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Volumn 43, Issue 3, 2010, Pages 388-396

Molecular dynamics simulations of the dimerization of transmembrane α-helices

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA2 INTEGRIN; GLYCOPHORIN; MEMBRANE PROTEIN;

EID: 77949509024     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar900211k     Document Type: Article
Times cited : (82)

References (53)
  • 1
    • 24644490119 scopus 로고    scopus 로고
    • Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
    • Nilsson, J.; Persson, B.; von Heijne, G. Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins: Struct., Funct., Bioinf. 2005, 60, 606-616.
    • (2005) Proteins: Struct., Funct., Bioinf. , vol.60 , pp. 606-616
    • Nilsson, J.1    Persson, B.2    Von Heijne, G.3
  • 2
    • 0033790343 scopus 로고    scopus 로고
    • Helical membrane protein folding, stability, and evolution
    • Popot, J. L.; Engelman, D. M. Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem. 2000, 69, 881-922.
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 881-922
    • Popot, J.L.1    Engelman, D.M.2
  • 3
    • 28444488355 scopus 로고    scopus 로고
    • Solving the membrane protein folding problem
    • Bowie, J. U. Solving the membrane protein folding problem. Nature 2005, 438, 581-589.
    • (2005) Nature , vol.438 , pp. 581-589
    • Bowie, J.U.1
  • 4
    • 4143085058 scopus 로고    scopus 로고
    • Folding of helical membrane proteins: The role of polar, GxxxG-likc and proline motifs
    • Senes, A.; Engel, D. E.; DeGrado, W. F. Folding of helical membrane proteins: The role of polar, GxxxG-likc and proline motifs. Curr. Opin. Struct. Biol. 2004, 14, 465-479.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 465-479
    • Senes, A.1    Engel, D.E.2    Degrado, W.F.3
  • 5
    • 67650069254 scopus 로고    scopus 로고
    • Interaction and conformational dynamics of membranespanning protein helices
    • Langosch, D.; Arkin, I. T. Interaction and conformational dynamics of membranespanning protein helices. Protein Sci. 2009, 18, 1343-1358.
    • (2009) Protein Sci. , vol.18 , pp. 1343-1358
    • Langosch, D.1    Arkin, I.T.2
  • 7
    • 49549083949 scopus 로고    scopus 로고
    • Membrane proteins: Molecular dynamics simulations
    • Lindahl, E.; Sansom, M. S. P. Membrane proteins: Molecular dynamics simulations. Curr. Opin. Struct. Biol. 2008, 18, 425-431.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 425-431
    • Lindahl, E.1    Sansom, M.S.P.2
  • 10
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink, S. J.; de Vries, A. H.; Mark, A. E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. 02004, 108, 750-760.
    • (2004) J. Phys. Chem. 0 , vol.108 , pp. 750-760
    • Marrink, S.J.1    De Vries, A.H.2    Mark, A.E.3
  • 13
    • 11044233935 scopus 로고    scopus 로고
    • Coarse-grained simulations of lipid bilayers
    • Stevens, M. J. Coarse-grained simulations of lipid bilayers. J. Chem. Phys. 2004, 121, 11942-11948.
    • (2004) J. Chem. Phys. , vol.121 , pp. 11942-11948
    • Stevens, M.J.1
  • 16
    • 33847242278 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    • Bond, P. J.; Holyoake, J.; Ivelac, A.; Khalid, S.; Sansom, M. S. P. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 2007, 157, 593-605.
    • (2007) J. Struct. Biol. , vol.157 , pp. 593-605
    • Bond, P.J.1    Holyoake, J.2    Ivelac, A.3    Khalid, S.4    Sansom, M.S.P.5
  • 18
    • 0030932407 scopus 로고    scopus 로고
    • A transmembrane helix dimer: Structure and implications
    • MacKenzie, K. R.; Prestegard, J. H.; Engelman, D. M. A transmembrane helix dimer: Structure and implications. Science 1997, 276, 131-133.
    • (1997) Science , vol.276 , pp. 131-133
    • MacKenzie, K.R.1    Prestegard, J.H.2    Engelman, D.M.3
  • 19
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and assembly of membrane proteins via simulation
    • Bond, P. J.; Sansom, M. S. P. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 2006, 128, 2697-2704.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.P.2
  • 20
    • 53249150686 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer
    • Bond, P. J.; Wee, C. L.; Sansom, M. S. P. Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochemistry 2008, 47, 11321-11331.
    • (2008) Biochemistry , vol.47 , pp. 11321-11331
    • Bond, P.J.1    Wee, C.L.2    Sansom, M.S.P.3
  • 21
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: In serial and in parallel
    • Ayten, G. A.; Noid, W. G.; Voth, G. A. Multiscale modeling of biomolecular systems: In serial and in parallel. Curr. Opin. Struct. Biol. 2007, 17, 192-198.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 192-198
    • Ayten, G.A.1    Noid, W.G.2    Voth, G.A.3
  • 23
    • 44449124693 scopus 로고    scopus 로고
    • Fast procedure for reconstruction of full-atom protein models from reduced representations
    • Rotkicwicz, P.; Skolnick, J. Fast procedure for reconstruction of full-atom protein models from reduced representations. J. Comput Chem. 2008, 29, 1460-1465.
    • (2008) J. Comput Chem. , vol.29 , pp. 1460-1465
    • Rotkicwicz, P.1    Skolnick, J.2
  • 24
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7, 306-317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 29
    • 33846823909 scopus 로고
    • Particle mesh Ewald - An N.log(N) method for Ewald sums in large systems
    • Dardon, T.; York, D.; Pedersen, L. Particle mesh Ewald - an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Dardon, T.1    York, D.2    Pedersen, L.3
  • 30
  • 31
    • 53249119350 scopus 로고    scopus 로고
    • Helix-helix interactions in membrane proteins: Coarse-grained simulations of glycophorin A helix dimerization
    • Psachoulia, E.; Bond, P. J.; Fowler, P. W.; Sansom, M. S. P. Helix-helix interactions in membrane proteins: Coarse-grained simulations of glycophorin A helix dimerization. Biochemistry 2008, 47, 10503-10512.
    • (2008) Biochemistry , vol.47 , pp. 10503-10512
    • Psachoulia, E.1    Bond, P.J.2    Fowler, P.W.3    Sansom, M.S.P.4
  • 32
    • 0035811042 scopus 로고    scopus 로고
    • Structure of the transmembrane dimer interface of glycophorin A in membrane bilayers
    • Smith, S. O.; Song, D.; Shekar, S.; Groesbeek M.; Ziliox, M.; Aimoto, S. Structure of the transmembrane dimer interface of glycophorin A in membrane bilayers. Biochemistry 2001, 40, 6553-6558.
    • (2001) Biochemistry , vol.40 , pp. 6553-6558
    • Smith, S.O.1    Song, D.2    Shekar, S.3    Groesbeek, M.4    Ziliox, M.5    Aimoto, S.6
  • 34
    • 0027092981 scopus 로고
    • The glycophorin A transmembrane domain dimer: Sequence-specific propensity for a right-handed supercoil of helices
    • Treutiein, H. R.; Lemmon, M. A.; Engelman, D. M.; Brunger, A. T. The glycophorin A transmembrane domain dimer: Sequence-specific propensity for a right-handed supercoil of helices. Biochemistry 1992, 31, 12726-12733.
    • (1992) Biochemistry , vol.31 , pp. 12726-12733
    • Treutiein, H.R.1    Lemmon, M.A.2    Engelman, D.M.3    Brunger, A.T.4
  • 36
    • 0034711953 scopus 로고    scopus 로고
    • The GxxxG motif: A framework for transmembrane helix-helix association
    • Russ, W. P.; Engelman, D. M. The GxxxG motif: A framework for transmembrane helix-helix association. J. Mol. Biol. 2000, 296, 911-919.
    • (2000) J. Mol. Biol. , vol.296 , pp. 911-919
    • Russ, W.P.1    Engelman, D.M.2
  • 37
    • 33750022623 scopus 로고    scopus 로고
    • The structure of the ξξ transmembrane dimer reveals features essential for its assembly with the T cell receptor
    • Call, M. E.; Schnell, J. R.; Xu, C. Q.; Lutz, R. A.; Chou, J. J.; Wucherpfennig, K. W. The structure of the ξξ transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 2006, 127, 355-368.
    • (2006) Cell , vol.127 , pp. 355-368
    • Call, M.E.1    Schnell, J.R.2    Xu, C.Q.3    Lutz, R.A.4    Chou, J.J.5    Wucherpfennig, K.W.6
  • 38
    • 6344236852 scopus 로고    scopus 로고
    • Complex interactions at the helix-helix interface stabilize the glycophorin A transmembrane dimer
    • Doura, A. K.; Fleming, K. G. Complex interactions at the helix-helix interface stabilize the glycophorin A transmembrane dimer. J. Mol. Biol. 2004, 343, 1487-1497.
    • (2004) J. Mol. Biol. , vol.343 , pp. 1487-1497
    • Doura, A.K.1    Fleming, K.G.2
  • 39
    • 20444499328 scopus 로고    scopus 로고
    • Insights into the recognition and association of transmembrane α-helices. the free energy of α-helix dimerization in glycophorin A
    • Hénin, J.; Pohonilo, A.; Chipot, C. Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A. J. Am. Chem. Soc. 2005, 127, 8478-8484.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 8478-8484
    • Hénin, J.1    Pohonilo, A.2    Chipot, C.3
  • 40
    • 33845316118 scopus 로고    scopus 로고
    • Transmembrane helix-helix interactions: Comparative simulations of the glycophorin A dimer
    • Cuthbertson, J. M.; Bond, P. J.; Sansom, M. S. P. Transmembrane helix-helix interactions: Comparative simulations of the glycophorin A dimer. Biochemistry 2006, 45, 14298-14310.
    • (2006) Biochemistry , vol.45 , pp. 14298-14310
    • Cuthbertson, J.M.1    Bond, P.J.2    Sansom, M.S.P.3
  • 41
    • 0034711958 scopus 로고    scopus 로고
    • Statistical analysis of amino acid patterns in transmembrane helices: The GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions
    • Senes, A.; Gerstein, M.; Engelman, D. M. Statistical analysis of amino acid patterns in transmembrane helices: The GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J. Mol. Biol. 2000, 296, 921-936.
    • (2000) J. Mol. Biol. , vol.296 , pp. 921-936
    • Senes, A.1    Gerstein, M.2    Engelman, D.M.3
  • 42
    • 16244380777 scopus 로고    scopus 로고
    • Syndecans: New kids on the signaling block
    • Tkachonko, E.; Rhodes, J. M.; Simons, M. Syndecans: New kids on the signaling block. Circ. Res. 2005, 96, 488-500.
    • (2005) Circ. Res. , vol.96 , pp. 488-500
    • Tkachonko, E.1    Rhodes, J.M.2    Simons, M.3
  • 43
    • 38049174634 scopus 로고    scopus 로고
    • Transmembrane domains of the syndecan family of growth factor corecepters display a hierarchy of homotypic and heterotypic interactions
    • Dews, I. C.; Mackenzie, K. R. Transmembrane domains of the syndecan family of growth factor corecepters display a hierarchy of homotypic and heterotypic interactions. Proc. Nail. Acad. Sci. U.S.A. 2007, 104, 20782-20787.
    • (2007) Proc. Nail. Acad. Sci. U.S.A. , vol.104 , pp. 20782-20787
    • Dews, I.C.1    Mackenzie, K.R.2
  • 44
    • 0037145037 scopus 로고    scopus 로고
    • Integrins: Bidirectional, allosteric signaling machines
    • Hynes, R. O. Integrins: Bidirectional, allosteric signaling machines. Cell 2002, 110, 673-687.
    • (2002) Cell , vol.110 , pp. 673-687
    • Hynes, R.O.1
  • 45
    • 14844323604 scopus 로고    scopus 로고
    • Transmembrane domain helix packing stabilizes integrin αllbß3 in the low affinity state
    • Partridge, A. W.; Liu, S.; Kim, S.; Bowie, J. U.; Ginsberg, M. H. Transmembrane domain helix packing stabilizes integrin αllbß3 in the low affinity state. J. Biol. Chem. 2005, 280, 7294-7300.
    • (2005) J. Biol. Chem. , vol.280 , pp. 7294-7300
    • Partridge, A.W.1    Liu, S.2    Kim, S.3    Bowie, J.U.4    Ginsberg, M.H.5
  • 46
    • 65649127175 scopus 로고    scopus 로고
    • The structure of the integrin αllbßB transmembrane complex explains integrin transmembrane signalling
    • Lau, T. L.; Kim, C.; Ginsberg, M. H.; Ulmer, T. S. The structure of the integrin αllbßB transmembrane complex explains integrin transmembrane signalling. EMBO J. 2009, 28, 1351-1361.
    • (2009) EMBO J. , vol.28 , pp. 1351-1361
    • Lau, T.L.1    Kim, C.2    Ginsberg, M.H.3    Ulmer, T.S.4
  • 47
    • 70449566822 scopus 로고    scopus 로고
    • Structure of an integrin αllbß3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation
    • Yang, J.; Ma, Y. Q.; Page, R. C.; Misra, S.; Plow, E. F.; Qin, J. Structure of an integrin αllbß3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 17729-17734.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 17729-17734
    • Yang, J.1    Ma, Y.Q.2    Page, R.C.3    Misra, S.4    Plow, E.F.5    Qin, J.6
  • 49
    • 48249125437 scopus 로고    scopus 로고
    • Transmembrane and cytoplasmic domains in integrin activation and protein-protein interactions (Review)
    • Wegener, K. L.; Campbell, I. D. Transmembrane and cytoplasmic domains in integrin activation and protein-protein interactions (Review). Mol. Membr. Biol. 2008, 25, 376-387.
    • (2008) Mol. Membr. Biol. , vol.25 , pp. 376-387
    • Wegener, K.L.1    Campbell, I.D.2
  • 50
    • 36549085536 scopus 로고    scopus 로고
    • Dynamic equilibrium between multiple active and inactive conformations explains regulation and oncogenic mutations in ErbB receptors
    • Landau, M.; Ben-Tal, N. Dynamic equilibrium between multiple active and inactive conformations explains regulation and oncogenic mutations in ErbB receptors. Biochim. Biophys. Acta 2008, 1785, 12-31.
    • (2008) Biochim. Biophys. Acta , vol.1785 , pp. 12-31
    • Landau, M.1    Ben-Tal, N.2
  • 51
    • 54849405417 scopus 로고    scopus 로고
    • Self-assembly of a simple membrane protein: Coarse-grained molecular dynamics simulations of the influenza M2 channel
    • Carpenter, T.; Bond, P. J.; Khalid, S.; Sansom, M. S. P. Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. Biophys. J. 2008, 95, 3790-3801.
    • (2008) Biophys. J. , vol.95 , pp. 3790-3801
    • Carpenter, T.1    Bond, P.J.2    Khalid, S.3    Sansom, M.S.P.4
  • 52
    • 0035979146 scopus 로고    scopus 로고
    • The Cα-H⋯O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions
    • Senes, A.; Ubarretxena-Belandia, I.; Engelman, D. M. The Cα-H⋯O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 9056-9061.
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 9056-9061
    • Senes, A.1    Ubarretxena-Belandia, I.2    Engelman, D.M.3
  • 53
    • 38949159124 scopus 로고    scopus 로고
    • Strength of Cα-H ⋯ O=C hydrogen bonds in transmembrane proteins
    • Park, H.; Yoon, J.; Seok, C. Strength of Cα-H ⋯ O=C hydrogen bonds in transmembrane proteins. J. Phys. Chem. B 2008, 112, 1041-1048.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 1041-1048
    • Park, H.1    Yoon, J.2    Seok, C.3


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