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Volumn 7, Issue 1, 2010, Pages

Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane α-helical dimers: Ephrin receptor A1

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 77949865294     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/7/1/016014     Document Type: Article
Times cited : (10)

References (49)
  • 1
    • 33646889068 scopus 로고    scopus 로고
    • Role of receptor tyrosine kinase transmembrane domains in cell signaling and human pathologies
    • Li E and Hristova K 2006 Role of receptor tyrosine kinase transmembrane domains in cell signaling and human pathologies Biochemistry 45 6241-51
    • (2006) Biochemistry , vol.45 , pp. 6241-6251
    • Li, E.1    Hristova, K.2
  • 2
    • 14844323604 scopus 로고    scopus 로고
    • Transmembrane domain helix packing stabilizes integrin alphaIIbbeta3 in the low affinity state
    • Partridge A W, Liu S, Kim S, Bowie J U and Ginsberg M H 2005 Transmembrane domain helix packing stabilizes integrin alphaIIbbeta3 in the low affinity state J. Biol. Chem. 280 7294-300
    • (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
  • 4
    • 34247476788 scopus 로고    scopus 로고
    • Peptides as transmembrane segments: Decrypting the determinants for helix-helix interactions in membrane proteins
    • Rath A, Johnson R M and Deber C M 2007 Peptides as transmembrane segments: decrypting the determinants for helix-helix interactions in membrane proteins Biopolymers 88 217-32
    • (2007) Biopolymers , vol.88 , pp. 217-232
    • Rath, A.1    Johnson, R.M.2    Deber, C.M.3
  • 5
    • 34548757937 scopus 로고    scopus 로고
    • Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: A molecular modeling study
    • Vereshaga Y A, Volynsky P E, Pustovalova J E, Nolde D E, Arseniev A S and Efremov R G 2007 Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study Proteins 69 309-25
    • (2007) Proteins , vol.69 , pp. 309-325
    • Vereshaga, Y.A.1    Volynsky, P.E.2    Pustovalova, J.E.3    Nolde, D.E.4    Arseniev, A.S.5    Efremov, R.G.6
  • 7
    • 0035903168 scopus 로고    scopus 로고
    • In vivo detection of hetero-association of glycophorin-A and its mutants within the membrane
    • Gerber D and Shai Y 2001 In vivo detection of hetero-association of glycophorin-A and its mutants within the membrane J. Biol. Chem. 276 31229-32
    • (2001) J. Biol. Chem , vol.276 , pp. 31229-31232
    • Gerber, D.1    Shai, Y.2
  • 8
    • 2442647912 scopus 로고    scopus 로고
    • Two motifs within a transmembrane domain, one for homodimerization and the other for heterodimerization
    • Gerber D, Sal-Man N and Shai Y 2004 Two motifs within a transmembrane domain, one for homodimerization and the other for heterodimerization J. Biol. Chem. 279 21177-82
    • (2004) J. Biol. Chem , vol.279 , pp. 21177-21182
    • Gerber, D.1    Sal-Man, N.2    Shai, Y.3
  • 11
    • 49749131164 scopus 로고    scopus 로고
    • Computationally designed peptide inhibitors of protein-protein interactions in membranes
    • Caputo G A, Litvinov R I, Li W, Bennett J S, Degrado W F and Yin H 2008 Computationally designed peptide inhibitors of protein-protein interactions in membranes Biochemistry 47 8600-06
    • (2008) Biochemistry , vol.47 , pp. 8600-8606
    • Caputo, G.A.1    Litvinov, R.I.2    Li, W.3    Bennett, J.S.4    Degrado, W.F.5    Yin, H.6
  • 12
    • 0030932407 scopus 로고    scopus 로고
    • A transmembrane helix dimer: Structure and implications
    • MacKenzie K R, Prestegard J H and Engelman D M 1997 A transmembrane helix dimer: structure and implications Science 276 131-3
    • (1997) Science , vol.276 , pp. 131-133
    • MacKenzie, K.R.1    Prestegard, J.H.2    Engelman, D.M.3
  • 15
    • 34447523353 scopus 로고    scopus 로고
    • Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger
    • Bocharov E V et al 2007 Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger J. Biol. Chem. 282 16256-66
    • (2007) J. Biol. Chem , vol.282 , pp. 16256-16266
    • Bocharov, E.V.1
  • 16
    • 33750022623 scopus 로고    scopus 로고
    • The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor
    • Call M E, Schnell J R, Xu C, Lutz R A, Chou J J and Wucherpfennig K W 2006 The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor Cell 127 355-68
    • (2006) Cell , vol.127 , pp. 355-368
    • Call, M.E.1    Schnell, J.R.2    Xu, C.3    Lutz, R.A.4    Chou, J.J.5    Wucherpfennig, K.W.6
  • 17
    • 0242322528 scopus 로고    scopus 로고
    • An implicit membrane generalized Born theory for the study of structure, stability and interactions of membrane proteins
    • Im W, Feig M and Brooks C L III 2003 An implicit membrane generalized Born theory for the study of structure, stability and interactions of membrane proteins Biophys. J. 85 2900-18
    • (2003) Biophys. J , vol.85 , pp. 2900-2918
    • Im, W.1    Feig, M.2    Brooks III, C.L.3
  • 18
    • 33845316118 scopus 로고    scopus 로고
    • Transmembrane helix-helix interactions: Comparative simulations of the glycophorin a dimer
    • Cuthbertson J M, Bond P J and Sansom M S 2006 Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer Biochemistry 45 14298-310
    • (2006) Biochemistry , vol.45 , pp. 14298-14310
    • Cuthbertson, J.M.1    Bond, P.J.2    Sansom, M.S.3
  • 19
    • 0038730774 scopus 로고    scopus 로고
    • A simple method for modeling transmembrane helix oligomers
    • Kim S, Chamberlain A K and Bowie J U 2003 A simple method for modeling transmembrane helix oligomers J. Mol. Biol. 329 831-40
    • (2003) J. Mol. Biol , vol.329 , pp. 831-840
    • Kim, S.1    Chamberlain, A.K.2    Bowie, J.U.3
  • 22
    • 0034703270 scopus 로고    scopus 로고
    • Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: Molecular dynamics calculations
    • Petrache H I, Grossfield A, MacKenzie K R, Engelman D M and Woolf T B 2000 Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations J. Mol. Biol. 302 727-46
    • (2000) J. Mol. Biol , vol.302 , pp. 727-746
    • Petrache, H.I.1    Grossfield, A.2    MacKenzie, K.R.3    Engelman, D.M.4    Woolf, T.B.5
  • 23
    • 33947401373 scopus 로고    scopus 로고
    • Mutagenesis data in the automated prediction of transmembrane helix dimers
    • Metcalf D G, Law P B and DeGrado W F 2007 Mutagenesis data in the automated prediction of transmembrane helix dimers Proteins 67 375-84
    • (2007) Proteins , vol.67 , pp. 375-384
    • Metcalf, D.G.1    Law, P.B.2    DeGrado, W.F.3
  • 24
    • 0034711953 scopus 로고    scopus 로고
    • The GxxxG motif: A framework for transmembrane helix-helix association
    • Russ W P and Engelman D M 2000 The GxxxG motif: a framework for transmembrane helix-helix association J. Mol. Biol. 296 911-9
    • (2000) J. Mol. Biol , vol.296 , pp. 911-919
    • Russ, W.P.1    Engelman, D.M.2
  • 25
    • 18744378545 scopus 로고    scopus 로고
    • A putative molecular-activation switch in the transmembrane domain of erbB2
    • Fleishman S J, Schlessinger J and Ben-Tal N 2002 A putative molecular-activation switch in the transmembrane domain of erbB2 Proc. Natl Acad. Sci. USA 99 15937-40
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 15937-15940
    • Fleishman, S.J.1    Schlessinger, J.2    Ben-Tal, N.3
  • 26
    • 33847118661 scopus 로고    scopus 로고
    • A dimerization hierarchy in the transmembrane domains of the HER receptor family
    • Duneau J P, Vegh A P and Sturgis J N 2007 A dimerization hierarchy in the transmembrane domains of the HER receptor family Biochemistry 46 2010-9
    • (2007) Biochemistry , vol.46 , pp. 2010-2019
    • Duneau, J.P.1    Vegh, A.P.2    Sturgis, J.N.3
  • 30
    • 2442701289 scopus 로고    scopus 로고
    • The ErbB/HER receptor protein-tyrosine kinases and cancer
    • Roskoski R Jr 2004 The ErbB/HER receptor protein-tyrosine kinases and cancer Biochem. Biophys. Res. Commun. 319 1-11
    • (2004) Biochem. Biophys. Res. Commun , vol.319 , pp. 1-11
    • Roskoski Jr, R.1
  • 32
    • 84986486657 scopus 로고
    • Efficient search for all low energy conformations of polypeptides by Monte Carlo methods
    • von Freyberg B and Braun W 1991 Efficient search for all low energy conformations of polypeptides by Monte Carlo methods J. Comput. Chem. 12 1065-76
    • (1991) J. Comput. Chem , vol.12 , pp. 1065-1076
    • von Freyberg, B.1    Braun, W.2
  • 33
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogenbonded and geometrical features
    • Kabsch W and Sander C 1983 Dictionary of protein secondary structure: pattern recognition of hydrogenbonded and geometrical features Biopolymers 22 2577-637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 35
    • 0006161383 scopus 로고    scopus 로고
    • On the choice of dihedral angle potential energy functions for n-alkanes
    • Schuler L D and van Gunsteren W F 2000 On the choice of dihedral angle potential energy functions for n-alkanes Mol. Simul. 25 301-19
    • (2000) Mol. Simul , vol.25 , pp. 301-319
    • Schuler, L.D.1    van Gunsteren, W.F.2
  • 37
    • 0032714393 scopus 로고    scopus 로고
    • Factors important for fusogenic activity of peptides: Molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin
    • Efremov R G, Nolde D E, Volynsky P E, Chernyavsky A A, Dubovskii P V and Arseniev A S 1999 Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin FEBS Lett. 462 205-10
    • (1999) FEBS Lett , vol.462 , pp. 205-210
    • Efremov, R.G.1    Nolde, D.E.2    Volynsky, P.E.3    Chernyavsky, A.A.4    Dubovskii, P.V.5    Arseniev, A.S.6
  • 38
    • 0035824509 scopus 로고    scopus 로고
    • In vitro selection of membrane-spanning leucine zipper protein-protein interaction motifs using POSSYCCAT
    • Gurezka R and Langosch D 2001 In vitro selection of membrane-spanning leucine zipper protein-protein interaction motifs using POSSYCCAT J. Biol. Chem. 276 45580-87
    • (2001) J. Biol. Chem , vol.276 , pp. 45580-45587
    • Gurezka, R.1    Langosch, D.2
  • 39
    • 0002972659 scopus 로고
    • ed J H Miller (New York: CSH Laboratory Press) pp
    • Miller J H 1972 Experiments in Molecular Genetics ed J H Miller (New York: CSH Laboratory Press) pp 352-5
    • (1972) Experiments in Molecular Genetics , pp. 352-355
    • Miller, J.H.1
  • 40
    • 33646854383 scopus 로고    scopus 로고
    • One-step high-throughput assay for quantitative detection of β-galactosidase activity in intact gram-negative bacteria, yeast, and mammalian cells
    • Vidal-Aroca F, Giannattasio M, Brunelli E, Vezzoli A, Plevani P, Muzi-Falconi M and Bertoni G 2006 One-step high-throughput assay for quantitative detection of β-galactosidase activity in intact gram-negative bacteria, yeast, and mammalian cells Biotechniques 40 433-40
    • (2006) Biotechniques , vol.40 , pp. 433-440
    • Vidal-Aroca, F.1    Giannattasio, M.2    Brunelli, E.3    Vezzoli, A.4    Plevani, P.5    Muzi-Falconi, M.6    Bertoni, G.7
  • 42
    • 0033514311 scopus 로고    scopus 로고
    • Russ W P and Engelman D M 1999 TOXCAT: a measure of transmembrane helix association in a biological membrane Proc. Natl Acad. Sci. USA 96 863-8
    • Russ W P and Engelman D M 1999 TOXCAT: a measure of transmembrane helix association in a biological membrane Proc. Natl Acad. Sci. USA 96 863-8
  • 43
    • 26444611461 scopus 로고    scopus 로고
    • Kim S, Jeon T J, Oberai A, Yang D, Schmidt J J and Bowie J U 2005 Transmembrane glycine zippers: physiological and pathological roles in membrane proteins Proc. Natl Acad. Sci. USA 102 14278-83
    • Kim S, Jeon T J, Oberai A, Yang D, Schmidt J J and Bowie J U 2005 Transmembrane glycine zippers: physiological and pathological roles in membrane proteins Proc. Natl Acad. Sci. USA 102 14278-83
  • 44
    • 0030575833 scopus 로고
    • Dimerisation of the glycophorin A transmembrane segment in membranes probed with the ToxR transcription activator
    • Langosch D, Brosig B, Kolmar H and Fritz H-J 1995 Dimerisation of the glycophorin A transmembrane segment in membranes probed with the ToxR transcription activator J. Mol. Biol. 263 525-30
    • (1995) J. Mol. Biol , vol.263 , pp. 525-530
    • Langosch, D.1    Brosig, B.2    Kolmar, H.3    Fritz, H.-J.4
  • 45
  • 46
    • 0031956790 scopus 로고    scopus 로고
    • The dimerization motif of the glycophorin A transmembrane segment in membranes: Importance of glycine residues
    • Brosig B and Langosch D 1998 The dimerization motif of the glycophorin A transmembrane segment in membranes: importance of glycine residues Protein Sci. 7 1052-56
    • (1998) Protein Sci , vol.7 , pp. 1052-1056
    • Brosig, B.1    Langosch, D.2
  • 47
    • 33751088317 scopus 로고    scopus 로고
    • Sequence dependence of BNIP3 transmembrane domain dimerization implicates side-chain hydrogen bonding and a tandem GxxxG motif in specific helix-helix interactions
    • Sulistijo E S and MacKenzie K R 2006 Sequence dependence of BNIP3 transmembrane domain dimerization implicates side-chain hydrogen bonding and a tandem GxxxG motif in specific helix-helix interactions J. Mol. Biol. 364 974-90
    • (2006) J. Mol. Biol , vol.364 , pp. 974-990
    • Sulistijo, E.S.1    MacKenzie, K.R.2
  • 48
    • 0029115282 scopus 로고
    • Membrane insertion of the bacterial signal transduction protein ToxR and requirements of transcription activation studied by modular replacement of different protein substructures
    • Kolmar H, Hennecke F, Gotze K, Janzer B, Vogt B, Mayer F and Fritz H J 1995 Membrane insertion of the bacterial signal transduction protein ToxR and requirements of transcription activation studied by modular replacement of different protein substructures EMBO J. 14 3895-904
    • (1995) EMBO J , vol.14 , pp. 3895-3904
    • Kolmar, H.1    Hennecke, F.2    Gotze, K.3    Janzer, B.4    Vogt, B.5    Mayer, F.6    Fritz, H.J.7
  • 49
    • 84929955547 scopus 로고    scopus 로고
    • Berendsen H J C, Postma J P M, van Gunsteren W F and Hermans J 1981 Interaction models of water in relation to protein hydration Intermolecular Forces ed B Pullman and D Reidel (Dordrecht: Kluwer)
    • Berendsen H J C, Postma J P M, van Gunsteren W F and Hermans J 1981 Interaction models of water in relation to protein hydration Intermolecular Forces ed B Pullman and D Reidel (Dordrecht: Kluwer)


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