메뉴 건너뛰기




Volumn 45, Issue 30, 2006, Pages 9053-9058

MD simulations of mistic: Conformational stability in detergent micelles and water

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; HYDROPHOBICITY; MICELLES; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; WATER;

EID: 33746657174     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0608818     Document Type: Article
Times cited : (18)

References (40)
  • 2
    • 0026504192 scopus 로고
    • A protein of the endoplasmic reticulum involved early in polypeptide translocation
    • Gorlich, D., Hartmann, E., Prehn, S., and Rapoport, T. A. (1992) A protein of the endoplasmic reticulum involved early in polypeptide translocation, Nature 357, 47-52.
    • (1992) Nature , vol.357 , pp. 47-52
    • Gorlich, D.1    Hartmann, E.2    Prehn, S.3    Rapoport, T.A.4
  • 3
    • 0026466143 scopus 로고
    • A mammalian homolog of SEC61p and SECYp is associated with ribosomes and nascent polypeptides during translocation
    • Gorlich, D., Prehn, S., Hartmann, E., Kalies, K. U., and Rapoport, T. A. (1992) A mammalian homolog of SEC61p and SECYp is associated with ribosomes and nascent polypeptides during translocation, Cell 71, 489-503.
    • (1992) Cell , vol.71 , pp. 489-503
    • Gorlich, D.1    Prehn, S.2    Hartmann, E.3    Kalies, K.U.4    Rapoport, T.A.5
  • 5
    • 14544292475 scopus 로고    scopus 로고
    • NMR structure of Mistic, a membrane-integrating protein for membrane protein expression
    • Roosild, T. P., Greenwald, J., Vega, M., Castronovo, S., Riek, R., and Choe, S. (2005) NMR structure of Mistic, a membrane-integrating protein for membrane protein expression, Science 307, 1317-1321.
    • (2005) Science , vol.307 , pp. 1317-1321
    • Roosild, T.P.1    Greenwald, J.2    Vega, M.3    Castronovo, S.4    Riek, R.5    Choe, S.6
  • 6
    • 0035979797 scopus 로고    scopus 로고
    • Overexpression of mammalian integral membrane proteins for structural studies
    • Tate, C. G. (2001) Overexpression of mammalian integral membrane proteins for structural studies, FEBS. Lett. 504, 94-98.
    • (2001) FEBS. Lett. , vol.504 , pp. 94-98
    • Tate, C.G.1
  • 7
    • 0035980050 scopus 로고    scopus 로고
    • Detergents as tools in membrane biochemistry
    • Garavito, R., and Ferguson-Miller, S. (2001) Detergents as tools in membrane biochemistry, J. Biol. Chem. 276, 32403-32406.
    • (2001) J. Biol. Chem. , vol.276 , pp. 32403-32406
    • Garavito, R.1    Ferguson-Miller, S.2
  • 8
    • 0035795721 scopus 로고    scopus 로고
    • Amino acid distributions in integral membrane protein structures
    • Ulmschneider, M. B., and Sansom, M. S. P. (2001) Amino acid distributions in integral membrane protein structures, Biochim. Biophys. Acta 1512, 1-14.
    • (2001) Biochim. Biophys. Acta , vol.1512 , pp. 1-14
    • Ulmschneider, M.B.1    Sansom, M.S.P.2
  • 9
    • 21744454309 scopus 로고    scopus 로고
    • Transmembrane helix prediction: A comparative evaluation and analysis
    • Cuthbertson, J. M., Doyle, D. A., and Sansom, M. S. P. (2005) Transmembrane helix prediction: a comparative evaluation and analysis, Protein Eng. Des. Sel. 18, 295-308.
    • (2005) Protein Eng. Des. Sel. , vol.18 , pp. 295-308
    • Cuthbertson, J.M.1    Doyle, D.A.2    Sansom, M.S.P.3
  • 10
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M. J., and McCammon, J. A. (2002) Molecular dynamics simulations of biomolecules, Nat. Struct. Biol. 9, 646-652.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.J.1    McCammon, J.A.2
  • 11
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods for simulating the activity of proteins
    • Adcock, S. A., and McCammon, J. A. (2006) Molecular dynamics: survey of methods for simulating the activity of proteins, Chem. Rev. 106, 1589-1615.
    • (2006) Chem. Rev. , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 12
    • 7044224837 scopus 로고    scopus 로고
    • Computer simulations of membrane proteins, Biochim
    • Ash, W. L., Zlomislic, M. R., Oloo, E. O., and Tieleman, D. P. (2004) Computer simulations of membrane proteins, Biochim. Biophys. Acta 1666, 158-189.
    • (2004) Biophys. Acta , vol.1666 , pp. 158-189
    • Ash, W.L.1    Zlomislic, M.R.2    Oloo, E.O.3    Tieleman, D.P.4
  • 13
    • 0038724257 scopus 로고    scopus 로고
    • Membrane protein dynamics vs. environment: Simulations of OmpA in a micelle and in a bilayer
    • Bond, P. J., and Sansom, M. S. P. (2003) Membrane protein dynamics vs. environment: simulations of OmpA in a micelle and in a bilayer, J. Mol. Biol. 329, 1035-1053.
    • (2003) J. Mol. Biol. , vol.329 , pp. 1035-1053
    • Bond, P.J.1    Sansom, M.S.P.2
  • 14
    • 12344261864 scopus 로고    scopus 로고
    • Molecular dynamics simulations of G1pF in a micelle vs. in a bilayer: Conformational dynamics of a membrane protein as a function of environment
    • Patargias, G., Bond, P. J., Deol, S. D., and Sansom, M. S. P. (2005) Molecular dynamics simulations of G1pF in a micelle vs. in a bilayer: conformational dynamics of a membrane protein as a function of environment, J. Phys. Chem. B 109, 575-582.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 575-582
    • Patargias, G.1    Bond, P.J.2    Deol, S.D.3    Sansom, M.S.P.4
  • 15
    • 10344247720 scopus 로고    scopus 로고
    • MD simulations of spontaneous membrane protein/detergent micelle formation
    • Bond, P. J., Cuthbertson, J. M., Deol, S. D., and Sansom, M. S. P. (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.D.3    Sansom, M.S.P.4
  • 16
    • 4143150532 scopus 로고    scopus 로고
    • Molecular dynamics simulations of micelle formation around dimeric Glycophorin a transmembrane helices
    • Braun, R., Engelman, D. M., and Schulten, K. (2004) Molecular dynamics simulations of micelle formation around dimeric Glycophorin A transmembrane helices, Biophys. J. 87, 754-763.
    • (2004) Biophys. J. , vol.87 , pp. 754-763
    • Braun, R.1    Engelman, D.M.2    Schulten, K.3
  • 17
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., Hess, B., and van der Spoel, D. (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
  • 20
    • 33846823909 scopus 로고
    • Particle mesh Ewald - An N log(N) method for Ewald sums in large systems
    • Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald - an N log(N) method for Ewald sums in large systems, J. Chem. Phys. 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 23
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess, B., Bekker, H., Berendsen, H. J. C., and Fraaije, J. G. E. M. (1997) LINCS: A linear constraint solver for molecular simulations, J. Comput. Chem. 18, 1463-1472.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.G.E.M.4
  • 24
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern-recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and Sander, C. (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
  • 26
    • 0034567210 scopus 로고    scopus 로고
    • Comparative protein structure modeling. Introduction and practical examples with modeller
    • Sanchez, R., and Sali, A. (2000) Comparative protein structure modeling. Introduction and practical examples with modeller, Methods Mol. Biol. 143, 97-129.
    • (2000) Methods Mol. Biol. , vol.143 , pp. 97-129
    • Sanchez, R.1    Sali, A.2
  • 28
    • 0030158429 scopus 로고    scopus 로고
    • PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
    • van Aalten, D. M., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., and Vriend, G. (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules, J. Comput.-Aided Mol. Des. 10, 255-262.
    • (1996) J. Comput.-Aided Mol. Des. , vol.10 , pp. 255-262
    • Van Aalten, D.M.1    Bywater, R.2    Findlay, J.B.3    Hendlich, M.4    Hooft, R.W.5    Vriend, G.6
  • 29
    • 0007229077 scopus 로고
    • Micellar properties of some zwitterionic surfactants
    • Herrmann, K. W. (1966) Micellar properties of some zwitterionic surfactants, J. Colloid Interface Sci. 22, 352-359.
    • (1966) J. Colloid Interface Sci. , vol.22 , pp. 352-359
    • Herrmann, K.W.1
  • 30
    • 0034229640 scopus 로고    scopus 로고
    • Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: Micellar structure and chain relaxation
    • Tieleman, D. P., van der Spoel, D., and Berendsen, H. J. C. (2000) Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: Micellar structure and chain relaxation, J. Phys. Chem. B 104, 6380-6388.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6380-6388
    • Tieleman, D.P.1    Van Der Spoel, D.2    Berendsen, H.J.C.3
  • 31
    • 0033718963 scopus 로고    scopus 로고
    • Molecular dynamics simulations of octyl glucoside micelles: Structural properties
    • Bogusz, S., Venable, R. M., and Pastor, R. W. (2000) Molecular dynamics simulations of octyl glucoside micelles: Structural properties, J. Phys. Chem. B 104, 5462-5470.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 5462-5470
    • Bogusz, S.1    Venable, R.M.2    Pastor, R.W.3
  • 32
    • 0035818094 scopus 로고    scopus 로고
    • Molecular dynamics simulations of octyl glucoside micelles: Dynamic properties
    • Bogusz, S., Venable, R. M., and Pastor, R. W. (2001) Molecular dynamics simulations of octyl glucoside micelles: Dynamic properties, J. Phys. Chem. B 105, 8312-8321.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 8312-8321
    • Bogusz, S.1    Venable, R.M.2    Pastor, R.W.3
  • 33
    • 12344269582 scopus 로고    scopus 로고
    • Molecular dynamics studies of sodium dodecyl sulfate aggregation about glycophorin-A transmembrane domain
    • Braun, R., and Schulten, K. (2004) Molecular dynamics studies of sodium dodecyl sulfate aggregation about glycophorin-A transmembrane domain, Biophys. J. 86, 560A.
    • (2004) Biophys. J. , vol.86
    • Braun, R.1    Schulten, K.2
  • 34
    • 17844410935 scopus 로고    scopus 로고
    • Spontaneous formation of detergent micelles around the outer membrane protein OmpX
    • Böckmann, R. A., and Caflisch, A. (2005) Spontaneous formation of detergent micelles around the outer membrane protein OmpX, Biophys. J. 86, 3191-3204.
    • (2005) Biophys. J. , vol.86 , pp. 3191-3204
    • Böckmann, R.A.1    Caflisch, A.2
  • 35
    • 0026050639 scopus 로고
    • Crystal structure of insecticidal δ endotoxin from Bacillus thuringiensis at 2.5 Å resolution
    • Li, J., Carroll, J., and Ellar, D. J. (1991) Crystal structure of insecticidal δ endotoxin from Bacillus thuringiensis at 2.5 Å resolution, Nature 353, 815-821.
    • (1991) Nature , vol.353 , pp. 815-821
    • Li, J.1    Carroll, J.2    Ellar, D.J.3
  • 37
    • 17844379740 scopus 로고    scopus 로고
    • Structure and dynamics of model pore insertion into a membrane
    • Lopez, C. F., Nielsen, S. O., Ensing, B., Moore, P. B., and Klein, M. L. (2005) Structure and dynamics of model pore insertion into a membrane, Biophys. J. 88, 3083-3094.
    • (2005) Biophys. J. , vol.88 , pp. 3083-3094
    • Lopez, C.F.1    Nielsen, S.O.2    Ensing, B.3    Moore, P.B.4    Klein, M.L.5
  • 38
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and assembly of membrane proteins via simulation
    • Bond, P. J., and Sansom, M. S. P. (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.P.2
  • 39
    • 1642525904 scopus 로고    scopus 로고
    • Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods
    • Kastenholz, M. A., and Hünenberger, P. H. (2004) Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods, J. Phys. Chem. B 108, 774-788.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 774-788
    • Kastenholz, M.A.1    Hünenberger, P.H.2
  • 40
    • 12144275299 scopus 로고    scopus 로고
    • Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
    • Beck, D. A. C., Armen, R. S., and Daggett, V. (2005) Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides, Biochemistry 44, 609-616.
    • (2005) Biochemistry , vol.44 , pp. 609-616
    • Beck, D.A.C.1    Armen, R.S.2    Daggett, V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.