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Volumn 76, Issue 5, 1999, Pages 2448-2459

A solvent model for simulations of peptides in bilayers. I. Membrane- promoting α-helix formation

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOHEXANE; GLYCINE; ISOLEUCINE; LEUCINE; MEMBRANE PROTEIN; OCTANOL; PEPTIDE; SOLVENT; VALINE; WATER;

EID: 0032991265     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77400-X     Document Type: Article
Times cited : (57)

References (51)
  • 1
    • 0029847652 scopus 로고    scopus 로고
    • Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching
    • Adams, P. D., D. M. Engelman, and A. T. Brúnger. 1996. Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching. Proteins. 26:257-261.
    • (1996) Proteins , vol.26 , pp. 257-261
    • Adams, P.D.1    Engelman, D.M.2    Brúnger, A.T.3
  • 2
    • 0029762032 scopus 로고    scopus 로고
    • Insertion and hairpin formation of membrane proteins: A Monte Carlo study
    • Baumgärtner, A. 1996. Insertion and hairpin formation of membrane proteins: a Monte Carlo study. Biophys. J. 71:1248-1255.
    • (1996) Biophys. J. , vol.71 , pp. 1248-1255
    • Baumgärtner, A.1
  • 3
    • 0029669955 scopus 로고    scopus 로고
    • Free energy determinants of α-helix insertion into lipid bilayers
    • Ben-Tal, N., A. Ben-Shaul, A. Nicholls, and B. Honig. 1996. Free energy determinants of α-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
  • 4
    • 0027236794 scopus 로고
    • Structural basis of amino acid α-helix propensity
    • Blaber, M., X.-J. Zhang, and B. W. Matthews. 1993. Structural basis of amino acid α-helix propensity. Science. 260:1637-1643.
    • (1993) Science , vol.260 , pp. 1637-1643
    • Blaber, M.1    Zhang, X.-J.2    Matthews, B.W.3
  • 5
    • 0027098088 scopus 로고
    • An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin
    • Chou, K.-C., L. Carlacci, G. M. Maggiora, L. A. Parodi, and M. W. Schulz. 1992. An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin. Protein Sci. 1:810-827.
    • (1992) Protein Sci. , vol.1 , pp. 810-827
    • Chou, K.-C.1    Carlacci, L.2    Maggiora, G.M.3    Parodi, L.A.4    Schulz, M.W.5
  • 6
    • 0028863592 scopus 로고
    • Atomic solvation parameters in the analysis of protein-protein docking results
    • Cummings, M. D., T. N. Hart, and R. J. Read. 1995. Atomic solvation parameters in the analysis of protein-protein docking results. Protein Sci. 4:2087-2099.
    • (1995) Protein Sci. , vol.4 , pp. 2087-2099
    • Cummings, M.D.1    Hart, T.N.2    Read, R.J.3
  • 7
    • 0029766187 scopus 로고    scopus 로고
    • Folding proteins into membranes
    • Deber, C. M., and N. K. Goto. 1996. Folding proteins into membranes. Nat. Struct. Biol. 3:815-818.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 815-818
    • Deber, C.M.1    Goto, N.K.2
  • 8
    • 0029153215 scopus 로고
    • Peptides in membranes: Helicity and hydrophobicity
    • Deber, C. M., and S.-C. Li. 1995. Peptides in membranes: helicity and hydrophobicity. Biopolymers. 37:295-318.
    • (1995) Biopolymers , vol.37 , pp. 295-318
    • Deber, C.M.1    Li, S.-C.2
  • 9
    • 0000341366 scopus 로고
    • Molecular dynamics simulation of galanin in aqueous and non-aqueous solution
    • De Loof, H., L. Nilsson, and R. Rigler. 1992. Molecular dynamics simulation of galanin in aqueous and non-aqueous solution. J. Am. Chem. Soc. 114:4028-4035.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 4028-4035
    • De Loof, H.1    Nilsson, L.2    Rigler, R.3
  • 10
    • 0032032107 scopus 로고    scopus 로고
    • IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies
    • Ducarme, P., N. Rahman, and R. Brasseur. 1998. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins. 30:357-371.
    • (1998) Proteins , vol.30 , pp. 357-371
    • Ducarme, P.1    Rahman, N.2    Brasseur, R.3
  • 11
    • 0024288356 scopus 로고
    • The structure of a membrane-spanning polypeptide studied by molecular dynamics
    • Edholm, O., and F. Jahnig. 1988. The structure of a membrane-spanning polypeptide studied by molecular dynamics. Biophys. Chem. 30: 279-292.
    • (1988) Biophys. Chem. , vol.30 , pp. 279-292
    • Edholm, O.1    Jahnig, F.2
  • 12
    • 0027768907 scopus 로고
    • Environmental properties of residues in proteins
    • Efremov, R. G., and A. J. P. Alix. 1993. Environmental properties of residues in proteins. J. Biomol. Struct. Dyn. 6:483-507.
    • (1993) J. Biomol. Struct. Dyn. , vol.6 , pp. 483-507
    • Efremov, R.G.1    Alix, A.J.P.2
  • 13
    • 0000717364 scopus 로고
    • Hydrophobic nature of membrane-spanning α-helical peptides as revealed by Monte Carlo simulations and molecular hydrophobicity potential analysis
    • Efremov, R. G., and G. Vergoten. 1995. Hydrophobic nature of membrane-spanning α-helical peptides as revealed by Monte Carlo simulations and molecular hydrophobicity potential analysis. J. Phys. Chem. 99: 10658-10666.
    • (1995) J. Phys. Chem. , vol.99 , pp. 10658-10666
    • Efremov, R.G.1    Vergoten, G.2
  • 14
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg, D., and A. D. McLachlan. 1986. Solvation energy in protein folding and binding. Nature (Lond.). 319:199-203.
    • (1986) Nature (Lond.) , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 15
    • 0029970351 scopus 로고    scopus 로고
    • An efficient solvation force model for use in molecular dynamics simulations of proteins in aqueous solution
    • Fraternali, F., and W. F. van Gunsteren. 1996. An efficient solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. J. Mol. Biol. 256:939-948.
    • (1996) J. Mol. Biol. , vol.256 , pp. 939-948
    • Fraternali, F.1    Van Gunsteren, W.F.2
  • 16
    • 0344046737 scopus 로고
    • Computational studies of protein adsorption at bilayer interfaces
    • Gersappe, D., W. Li, and A. C. Balazs. 1993. Computational studies of protein adsorption at bilayer interfaces. J. Chem. Phys. 99:7209-7213.
    • (1993) J. Chem. Phys. , vol.99 , pp. 7209-7213
    • Gersappe, D.1    Li, W.2    Balazs, A.C.3
  • 17
    • 0005434387 scopus 로고
    • Simulation of water around a model protein helix. 2. The relative contributions of packing, hydrophobicity, and hydrogen bonding
    • Gerstein, M., and R. M. Lynden-Bell. 1993. Simulation of water around a model protein helix. 2. The relative contributions of packing, hydrophobicity, and hydrogen bonding. J. Phys. Chem. 97:2991-2999.
    • (1993) J. Phys. Chem. , vol.97 , pp. 2991-2999
    • Gerstein, M.1    Lynden-Bell, R.M.2
  • 18
    • 84988109729 scopus 로고
    • Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity
    • Ghose, A. K., and G. M. Crippen. 1986. Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity. J. Comput. Chem. 7:565-577.
    • (1986) J. Comput. Chem. , vol.7 , pp. 565-577
    • Ghose, A.K.1    Crippen, G.M.2
  • 19
    • 0024558250 scopus 로고
    • The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices
    • Jacobs, R. E., and S. H. White. 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
  • 20
    • 0026761782 scopus 로고
    • Modeling of the structure of bacteriorhodopsin. A molecular dynamics study
    • Jähnig, F., and O. Edholm. 1992. Modeling of the structure of bacteriorhodopsin. A molecular dynamics study. J. Mol. Biol. 226:837-850.
    • (1992) J. Mol. Biol. , vol.226 , pp. 837-850
    • Jähnig, F.1    Edholm, O.2
  • 21
    • 0028818570 scopus 로고
    • Comparison of atomic solvation parameters sets: Applicability and limitations in protein folding and design
    • Juffer, A., F. Eisenhaber, S. Hubbard, D. Walther, and P. Argos. 1995. Comparison of atomic solvation parameters sets: applicability and limitations in protein folding and design. Protein Sci. 4:2499-2509.
    • (1995) Protein Sci. , vol.4 , pp. 2499-2509
    • Juffer, A.1    Eisenhaber, F.2    Hubbard, S.3    Walther, D.4    Argos, P.5
  • 22
    • 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
  • 23
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., M. Billeter, and K. Wüthrich. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics. 14:51-55.
    • (1996) J. Mol. Graphics , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3
  • 24
    • 0028904088 scopus 로고
    • The effect of environment on the stability of an integral membrane helix: Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water
    • Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. J. Mol. Biol. 247:808-822.
    • (1995) J. Mol. Biol. , vol.247 , pp. 808-822
    • Kovacs, H.1    Mark, A.E.2    Johansson, J.3    Van Gunsteren, W.F.4
  • 26
    • 0030249150 scopus 로고    scopus 로고
    • Threshold hydrophobicity dictates helical conformations of peptides in membrane environments
    • Liu, L.-P., S.-C. Li, N. K. Goto, and C. M. Deber. 1996. Threshold hydrophobicity dictates helical conformations of peptides in membrane environments. Biopolymers. 39:465-470.
    • (1996) Biopolymers , vol.39 , pp. 465-470
    • Liu, L.-P.1    Li, S.-C.2    Goto, N.K.3    Deber, C.M.4
  • 28
    • 0027390459 scopus 로고
    • Insertion of peptide chains into lipid membranes: An off-lattice Monte Carlo dynamics model
    • Milik, M., and J. Skolnick. 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
  • 29
    • 0029099311 scopus 로고
    • A Monte Carlo model of fd and Pfl proteins in lipid membranes
    • Milik, M., and J. Skolnick. 1995. A Monte Carlo model of fd and Pfl proteins in lipid membranes. Biophys. J. 69:1382-1386.
    • (1995) Biophys. J. , vol.69 , pp. 1382-1386
    • Milik, M.1    Skolnick, J.2
  • 30
    • 33845550595 scopus 로고
    • Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
    • Némethy, G., M. S. Pottle, and H. A. Sheraga. 1983. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87:1883-1887.
    • (1983) J. Phys. Chem. , vol.87 , pp. 1883-1887
    • Némethy, G.1    Pottle, M.S.2    Sheraga, H.A.3
  • 31
    • 0025222978 scopus 로고
    • A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
    • O'Neil, K. T., and W. F. DeGrado. 1990. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science. 250:646-651.
    • (1990) Science , vol.250 , pp. 646-651
    • O'Neil, K.T.1    Degrado, W.F.2
  • 32
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • Ooi, T., M. Oobatake, G. Némethy, and H. A. Sheraga. 1987. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. USA. 84:3086-3090.
    • (1987) Proc. Natl. Acad. Sci. USA. , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Némethy, G.3    Sheraga, H.A.4
  • 34
    • 0026581661 scopus 로고
    • Refined structure of the pore-forming domain of colicin A at 2.4 Å resolution
    • Parker, M. W., J. P. M. Postma, F. Pattus, A. D. Tucker, and D. Tsernoglou. 1992. Refined structure of the pore-forming domain of colicin A at 2.4 Å resolution. J. Mol. Biol. 224:639-657.
    • (1992) J. Mol. Biol. , vol.224 , pp. 639-657
    • Parker, M.W.1    Postma, J.P.M.2    Pattus, F.3    Tucker, A.D.4    Tsernoglou, D.5
  • 35
    • 0028124519 scopus 로고
    • Molecular dynamics and Monte Carlo simulations of lipid bilayers
    • Pastor, R. W. 1994. Molecular dynamics and Monte Carlo simulations of lipid bilayers. Curr. Opin. Struct. Biol. 4:486-492.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 486-492
    • Pastor, R.W.1
  • 36
    • 0029926518 scopus 로고    scopus 로고
    • Dynamics of proteins in different solvent systems: Analysis of essential motion in lipases
    • Peters, G. H., D. M. F. van Aalten, O. Edholm, S. Toxvaerg, and R. Bywater. 1996. Dynamics of proteins in different solvent systems: analysis of essential motion in lipases. Biophys. J. 71:2245-2255.
    • (1996) Biophys. J. , vol.71 , pp. 2245-2255
    • Peters, G.H.1    Van Aalten, D.M.F.2    Edholm, O.3    Toxvaerg, S.4    Bywater, R.5
  • 37
    • 0028321565 scopus 로고
    • Molecular dynamics simulations of the gramicidin channel
    • Roux, B., and M. Karplus. 1994. Molecular dynamics simulations of the gramicidin channel. Annu. Rev. Biophys. Biomol. Struct. 23:731-761.
    • (1994) Annu. Rev. Biophys. Biomol. Struct. , vol.23 , pp. 731-761
    • Roux, B.1    Karplus, M.2
  • 38
    • 0027883012 scopus 로고
    • Protein structure prediction with a combined solvation free energy-molecular mechanics force field
    • Schiffer, C., J. W. Caldwell, P. A. Kollman, and R. M. Stroud. 1993. Protein structure prediction with a combined solvation free energy-molecular mechanics force field. Mol. Simul. 10:121-149.
    • (1993) Mol. Simul. , vol.10 , pp. 121-149
    • Schiffer, C.1    Caldwell, J.W.2    Kollman, P.A.3    Stroud, R.M.4
  • 39
    • 0344046729 scopus 로고
    • A two-lattice model of membrane proteins: Configuration as a function of sequence
    • Seagraves, C., and W. P. Reinhardt. 1995. A two-lattice model of membrane proteins: configuration as a function of sequence. J. Chem. Phys. 103:5091-5101.
    • (1995) J. Chem. Phys. , vol.103 , pp. 5091-5101
    • Seagraves, C.1    Reinhardt, W.P.2
  • 40
    • 0026076664 scopus 로고
    • Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models
    • Sharp, K. A., A. Nicholls, R. Friedman, and B. Honig. 1991. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry. 30:9686-9697.
    • (1991) Biochemistry , vol.30 , pp. 9686-9697
    • Sharp, K.A.1    Nicholls, A.2    Friedman, R.3    Honig, B.4
  • 41
    • 0027804108 scopus 로고
    • An effective solvation term based on atomic occupancies for use in protein simulations
    • Stouten, P. F. W., C. Frommel, H. Nakamura, and C. Sander. 1993. An effective solvation term based on atomic occupancies for use in protein simulations. Mol. Simul. 10:97-120.
    • (1993) Mol. Simul. , vol.10 , pp. 97-120
    • Stouten, P.F.W.1    Frommel, C.2    Nakamura, H.3    Sander, C.4
  • 42
    • 0030029471 scopus 로고    scopus 로고
    • Direct determination of the membrane affinities of individual amino acids
    • Thorgeirsson, T. E., C. J. Russel, D. S. King, and Y.-K. Shin. 1996. Direct determination of the membrane affinities of individual amino acids. Biochemistry. 35:1803-1809.
    • (1996) Biochemistry , vol.35 , pp. 1803-1809
    • Thorgeirsson, T.E.1    Russel, C.J.2    King, D.S.3    Shin, Y.-K.4
  • 43
    • 0025858688 scopus 로고
    • Molecular dynamics simulations of the unfolding of an α-helical analogue of ribonuclease A S-peptide in water
    • Tirado-Rives, J., and W. L. Jorgensen. 1991. Molecular dynamics simulations of the unfolding of an α-helical analogue of ribonuclease A S-peptide in water. Biochemistry. 30:3864-3871.
    • (1991) Biochemistry , vol.30 , pp. 3864-3871
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 44
    • 0027642798 scopus 로고
    • Molecular dynamics simulation of the stability of a 22-residue α-helix in water and 30% trifluoroethanol
    • van Buuren, A. R., and H. J. C. Berendsen. 1993. Molecular dynamics simulation of the stability of a 22-residue α-helix in water and 30% trifluoroethanol. Biopolymers. 33:1159-1166.
    • (1993) Biopolymers , vol.33 , pp. 1159-1166
    • Van Buuren, A.R.1    Berendsen, H.J.C.2
  • 45
    • 84986486657 scopus 로고
    • Efficient search for all low energy conformations of polypeptides by Monte Carlo methods
    • von Freyberg, B., and W. Braun. 1991. Efficient search for all low energy conformations of polypeptides by Monte Carlo methods. J. Comp. Chem. 12:1065-1076.
    • (1991) J. Comp. Chem. , vol.12 , pp. 1065-1076
    • Von Freyberg, B.1    Braun, W.2
  • 46
    • 0027432959 scopus 로고
    • Surface area included in energy refinement of proteins
    • von Freyberg, B., T. J. Richmond, and W. Braun. 1993. Surface area included in energy refinement of proteins. J. Mol. Biol. 233:275-292.
    • (1993) J. Mol. Biol. , vol.233 , pp. 275-292
    • Von Freyberg, B.1    Richmond, T.J.2    Braun, W.3
  • 48
    • 0025989688 scopus 로고
    • Do helices in membranes prefer to form bundles or stay dispersed in the lipid phase
    • Wang, J., and A. Pullman. 1991. Do helices in membranes prefer to form bundles or stay dispersed in the lipid phase. Biochim. Biophys. Acta. 1070:493-496.
    • (1991) Biochim. Biophys. Acta. , vol.1070 , pp. 493-496
    • Wang, J.1    Pullman, A.2
  • 49
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to molecular dynamics of proteins in solution
    • Wesson, L., and D. Eisenberg. 1992. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1:227-235.
    • (1992) Protein Sci. , vol.1 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2
  • 50
    • 0029738872 scopus 로고    scopus 로고
    • Experimentally determined hydrophobicity scale for proteins at membrane interfaces
    • Wimley, W. C, and S. H. White. 1996. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3:842-848.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 842-848
    • Wimley, W.C.1    White, S.H.2
  • 51
    • 0024381371 scopus 로고
    • Monte Carlo studies of lipid chains and gramicidin A in a model membrane
    • Xing, J., and H. L. Scott. 1989. Monte Carlo studies of lipid chains and gramicidin A in a model membrane. Biochem. Biophys. Res. Commun. 165:1-6.
    • (1989) Biochem. Biophys. Res. Commun. , vol.165 , pp. 1-6
    • Xing, J.1    Scott, H.L.2


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