메뉴 건너뛰기




Volumn 95, Issue 11, 2008, Pages 5021-5029

Free-energy profiles of membrane insertion of the M2 transmembrane peptide from influenza A virus

Author keywords

[No Author keywords available]

Indexed keywords

M2 PROTEIN, INFLUENZA A VIRUS; MATRIX PROTEIN; PEPTIDE FRAGMENT; UNCLASSIFIED DRUG; WATER;

EID: 58149356759     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.133579     Document Type: Article
Times cited : (18)

References (52)
  • 2
    • 0036441135 scopus 로고    scopus 로고
    • Membrane traffic exploited by protein toxins
    • Sandvig, K., and B. van Deurs. 2002. Membrane traffic exploited by protein toxins. Annu. Rev. Cell Dev. Biol. 18:1-24.
    • (2002) Annu. Rev. Cell Dev. Biol , vol.18 , pp. 1-24
    • Sandvig, K.1    van Deurs, B.2
  • 3
    • 0037371597 scopus 로고    scopus 로고
    • Mechanisms of antimicrobial peptide action and resistance
    • Yeaman, M. R., and N. Y. Yount. 2003. Mechanisms of antimicrobial peptide action and resistance. Pharmacol. Rev. 55:27-55.
    • (2003) Pharmacol. Rev , vol.55 , pp. 27-55
    • Yeaman, M.R.1    Yount, N.Y.2
  • 6
    • 3042621274 scopus 로고    scopus 로고
    • The progress of membrane protein structure determination
    • White, S. H. 2004. The progress of membrane protein structure determination. Protein Sci. 13:1948-19.
    • (2004) Protein Sci , vol.13 , pp. 1948-2019
    • White, S.H.1
  • 7
    • 33746647787 scopus 로고    scopus 로고
    • Peptides in lipid bilayers: The power of simple models
    • Killian, J. A., and T. K. M. Nyholm. 2006. Peptides in lipid bilayers: the power of simple models. Curr. Opin. Struct. Biol. 16:473-479.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 473-479
    • Killian, J.A.1    Nyholm, T.K.M.2
  • 8
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: Physical principles
    • White, S. H., and W. C. Wimley. 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
  • 9
    • 18744403982 scopus 로고    scopus 로고
    • Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations
    • Im, W., and C. L. Brooks. 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, C.L.2
  • 10
    • 33750288787 scopus 로고    scopus 로고
    • Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics
    • Lopez, C. F., S. O. Nielsen, G. Srinivas, W. F. DeGrado, and M. L. Klein. 2006. Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics. J. Chem. Theory Comput. 2:649-655.
    • (2006) J. Chem. Theory Comput , vol.2 , pp. 649-655
    • Lopez, C.F.1    Nielsen, S.O.2    Srinivas, G.3    DeGrado, W.F.4    Klein, M.L.5
  • 11
    • 18844362955 scopus 로고    scopus 로고
    • Folding is not required for bilayer insertion: Replica exchange simulations of an α-helical peptide with an explicit lipid bilayer
    • Nymeyer, H., T. B. Woolf, and A. E. García. 2005. Folding is not required for bilayer insertion: replica exchange simulations of an α-helical peptide with an explicit lipid bilayer. Proteins. 59:783-790.
    • (2005) Proteins , vol.59 , pp. 783-790
    • Nymeyer, H.1    Woolf, T.B.2    García, A.E.3
  • 12
    • 34548718755 scopus 로고    scopus 로고
    • Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane
    • Ulmschneider, J. P., M. B. Ulmschneider, and A. Di Nola. 2007. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Proteins. 69:297-308.
    • (2007) Proteins , vol.69 , pp. 297-308
    • Ulmschneider, J.P.1    Ulmschneider, M.B.2    Di Nola, A.3
  • 13
    • 33646138957 scopus 로고    scopus 로고
    • Evaluating tilt angles of membrane-associated helices: Comparison of computational and NMR techniques
    • Ulmschneider, M. B., M. S. P. Sansom, and A. Di Nola. 2006. Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. Biophys. J. 90:1650-1660.
    • (2006) Biophys. J , vol.90 , pp. 1650-1660
    • Ulmschneider, M.B.1    Sansom, M.S.P.2    Di Nola, A.3
  • 14
    • 34047240165 scopus 로고    scopus 로고
    • A generalized Born implicit-membrane representation compared to experimental insertion free energies
    • Ulmschneider, M. B., J. P. Ulmschneider, M. S. P. Sansom, and A. Di Nola. 2007. A generalized Born implicit-membrane representation compared to experimental insertion free energies. Biophys. J. 92:2338-2349.
    • (2007) Biophys. J , vol.92 , pp. 2338-2349
    • Ulmschneider, M.B.1    Ulmschneider, J.P.2    Sansom, M.S.P.3    Di Nola, A.4
  • 15
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314:141-151.
    • (1999) Chem. Phys. Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 16
    • 33646932780 scopus 로고    scopus 로고
    • The M2 proton channels of influenza A and B viruses
    • Pinto, L. H., and R. A. Lamb. 2006. The M2 proton channels of influenza A and B viruses. J. Biol. Chem. 281:8997-9000.
    • (2006) J. Biol. Chem , vol.281 , pp. 8997-9000
    • Pinto, L.H.1    Lamb, R.A.2
  • 17
    • 0026785994 scopus 로고
    • The transmembrane domain of influenza-A M2 protein forms amantadine-sensitive proton channels in planar lipid bilayers
    • Duff, K. C., and R. H. Ashley. 1992. The transmembrane domain of influenza-A M2 protein forms amantadine-sensitive proton channels in planar lipid bilayers. Virology. 190:485-489.
    • (1992) Virology , vol.190 , pp. 485-489
    • Duff, K.C.1    Ashley, R.H.2
  • 19
    • 38749106195 scopus 로고    scopus 로고
    • Structure and mechanism of the M2 proton channel of influenza A virus
    • Schnell, J. R., and J. J. Chou. 2008. Structure and mechanism of the M2 proton channel of influenza A virus. Nature. 451:591-595.
    • (2008) Nature , vol.451 , pp. 591-595
    • Schnell, J.R.1    Chou, J.J.2
  • 21
    • 0034039757 scopus 로고    scopus 로고
    • Computer simulation of ion channel gating: The M-2 channel of influenza A virus in a lipid bilayer
    • Schweighofer, K. J., and A. Pohorille. 2000. Computer simulation of ion channel gating: the M-2 channel of influenza A virus in a lipid bilayer. Biophys. J. 78:150-163.
    • (2000) Biophys. J , vol.78 , pp. 150-163
    • Schweighofer, K.J.1    Pohorille, A.2
  • 22
    • 0036789499 scopus 로고    scopus 로고
    • Molecular dynamics simulation of proton transport through the influenza A virus M2 channel
    • Smondyrev, A. M., and G. A. Voth. 2002. Molecular dynamics simulation of proton transport through the influenza A virus M2 channel. Biophys. J. 83:1987-1996.
    • (2002) Biophys. J , vol.83 , pp. 1987-1996
    • Smondyrev, A.M.1    Voth, G.A.2
  • 23
    • 33846804141 scopus 로고    scopus 로고
    • Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations
    • Bu, L. T., W. Im, and L. I. Charles. 2007. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys. J. 92:854-863.
    • (2007) Biophys. J , vol.92 , pp. 854-863
    • Bu, L.T.1    Im, W.2    Charles, L.I.3
  • 24
    • 0034614541 scopus 로고    scopus 로고
    • Helix tilt of the M2 transmembrane peptide from influenza A virus: An intrinsic property
    • Kovacs, F. A., J. K. Denny, Z. Song, J. R. Quine, and T. A. Cross. 2000. Helix tilt of the M2 transmembrane peptide from influenza A virus: an intrinsic property. J. Mol. Biol. 295:117-125.
    • (2000) J. Mol. Biol , vol.295 , pp. 117-125
    • Kovacs, F.A.1    Denny, J.K.2    Song, Z.3    Quine, J.R.4    Cross, T.A.5
  • 25
    • 0242322528 scopus 로고    scopus 로고
    • An implicit membrane generalized Born theory for the study of structure stability and interactions of membrane proteins
    • Im, W., M. Feig, and C. L. Brooks. 2003. An implicit membrane generalized Born theory for the study of structure stability and interactions of membrane proteins. Biophys. J. 85:2900-2918.
    • (2003) Biophys. J , vol.85 , pp. 2900-2918
    • Im, W.1    Feig, M.2    Brooks, C.L.3
  • 26
    • 34247633528 scopus 로고    scopus 로고
    • On the thermodynamic stability of a charged arginine side chain in a transmembrane helix
    • Dorairaj, S., and T. W. Allen. 2007. On the thermodynamic stability of a charged arginine side chain in a transmembrane helix. Proc. Natl. Acad. Sci. USA. 104:4943-4948.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 4943-4948
    • Dorairaj, S.1    Allen, T.W.2
  • 27
    • 34547622288 scopus 로고    scopus 로고
    • Modeling charged protein side chains in lipid membranes
    • Allen, T. W. 2007. Modeling charged protein side chains in lipid membranes. J. Gen. Physiol. 130:237-240.
    • (2007) J. Gen. Physiol , vol.130 , pp. 237-240
    • Allen, T.W.1
  • 28
    • 43649094583 scopus 로고    scopus 로고
    • Distribution of amino acids in a lipid bilayer from computer simulations
    • MacCallum, J. L., W. F. D. Bennett, and D. P. Tieleman. 2008. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 94:3393-3404.
    • (2008) Biophys. J , vol.94 , pp. 3393-3404
    • MacCallum, J.L.1    Bennett, W.F.D.2    Tieleman, D.P.3
  • 29
    • 34247626293 scopus 로고    scopus 로고
    • Partitioning of amino acid side chains into lipid bilayers: Results from computer simulations and comparison to experiment
    • MacCallum, J. L., W. F. D. Bennett, and D. P. Tieleman. 2007. Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J. Gen. Physiol. 129:371-377.
    • (2007) J. Gen. Physiol , vol.129 , pp. 371-377
    • MacCallum, J.L.1    Bennett, W.F.D.2    Tieleman, D.P.3
  • 30
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer-simulations
    • Roux, B. 1995. The calculation of the potential of mean force using computer-simulations. Comput. Phys. Commun. 91:275-282.
    • (1995) Comput. Phys. Commun , vol.91 , pp. 275-282
    • Roux, B.1
  • 32
    • 0030782840 scopus 로고    scopus 로고
    • Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties
    • MacKerell, A. D. 1997. Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties. J. Phys. Chem. B. 101:646-650.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 646-650
    • MacKerell, A.D.1
  • 33
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
    • MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
  • 34
    • 0034775070 scopus 로고    scopus 로고
    • Structure of the transmembrane region of the M2 protein H channel
    • Wang, J. F., S. Kim, F. Kovacs, and T. A. Cross. 2001. Structure of the transmembrane region of the M2 protein H channel. Protein Sci. 10:2241-2250.
    • (2001) Protein Sci , vol.10 , pp. 2241-2250
    • Wang, J.F.1    Kim, S.2    Kovacs, F.3    Cross, T.A.4
  • 35
    • 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. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 36
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • Feig, M., J. Karanicolas, and C. L. Brooks. 2004. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J. Mol. Graph. Model. 22:377-395.
    • (2004) J. Mol. Graph. Model , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks, C.L.3
  • 37
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method
    • Kumar, S., D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method. J. Comput. Chem. 13:1011-1021.
    • (1992) J. Comput. Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 38
    • 17444366185 scopus 로고    scopus 로고
    • Temperature weighted histogram analysis method, replica exchange, and transition paths
    • Gallicchio, E., M. Andrec, A. K. Felts, and R. M. Levy. 2005. Temperature weighted histogram analysis method, replica exchange, and transition paths. J. Phys. Chem. B. 109:6722-6731.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 6722-6731
    • Gallicchio, E.1    Andrec, M.2    Felts, A.K.3    Levy, R.M.4
  • 39
    • 0034683242 scopus 로고    scopus 로고
    • Conformational diffusion and helix formation kinetics
    • Hummer, G., A. E. García, and S. Garde. 2000. Conformational diffusion and helix formation kinetics. Phys. Rev. Lett. 85:2637-2640.
    • (2000) Phys. Rev. Lett , vol.85 , pp. 2637-2640
    • Hummer, G.1    García, A.E.2    Garde, S.3
  • 41
    • 24144475875 scopus 로고    scopus 로고
    • Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations
    • Heise, H., S. Luca, B. L. de Groot, H. Grubmueller, and M. Baldus. 2005. Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys. J. 89:2113-2120.
    • (2005) Biophys. J , vol.89 , pp. 2113-2120
    • Heise, H.1    Luca, S.2    de Groot, B.L.3    Grubmueller, H.4    Baldus, M.5
  • 42
    • 57449092529 scopus 로고    scopus 로고
    • Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models
    • In press
    • Yeh, I.-C., M. S. Lee, and M. A. Olson. 2008. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models. J. Phys. Chem. B. In press.
    • (2008) J. Phys. Chem. B
    • Yeh, I.-C.1    Lee, M.S.2    Olson, M.A.3
  • 43
    • 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
  • 46
    • 11144233948 scopus 로고    scopus 로고
    • A quantitative assessment of models for voltage-dependent gating of ion channels
    • Grabe, M., H. Lecar, Y. N. Jan, and L. Y. Jan. 2004. A quantitative assessment of models for voltage-dependent gating of ion channels. Proc. Natl. Acad. Sci. USA. 101:17640-17645.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 17640-17645
    • Grabe, M.1    Lecar, H.2    Jan, Y.N.3    Jan, L.Y.4
  • 47
    • 17444426051 scopus 로고    scopus 로고
    • A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes
    • Tanizaki, S., and M. Feig. 2005. A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. J. Chem. Phys. 122:124706.
    • (2005) J. Chem. Phys , vol.122 , pp. 124706
    • Tanizaki, S.1    Feig, M.2
  • 48
    • 0000206982 scopus 로고    scopus 로고
    • Computer simulations of bilayer membranes: Self-assembly and interfacial tension
    • Goetz, R., and R. Lipowsky. 1998. Computer simulations of bilayer membranes: self-assembly and interfacial tension. J. Chem. Phys. 108:7397-7409.
    • (1998) J. Chem. Phys , vol.108 , pp. 7397-7409
    • Goetz, R.1    Lipowsky, R.2
  • 49
    • 14544291957 scopus 로고    scopus 로고
    • A multiscale coarse-graining method for biomolecular systems
    • Izvekov, S., and G. A. Voth. 2005. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B. 109:2469-2473.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 2469-2473
    • Izvekov, S.1    Voth, G.A.2
  • 50
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink, S. J., A. H. de Vries, and A. E. Mark. 2004. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B. 108:750-760.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 750-760
    • Marrink, S.J.1    de Vries, A.H.2    Mark, A.E.3
  • 52
    • 33644893631 scopus 로고    scopus 로고
    • Coarse grained protein-lipid model with application to lipoprotein particles
    • Shih, A. Y., A. Arkhipov, P. L. Freddolino, and K. Schulten. 2006. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B. 110:3674-3684.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3674-3684
    • Shih, A.Y.1    Arkhipov, A.2    Freddolino, P.L.3    Schulten, K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.