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Volumn 51, Issue 6, 2012, Pages 1061-1069

Molecular dynamics simulation of the unfolding of individual bacteriorhodopsin helices in sodium dodecyl sulfate micelles

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; CHARGED RESIDUES; IN-SILICO; IN-VITRO; MOLECULAR DYNAMICS SIMULATIONS; PARTIAL DENATURATION; POLAR GROUPS; SAMPLING TIME; SECONDARY STRUCTURES; SIMULATION TIME; SODIUM DODECYL SULFATE MICELLES; STRUCTURAL INSTABILITY; STRUCTURAL PERTURBATION; TRANSMEMBRANE SEGMENTS;

EID: 84856846248     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201770y     Document Type: Article
Times cited : (18)

References (53)
  • 3
    • 0029943869 scopus 로고    scopus 로고
    • Retinal binding during folding and assembly of the membrane protein bacteriorhodopsin
    • DOI 10.1021/bi960129e
    • Booth, P. J., Farooq, A., and Flitsch, S. L. (1996) Retinal binding during folding and assembly of the membrane protein bacteriorhodopsin Biochemistry 35, 5902-5909 (Pubitemid 26143684)
    • (1996) Biochemistry , vol.35 , Issue.18 , pp. 5902-5909
    • Booth, P.J.1    Farooq, A.2    Flitsch, S.L.3
  • 4
    • 0030010795 scopus 로고    scopus 로고
    • Dual roles of DMPC and CHAPS in the refolding of bacterial opsins in vitro
    • Sugiyama, Y. and Mukohata, Y. (1996) Dual roles of DMPC and CHAPS in the refolding of bacterial opsins in vitro J. Biochem. 119, 1143-1149 (Pubitemid 26202629)
    • (1996) Journal of Biochemistry , vol.119 , Issue.6 , pp. 1143-1149
    • Sugiyama, Y.1    Mukohata, Y.2
  • 6
    • 0031302710 scopus 로고    scopus 로고
    • Folding α-helical membrane proteins: Kinetic studies on bacteriorhodopsin
    • Booth, P. J. (1997) Folding α-helical membrane proteins: Kinetic studies on bacteriorhodopsin Folding Des. 2, R85-R92
    • (1997) Folding Des. , vol.2
    • Booth, P.J.1
  • 7
    • 0031012140 scopus 로고    scopus 로고
    • Slow α helix formation during folding of a membrane protein
    • DOI 10.1021/bi962199r
    • Riley, M. L., Wallace, B. A., Flitsch, S. L., and Booth, P. J. (1997) Slow α helix formation during folding of a membrane protein Biochemistry 36, 192-196 (Pubitemid 27024692)
    • (1997) Biochemistry , vol.36 , Issue.1 , pp. 192-196
    • Riley, M.L.1    Wallace, B.A.2    Flitsch, S.L.3    Booth, P.J.4
  • 8
    • 0033587549 scopus 로고    scopus 로고
    • Modulation of folding and assembly of the membrane protein bacteriorhodopsin by intermolecular forces within the lipid bilayer
    • Curran, A. R., Templer, R. H., and Booth, P. J. (1999) Modulation of folding and assembly of the membrane protein bacteriorhodopsin by intermolecular forces within the lipid bilayer Biochemistry 38, 9328-9336
    • (1999) Biochemistry , vol.38 , pp. 9328-9336
    • Curran, A.R.1    Templer, R.H.2    Booth, P.J.3
  • 9
    • 0034716941 scopus 로고    scopus 로고
    • The final stages of folding of the membrane protein bacteriorhodopsin occur by kinetically indistinguishable parallel folding paths that are mediated by pH
    • Lu, H. and Booth, P. J. (2000) The final stages of folding of the membrane protein bacteriorhodopsin occur by kinetically indistinguishable parallel folding paths that are mediated by pH J. Mol. Biol. 299, 233-243
    • (2000) J. Mol. Biol. , vol.299 , pp. 233-243
    • Lu, H.1    Booth, P.J.2
  • 10
    • 0035957523 scopus 로고    scopus 로고
    • Structure and function in bacteriorhodopsin: The effect of the interhelical loops on the protein folding kinetics
    • DOI 10.1006/jmbi.2001.4604
    • Allen, S. J., Kim, J. M., Khorana, H. G., Lu, H., and Booth, P. J. (2001) Structure and function in bacteriorhodopsin: The effect of the interhelical loops on the protein folding kinetics J. Mol. Biol. 308, 423-435 (Pubitemid 33043579)
    • (2001) Journal of Molecular Biology , vol.308 , Issue.2 , pp. 423-435
    • Allen, S.J.1    Kim, J.-M.2    Khorana, H.G.3    Lu, H.4    Booth, P.J.5
  • 11
    • 33644772377 scopus 로고    scopus 로고
    • Kinetics of an individual transmembrane helix during bacteriorhodopsin folding
    • DOI 10.1016/j.jmb.2005.12.042, PII S0022283605016141
    • Compton, E. L., Farmer, N. A., Lorch, M., Mason, J. M., Moreton, K. M., and Booth, P. J. (2006) Kinetics of an individual transmembrane helix during bacteriorhodopsin folding J. Mol. Biol. 357, 325-338 (Pubitemid 43339334)
    • (2006) Journal of Molecular Biology , vol.357 , Issue.1 , pp. 325-338
    • Compton, E.L.R.1    Farmer, N.A.2    Lorch, M.3    Mason, J.M.4    Moreton, K.M.5    Booth, P.J.6
  • 12
    • 0035957526 scopus 로고    scopus 로고
    • Proline residues in transmembrane α helices affect the folding of bacteriorhodopsin
    • DOI 10.1006/jmbi.2001.4605
    • Lu, H., Marti, T., and Booth, P. J. (2001) Proline residues in transmembrane α helices affect the folding of bacteriorhodopsin J. Mol. Biol. 308, 437-446 (Pubitemid 33043580)
    • (2001) Journal of Molecular Biology , vol.308 , Issue.2 , pp. 437-446
    • Lu, H.1    Marti, T.2    Booth, P.J.3
  • 13
    • 0019887931 scopus 로고
    • Refolding of an integral membrane protein. Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments
    • Huang, K. S., Bayley, H., Liao, M. J., London, E., and Khorana, H. G. (1981) Refolding of an integral membrane protein. Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments J. Biol. Chem. 256, 3802-3809
    • (1981) J. Biol. Chem. , vol.256 , pp. 3802-3809
    • Huang, K.S.1    Bayley, H.2    Liao, M.J.3    London, E.4    Khorana, H.G.5
  • 15
    • 70449687854 scopus 로고    scopus 로고
    • Mapping the structure of an integral membrane protein under semi-denaturing conditions by laser-induced oxidative labeling and mass spectrometry
    • Pan, Y., Brown, L., and Konermann, L. (2009) Mapping the structure of an integral membrane protein under semi-denaturing conditions by laser-induced oxidative labeling and mass spectrometry J. Mol. Biol. 394, 968-981
    • (2009) J. Mol. Biol. , vol.394 , pp. 968-981
    • Pan, Y.1    Brown, L.2    Konermann, L.3
  • 16
    • 13844299352 scopus 로고    scopus 로고
    • Solution structure of human saposin C in a detergent environment
    • DOI 10.1016/j.jmb.2004.12.045
    • Hawkins, C. A., de Alba, E., and Tjandra, N. (2005) Solution structure of human saposin C in a detergent environment J. Mol. Biol. 346, 1381-1392 (Pubitemid 40248836)
    • (2005) Journal of Molecular Biology , vol.346 , Issue.5 , pp. 1381-1392
    • Hawkins, C.A.1    De Alba, E.2    Tjandra, N.3
  • 17
    • 0017335799 scopus 로고
    • Crystallographic studies of protein denaturation and renaturation. II. Sodium dodecyl sulfate induced structural changes in triclinic lysozyme
    • Yonath, A., Podjarny, A., Honig, B., Sielecki, A., and Traub, W. (1977) Crystallographic studies of protein denaturation and renaturation. 2. Sodium dodecyl sulfate induced structural changes in triclinic lysozyme Biochemistry 16, 1418-1424 (Pubitemid 8083113)
    • (1977) Biochemistry , vol.16 , Issue.7 , pp. 1418-1424
    • Yonath, A.1    Podjarny, A.2    Honig, B.3
  • 18
    • 79955574923 scopus 로고    scopus 로고
    • version 1.3r1 () Schrodinger, LLC, New York.
    • The PyMOL Molecular Graphics System, version 1.3r1 (2010) Schrodinger, LLC, New York.
    • (2010) The PyMOL Molecular Graphics System
  • 19
    • 33846352840 scopus 로고    scopus 로고
    • Dynamics of the nitroxide side chain in spin-labeled proteins
    • DOI 10.1021/jp0629487
    • Tombolato, F., Ferrarini, A., and Freed, J. H. (2006) Dynamics of the nitroxide side chain in spin-labeled proteins J. Phys. Chem. B 110, 26248-26259 (Pubitemid 46133346)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.51 , pp. 26248-26259
    • Tombolato, F.1    Ferrarini, A.2    Freed, J.H.3
  • 21
    • 0026654787 scopus 로고
    • Proton transfer and energy coupling in the bacteriorhodopsin photocycle
    • Lanyi, J. K. (1992) Proton transfer and energy coupling in the bacteriorhodopsin photocycle J. Bioenerg. Biomembr. 24, 169-179
    • (1992) J. Bioenerg. Biomembr. , vol.24 , pp. 169-179
    • Lanyi, J.K.1
  • 23
    • 0024278712 scopus 로고
    • Bacteriorhodopsin, a Membrane-Protein That Uses Light to Translocate Protons
    • Khorana, H. G. (1988) Bacteriorhodopsin, a Membrane-Protein That Uses Light to Translocate Protons J. Biol. Chem. 263, 7439-7442
    • (1988) J. Biol. Chem. , vol.263 , pp. 7439-7442
    • Khorana, H.G.1
  • 26
    • 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
  • 29
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. (1985) Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 31, 1695-1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 30
    • 85024083583 scopus 로고    scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosé, S. (2002) A molecular dynamics method for simulations in the canonical ensemble Mol. Phys. 100, 191-198
    • (2002) Mol. Phys. , vol.100 , pp. 191-198
    • Nosé, S.1
  • 31
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • DOI 10.1063/1.328693
    • Parrinello, M. and Rahman, A. (1981) Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 52, 7182-7190 (Pubitemid 12456820)
    • (1981) Journal of Applied Physics , vol.52 , Issue.12 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 33
    • 38749123962 scopus 로고    scopus 로고
    • P-LINCS: A parallel linear constraint solver for molecular simulation
    • Hess, B. (2008) P-LINCS: A parallel linear constraint solver for molecular simulation J. Chem. Theory Comput. 4, 116-122
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 116-122
    • Hess, B.1
  • 35
    • 0343614206 scopus 로고    scopus 로고
    • A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field
    • van der Spoel, D., van Maaren, P. J., and Berendsen, H. J. C. (1998) A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field J. Chem. Phys. 108, 10220-10230 (Pubitemid 128611093)
    • (1998) Journal of Chemical Physics , vol.108 , Issue.24 , pp. 10220-10230
    • Van Der Spoel, D.1    Van Maaren, P.J.2    Berendsen, H.J.C.3
  • 36
    • 35548982245 scopus 로고    scopus 로고
    • Structural properties of ionic detergent aggregates: A large-scale molecular dynamics study of sodium dodecyl sulfate
    • DOI 10.1021/jp072587a
    • Sammalkorpi, M., Karttunen, M., and Haataja, M. (2007) Structural properties of ionic detergent aggregates: A large-scale molecular dynamics study of sodium dodecyl sulfate J. Phys. Chem. B 111, 11722-11733 (Pubitemid 350010875)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.40 , pp. 11722-11733
    • Sammalkorpi, M.1    Karttunen, M.2    Haataja, M.3
  • 37
    • 0001480302 scopus 로고    scopus 로고
    • Simulation of sodium dodecyl sulfate at the water-vapor and water-carbon tetrachloride interfaces at low surface coverage
    • Schweighofer, K. J., Essmann, U., and Berkowitz, M. (1997) Simulation of sodium dodecyl sulfate at the water-vapor and water-carbon tetrachloride interfaces at low surface coverage J. Phys. Chem. B 101, 3793-3799 (Pubitemid 127581134)
    • (1997) Journal of Physical Chemistry B , vol.101 , Issue.19 , pp. 3793-3799
    • Schweighofer, K.J.1    Essmann, U.2    Berkowitz, M.3
  • 40
    • 1842687947 scopus 로고    scopus 로고
    • Role of counterion concentration in determining micelle aggregation: Evaluation of the combination of constraints from small-angle neutron scattering, electron paramagnetic resonance, and time-resolved fluorescence quenching
    • Griffiths, P. C., Paul, A., Heenan, R. K., Penfold, J., Ranganathan, R., and Bales, B. L. (2004) Role of counterion concentration in determining micelle aggregation: Evaluation of the combination of constraints from small-angle neutron scattering, electron paramagnetic resonance, and time-resolved fluorescence quenching J. Phys. Chem. B 108, 3810-3816
    • (2004) J. Phys. Chem. B , vol.108 , pp. 3810-3816
    • Griffiths, P.C.1    Paul, A.2    Heenan, R.K.3    Penfold, J.4    Ranganathan, R.5    Bales, B.L.6
  • 42
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
    • Wimley, W. C., Creamer, T. P., and White, S. H. (1996) Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides Biochemistry 35, 5109-5124
    • (1996) Biochemistry , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 43
    • 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
  • 44
    • 46249089993 scopus 로고    scopus 로고
    • Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins
    • Joh, N. H., Min, A., Faham, S., Whitelegge, J. P., Yang, D., Woods, V. L., and Bowie, J. U. (2008) Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins Nature 453, 1266-1273
    • (2008) Nature , vol.453 , pp. 1266-1273
    • Joh, N.H.1    Min, A.2    Faham, S.3    Whitelegge, J.P.4    Yang, D.5    Woods, V.L.6    Bowie, J.U.7
  • 45
    • 73149116645 scopus 로고    scopus 로고
    • SDS Micelles as a Membrane-Mimetic Environment for Transmembrane Segments
    • Tulumello, D. V. and Deber, C. M. (2009) SDS Micelles as a Membrane-Mimetic Environment for Transmembrane Segments Biochemistry 48, 12096-12103
    • (2009) Biochemistry , vol.48 , pp. 12096-12103
    • Tulumello, D.V.1    Deber, C.M.2
  • 46
    • 36248978178 scopus 로고    scopus 로고
    • The Control of Transmembrane Helix Transverse Position in Membranes by Hydrophilic Residues
    • DOI 10.1016/j.jmb.2007.10.032, PII S0022283607013708
    • Krishnakumar, S. S. and London, E. (2007) The control of transmembrane helix transverse position in membranes by hydrophilic residues J. Mol. Biol. 374, 1251-1269 (Pubitemid 350122550)
    • (2007) Journal of Molecular Biology , vol.374 , Issue.5 , pp. 1251-1269
    • Krishnakumar, S.S.1    London, E.2
  • 47
    • 0032582541 scopus 로고    scopus 로고
    • Secondary structure of bacteriorhodopsin fragments: External sequence constraints specify the conformation of transmembrane helices
    • DOI 10.1074/jbc.273.44.28822
    • Luneberg, J., Widmann, M., Dathe, M., and Marti, T. (1998) Secondary structure of bacteriorhodopsin fragments: External sequence constraints specify the conformation of transmembrane helices J. Biol. Chem. 273, 28822-28830 (Pubitemid 28507573)
    • (1998) Journal of Biological Chemistry , vol.273 , Issue.44 , pp. 28822-28830
    • Luneberg, J.1    Widmann, M.2    Dathe, M.3    Marti, T.4
  • 48
    • 0028085957 scopus 로고
    • Conformation of a peptide corresponding to T4 lysozyme residues 59-81 by NMR and CD spectroscopy
    • DOI 10.1021/bi00203a013
    • Mcleish, M. J., Nielsen, K. J., Najbar, L. V., Wade, J. D., Lin, F., Doughty, M. B., and Craik, D. J. (1994) Conformation of a Peptide Corresponding to T4 Lysozyme Residues 59-81 by NMR and CD Spectroscopy Biochemistry 33, 11174-11183 (Pubitemid 24304281)
    • (1994) Biochemistry , vol.33 , Issue.37 , pp. 11174-11183
    • McLeish, M.J.1    Nielsen, K.J.2    Najbar, L.V.3    Wade, J.D.4    Lin, F.5    Doughty, M.B.6    Craik, D.J.7
  • 49
    • 0029151291 scopus 로고
    • CD and NMR Determination of the Solution Structure of a Peptide Corresponding to T4 Lysozyme Residues 38-51
    • Najbar, L. V., Craik, D. J., Wade, J. D., Lin, F., and Mcleish, M. J. (1995) CD and NMR Determination of the Solution Structure of a Peptide Corresponding to T4 Lysozyme Residues 38-51 Biochim. Biophys. Acta 1250, 163-170
    • (1995) Biochim. Biophys. Acta , vol.1250 , pp. 163-170
    • Najbar, L.V.1    Craik, D.J.2    Wade, J.D.3    Lin, F.4    McLeish, M.J.5
  • 50
    • 0025325818 scopus 로고
    • 1H NMR
    • DOI 10.1021/bi00474a007
    • 1H NMR Biochemistry 29, 5265-5269 (Pubitemid 20193929)
    • (1990) Biochemistry , vol.29 , Issue.22 , pp. 5265-5269
    • Mammi, S.1    Peggion, E.2
  • 51
    • 0027180807 scopus 로고
    • Conformational behavior of Escherichia coli OmpA signal peptides in membrane mimetic environments
    • DOI 10.1021/bi00069a025
    • Rizo, J., Blanco, F. J., Kobe, B., Bruch, M. D., and Gierasch, L. M. (1993) Conformational Behavior of Escherichia coli Ompa Signal Peptides in Membrane Mimetic Environments Biochemistry 32, 4881-4894 (Pubitemid 23162046)
    • (1993) Biochemistry , vol.32 , Issue.18 , pp. 4881-4894
    • Rizo, J.1    Blanco, F.J.2    Kobe, B.3    Bruch, M.D.4    Gierasch, L.M.5
  • 52
    • 0033951896 scopus 로고    scopus 로고
    • Simulation studies on bacteriorhodopsin α-helices
    • Son, H. S. and Sansom, M. S. (2000) Simulation studies on bacteriorhodopsin α-helices Eur. Biophys. J. 28, 674-682
    • (2000) Eur. Biophys. J. , vol.28 , pp. 674-682
    • Son, H.S.1    Sansom, M.S.2
  • 53
    • 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. 1. Structure and dynamics Biophys. J. 73, 2376-2392 (Pubitemid 27471447)
    • (1997) Biophysical Journal , vol.73 , Issue.5 , pp. 2376-2392
    • Woolf, T.B.1


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