.3
  • 30
    • 0033747198 scopus 로고    scopus 로고
    • Calculations suggest a pathway for the transmembrane migration of a hydrophobic peptide
    • Kessel A, Schulten K, Ben-Tal N (2000b) Calculations suggest a pathway for the transmembrane migration of a hydrophobic peptide. Biophys J 79:2322-2330
    • (2000) Biophys J , vol.79 , pp. 2322-2330
    • Kessel, A.1    Schulten, K.2    Ben-Tal, N.3
  • 31
    • 0034995930 scopus 로고    scopus 로고
    • Continuum solvent model studies of the interactions of an anticonvulsant drug with lipid bilayers
    • Kessel A, Musafia B, Ben-Tal N (2001) Continuum solvent model studies of the interactions of an anticonvulsant drug with lipid bilayers. Biophys J 80:2535-2545
    • (2001) Biophys J , vol.80 , pp. 2535-2545
    • Kessel, A.1    Musafia, B.2    Ben-Tal, N.3
  • 32
    • 0034667495 scopus 로고    scopus 로고
    • A molecular model for lipid-mediated interaction between proteins in membranes
    • May S, Ben-Shaul A (2000) A molecular model for lipid-mediated interaction between proteins in membranes. Phys Chem Chem Phys 2:4494-4502
    • (2000) Phys Chem Chem Phys , vol.2 , pp. 4494-4502
    • May, S.1    Ben-Shaul, A.2
  • 33
    • 0027390459 scopus 로고
    • Insertion of peptide chains into lipid membranes: An off-lattice Monte Carlo dynamics model
    • Milik M, Skolnick J (1993) Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins 15:10-25
    • (1993) Proteins , vol.15 , pp. 10-25
    • Milik, M.1    Skolnick, J.2
  • 34
    • 0021474573 scopus 로고
    • Mattress model of lipid-protein interactions in membranes
    • Mouritsen OG, Bloom M (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
  • 35
    • 35448979574 scopus 로고    scopus 로고
    • The role of electrostatic and nonpolar interactions in the association of peripheral proteins with membranes
    • Simon S, McIntosh T (eds). Academic Press, San Diego
    • Murray D, Arbuzova A, Honig B, McLaughlin S (2002) The role of electrostatic and nonpolar interactions in the association of peripheral proteins with membranes. In: Simon S, McIntosh T (eds) Current topics in membranes, vol 52: peptide-lipid interactions. Academic Press, San Diego, pp 271-302
    • (2002) Current Topics in Membranes, Vol 52: Peptide-lipid Interactions , vol.52 , pp. 271-302
    • Murray, D.1    Arbuzova, A.2    Honig, B.3    McLaughlin, S.4
  • 36
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls A, Honig B (1991) A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem 12:435-445
    • (1991) J Comput Chem , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 37
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A, Sharp KA, Honig B (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11:281-296
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 39
    • 0034823225 scopus 로고    scopus 로고
    • The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers
    • Pitera JW, van Gunsteren WF (2001) The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers. J Am Chem Soc 123:3163-3164
    • (2001) J Am Chem Soc , vol.123 , pp. 3163-3164
    • Pitera, J.W.1    Van Gunsteren, W.F.2
  • 40
    • 0027817476 scopus 로고
    • Structure and function of channel-forming peptaibols
    • Sansom MS (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.1
  • 41
    • 0032054195 scopus 로고    scopus 로고
    • Models and simulations of ion channels and related membrane proteins
    • Sansom MS (1998) Models and simulations of ion channels and related membrane proteins. Curr Opin Struct Biol 8:237-244
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 237-244
    • Sansom, M.S.1
  • 42
    • 32844457567 scopus 로고
    • Acurate calculations of hydration free energies using macroscopic solvent models
    • Sitkoff D, Sharp K, Honig B (1994) Acurate calculations of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978-1988
    • (1994) J Phys Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.2    Honig, B.3
  • 43
    • 33748640631 scopus 로고    scopus 로고
    • Calculation of alkane to water solvation free energies using continuum solvent models
    • Sitkoff D, Ben-Tal N, Honig B (1996) Calculation of alkane to water solvation free energies using continuum solvent models. J Phys Chem 100:2744-2752
    • (1996) J Phys Chem , vol.100 , pp. 2744-2752
    • Sitkoff, D.1    Ben-Tal, N.2    Honig, B.3
  • 44
    • 0035811210 scopus 로고    scopus 로고
    • Molecular dynamics simulations of antimicrobial peptides: From membrane binding to transmembrane channels
    • Tieleman DP, Sansom MSP (2001) Molecular dynamics simulations of antimicrobial peptides: from membrane binding to transmembrane channels. Int J Quantum Chem 83:166-179
    • (2001) Int J Quantum Chem , vol.83 , pp. 166-179
    • Tieleman, D.P.1    Sansom, M.S.P.2
  • 45
    • 0032534843 scopus 로고    scopus 로고
    • Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: Molecular dynamics simulations
    • Tieleman DP, Forrest LR, Sansom MS, Berendsen HJ (1998) Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations. Biochemistry 37:17554-17561
    • (1998) Biochemistry , vol.37 , pp. 17554-17561
    • Tieleman, D.P.1    Forrest, L.R.2    Sansom, M.S.3    Berendsen, H.J.4
  • 46
    • 0033035249 scopus 로고    scopus 로고
    • An alamethicin channel in a lipid bilayer: Molecular dynamics simulations
    • Tieleman DP, Berendsen HJ, Sansom MS (1999) An alamethicin channel in a lipid bilayer: molecular dynamics simulations. Biophys J 76:1757-1769
    • (1999) Biophys J , vol.76 , pp. 1757-1769
    • Tieleman, D.P.1    Berendsen, H.J.2    Sansom, M.S.3
  • 47
    • 0036841855 scopus 로고    scopus 로고
    • Analysis and evaluation of channel models: Simulations of alamethicin
    • Tieleman DP, Hess B, Sansom MSP (2002) Analysis and evaluation of channel models: simulations of alamethicin. Biophys J 83:2393-2407
    • (2002) Biophys J , vol.83 , pp. 2393-2407
    • Tieleman, D.P.1    Hess, B.2    Sansom, M.S.P.3
  • 48
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: Physical principles
    • White SH, Wimley WC (1999) Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct 28:319-365
    • (1999) Annu Rev Biophys Biomol Struct , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.