메뉴 건너뛰기




Volumn 99, Issue 1, 2010, Pages 175-183

Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation

Author keywords

[No Author keywords available]

Indexed keywords

LIPID BILAYER; MEMBRANE PROTEIN;

EID: 77954371031     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.04.015     Document Type: Article
Times cited : (99)

References (42)
  • 1
    • 34347262391 scopus 로고    scopus 로고
    • Bilayer thickness and membrane protein function: An energetic perspective
    • DOI 10.1146/annurev.biophys.36.040306.132643
    • Andersen, O. S., and R. E. Koeppe, 2nd. 2007. Bilayer thickness and membrane protein function: an energetic perspective. Annu. Rev. Biophys. Biomol. Struct. 36:107-130. (Pubitemid 46998112)
    • (2007) Annual Review of Biophysics and Biomolecular Structure , vol.36 , pp. 107-130
    • Andersen, O.S.1    Koeppe II, R.E.2
  • 2
    • 0031740415 scopus 로고    scopus 로고
    • Hydrophobic mismatch between proteins and lipids in membranes
    • Killian, J. A, 1998. Hydrophobic mismatch between proteins and lipids in membranes. Biochim, Biophys. Acta. 1376:401-415.
    • (1998) Biochim, Biophys. Acta. , vol.1376 , pp. 401-415
    • Killian, J.A.1
  • 3
    • 0027489133 scopus 로고
    • Sorting of membrane proteins in the secretory pathway
    • Pelham, H. R. B., and S. Munro. 1993. Sorting of membrane proteins in the secretory pathway. Cell. 75:603-605.
    • (1993) Cell. , vol.75 , pp. 603-605
    • Pelham, H.R.B.1    Munro, S.2
  • 6
    • 0030837927 scopus 로고    scopus 로고
    • Are there dominant membrane protein, families with, a given number of helices?
    • Arkin, I. T., A. T. Brünger, and D. M. Engelman. 1997. Are there dominant membrane protein, families with, a given number of helices? Proteins: Struct. Funct. Gen. 28:465-466.
    • (1997) Proteins: Struct. Funct. Gen. , vol.28 , pp. 465-466
    • Arkin, I.T.1    Brünger, A.T.2    Engelman, D.M.3
  • 7
    • 38549107447 scopus 로고    scopus 로고
    • New insights into growth hormone receptor function and clinical, implications
    • Lichanska, A. M., and M. J. Waters. 2008. New insights into growth hormone receptor function and clinical, implications. Hormone Res Paed. 69:138-145.
    • (2008) Hormone Res Paed. , vol.69 , pp. 138-145
    • Lichanska, A.M.1    Waters, M.J.2
  • 9
    • 20444366208 scopus 로고    scopus 로고
    • Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch
    • Park, S. H., and S. J. Opella. 2005. Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch. J. Mol. Biol. 350:310-318.
    • (2005) J. Mol. Biol. , vol.350 , pp. 310-318
    • Park, S.H.1    Opella, S.J.2
  • 10
    • 0242659352 scopus 로고    scopus 로고
    • Protein-lipid interactions studied with designed transmembrane peptides: Role of hydrophobic matching and interfacial anchoring
    • de Planque, M. R. R., and J. A. Killian. 2003. Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol. Membr. Biol. 20:271-284, (Review).
    • (2003) Mol. Membr. Biol. , vol.20 , pp. 271-284
    • De Planque, M.R.R.1    Killian, J.A.2
  • 11
    • 33746647787 scopus 로고    scopus 로고
    • Peptides in lipid bilayers: The power of simple models
    • DOI 10.1016/j.sbi.2006.06.007, PII S0959440X06001114
    • Killian, J. A., and T. K. Nyholm. 2006. Peptides in lipid bilayers: the power of simple models. Curr. Opin. Struct. Biol, 16:473-479. (Pubitemid 44149068)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.4 , pp. 473-479
    • Killian, J.A.1    Nyholm, T.K.2
  • 14
    • 33646198955 scopus 로고    scopus 로고
    • Molecular dynamics simulations of model, trans-membrane peptides in lipid bilayers: A systematic investigation of hydrophobic mismatch
    • Kandasamy, S. K., and R. G. Larson. 2006. Molecular dynamics simulations of model, trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch. Biophys. J. 90:2326-2343.
    • (2006) Biophys. J. , vol.90 , pp. 2326-2343
    • Kandasamy, S.K.1    Larson, R.G.2
  • 17
    • 37349011230 scopus 로고    scopus 로고
    • The dynamic orientation of membrane-bound peptides: Bridging simulations and experiments
    • Esteban-Martín, S., and J. Salgado. 2007. The dynamic orientation of membrane-bound peptides: bridging simulations and experiments. Biophys. J. 93:4278-4288.
    • (2007) Biophys. J. , vol.93 , pp. 4278-4288
    • Esteban-Martín, S.1    Salgado, J.2
  • 18
    • 40749090459 scopus 로고    scopus 로고
    • Transmembrane helix tilting: Insights from calculating the potential of mean, force
    • Lee, J., and W. Im. 2008. Transmembrane helix tilting: insights from calculating the potential of mean, force. Phys. Rev. Lett. 100:018103.
    • (2008) Phys. Rev. Lett. , vol.100 , pp. 018103
    • Lee, J.1    Im, W.2
  • 19
    • 18744403982 scopus 로고    scopus 로고
    • Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations
    • Im, W., and C. L. Brooks, 3rd. 2005. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 102:6771-6776.
    • (2005) Proc. Natl. Acad. Sci. USA. , vol.102 , pp. 6771-6776
    • Im, W.1    Brooks III, C.L.2
  • 20
    • 70449125771 scopus 로고    scopus 로고
    • Tilt and rotation angles of a transmembrane model peptide as studied by fluorescence spectroscopy
    • Holt, A., R. B. M. Koehorst, ..., J. A. Killian. 2009. Tilt and rotation angles of a transmembrane model peptide as studied by fluorescence spectroscopy. Biophys. J. 97:2258-2266.
    • (2009) Biophys. J. , vol.97 , pp. 2258-2266
    • Holt, A.1    Koehorst, R.B.M.2    Killian, J.A.3
  • 21
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie, G. M., and J. P. Valleau. 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comp. Phys. 23:187-199.
    • (1977) J. Comp. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 22
    • 34249737504 scopus 로고    scopus 로고
    • Restraint potential and free energy decomposition formalism for helical tilting
    • Lee, J., and W. Im, 2007. Restraint potential and free energy decomposition formalism for helical tilting. Chem. Phys. Lett. 441:132-135.
    • (2007) Chem. Phys. Lett. , vol.441 , pp. 132-135
    • Lee, J.1    Im, W.2
  • 23
    • 33847678434 scopus 로고    scopus 로고
    • Implementation and application of helix-helix distance and crossing angle restraint potentials
    • Lee, J., and W. Im. 2007. Implementation and application of helix-helix distance and crossing angle restraint potentials. J. Comput. Chem. 28:669-680.
    • (2007) J. Comput. Chem. , vol.28 , pp. 669-680
    • Lee, J.1    Im, W.2
  • 24
    • 67650480197 scopus 로고    scopus 로고
    • Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function
    • Im, W., J. Lee, ..., H. Rui. 2009. Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. J. Comput. Chem. 30:1622-1633.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1622-1633
    • Im, W.1    Lee, J.2    Rui, H.3
  • 25
    • 68949149548 scopus 로고    scopus 로고
    • CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes
    • Jo, S., J. B. Lim, ..., W. Im. 2009. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys. J. 97:50-58.
    • (2009) Biophys. J. , vol.97 , pp. 50-58
    • Jo, S.1    Lim, J.B.2    Im, W.3
  • 26
    • 41149134824 scopus 로고    scopus 로고
    • Automated builder and database of protein/membrane complexes for molecular dynamics simulations
    • Jo, S., T. Kim, and W. Im. 2007. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One. 2:e880.
    • (2007) PLoS One. , vol.2
    • Jo, S.1    Kim, T.2    Im, W.3
  • 27
    • 47149096704 scopus 로고    scopus 로고
    • CHARMM-GUI: A web-based graphical user interface for CHARMM
    • Jo, S., T. Kim, ..., W. Im. 2008. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29:1859-1865.
    • (2008) J. Comput. Chem. , vol.29 , pp. 1859-1865
    • Jo, S.1    Kim, T.2    Im, W.3
  • 28
    • 67650500988 scopus 로고    scopus 로고
    • CHARMM: The biomolecular simulation program
    • Brooks, B. R., C. L. Brooks, 3rd, ..., M. Karplus. 2009. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30:1545-1614.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1545-1614
    • Brooks, B.R.1    Brooks III, C.L.2    Karplus, M.3
  • 29
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell, Jr., A. D., D. Bashford, ..., M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. .102:3586-3616.
    • (1998) J. Phys. Chem. B.. , vol.102 , pp. 3586-3616
    • Bashford, D.1    Karplus, M.2
  • 30
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • Mackerell Jr., A. D., M. Feig, and C. L. Brooks, 3rd. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • Mackerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 31
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W.L., J.Chandrasekhar, ..., M.L.Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Klein, M.L.3
  • 32
    • 15744368593 scopus 로고    scopus 로고
    • An ab initio study on the torsional, surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer
    • Klauda, J. B., B. R. Brooks, ..., R. W. Pastor. 2005. An ab initio study on the torsional, surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J. Phys. Chem. B. 109:5300-5311
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 5300-5311
    • Klauda, J.B.1    Brooks, B.R.2    Pastor, R.W.3
  • 34
    • 33646940952 scopus 로고
    • Numerical. integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-.P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical. integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 35
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium, phase-space distributions
    • Hoover, W. G. 1985. Canonical dynamics: equilibrium, phase-space distributions. Phys. Rev. A: At. Mol. Opt. Phys. 31:1695-1697.
    • (1985) Phys. Rev. A: At. Mol. Opt. Phys. , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 36
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston, method
    • Feller, S. E., Y. Zhang, ..., B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston, method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Brooks, B.R.3
  • 37
    • 12244255728 scopus 로고    scopus 로고
    • Hydrophobic mismatch between helices and lipid bilayers
    • Weiss, T. M., P. C. A. van der Wel, ..., H. W. Huang. 2003. Hydrophobic mismatch between helices and lipid bilayers. Biophys. J. 84:379-385.
    • (2003) Biophys. J. , vol.84 , pp. 379-385
    • Weiss, T.M.1    Van Der Wel, P.C.A.2    Huang, H.W.3
  • 38
    • 0026704101 scopus 로고
    • Combined influence of cholesterol, and synthetic amphiphilic peptides upon bilayer thickness in model membranes
    • Nezil, F. A., and M. Bloom. 1992. Combined influence of cholesterol, and synthetic amphiphilic peptides upon bilayer thickness in model membranes. Biophys. J. 61:1176-1183.
    • (1992) Biophys. J. , vol.61 , pp. 1176-1183
    • Nezil, F.A.1    Bloom, M.2
  • 39
  • 40
    • 0037008040 scopus 로고    scopus 로고
    • The effects of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane a-helical peptides depend on the nature of interfacially exposed aromatic and charged residues
    • de Planque, M. R. R., J.-W. P. Boots, ..., J. A. Killian. 2002. The effects of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane a-helical peptides depend on the nature of interfacially exposed aromatic and charged residues. Biochemistry. 41:8396-8404.
    • (2002) Biochemistry. , vol.41 , pp. 8396-8404
    • De Planque, M.R.R.1    Boots, J.-W.P.2    Killian, J.A.3
  • 41
    • 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. Mol Biol. 3:842-848.
    • (1996) Nat. Struct. Mol Biol. , vol.3 , pp. 842-848
    • Wimley, W.C.1    White, S.H.2
  • 42
    • 0038694994 scopus 로고    scopus 로고
    • Snorkeling of lysine side chains in transmembrane helices: How easy can it get?
    • DOI 10.1016/S0014-5793(03)00475-7
    • Strandberg, E., and J. A. Killian. 2003. Snorkeling of lysine side chains in transmembrane helices: how easy can it get? FEBS Lett. 544:69-73. (Pubitemid 36628038)
    • (2003) FEBS Letters , vol.544 , Issue.1-3 , pp. 69-73
    • Strandberg, E.1    Killian, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.