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Volumn 397, Issue 5, 2010, Pages 1156-1174

Comprehensive analysis of HAMP domains: Implications for transmembrane signal transduction

Author keywords

Classification; Cluster analysis; Protein evolution; Transmembrane signaling; Two component signal transduction

Indexed keywords

MEMBRANE PROTEIN; PROTEIN HAMP; PROTEIN HISTIDINE KINASE; UNCLASSIFIED DRUG;

EID: 77950492834     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.02.031     Document Type: Article
Times cited : (76)

References (51)
  • 2
    • 70349541000 scopus 로고    scopus 로고
    • Biological insights from structures of two-component proteins
    • Gao R., Stock A.M. Biological insights from structures of two-component proteins. Annu. Rev. Microbiol. 2009, 63:133-154.
    • (2009) Annu. Rev. Microbiol. , vol.63 , pp. 133-154
    • Gao, R.1    Stock, A.M.2
  • 3
    • 0033534368 scopus 로고    scopus 로고
    • Structure of CheA, a signal-transducing histidine kinase
    • Bilwes A.M., Alex L.A., Crane B.R., Simon M.I. Structure of CheA, a signal-transducing histidine kinase. Cell 1999, 96:131-141.
    • (1999) Cell , vol.96 , pp. 131-141
    • Bilwes, A.M.1    Alex, L.A.2    Crane, B.R.3    Simon, M.I.4
  • 4
    • 37749029507 scopus 로고    scopus 로고
    • Bacterial chemoreceptors: high-performance signaling in networked arrays
    • Hazelbauer G.L., Falke J.J., Parkinson J.S. Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem. Sci. 2008, 33:9-19.
    • (2008) Trends Biochem. Sci. , vol.33 , pp. 9-19
    • Hazelbauer, G.L.1    Falke, J.J.2    Parkinson, J.S.3
  • 5
    • 33847249975 scopus 로고    scopus 로고
    • Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors
    • Alexander R.P., Zhulin I.B. Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. Proc. Natl Acad. Sci. USA 2007, 104:2885-2890.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 2885-2890
    • Alexander, R.P.1    Zhulin, I.B.2
  • 7
    • 27144522004 scopus 로고    scopus 로고
    • Genetic and functional characterization of the Escherichia coli BarA-UvrY two-component system: point mutations in the HAMP linker of the BarA sensor give a dominant-negative phenotype
    • Tomenius H., Pernestig A.K., Méndez-Catalá C.F., Georgellis D., Normark S., Melefors O. Genetic and functional characterization of the Escherichia coli BarA-UvrY two-component system: point mutations in the HAMP linker of the BarA sensor give a dominant-negative phenotype. J. Bacteriol. 2005, 187:7317-7324.
    • (2005) J. Bacteriol. , vol.187 , pp. 7317-7324
    • Tomenius, H.1    Pernestig, A.K.2    Méndez-Catalá, C.F.3    Georgellis, D.4    Normark, S.5    Melefors, O.6
  • 8
    • 0032826834 scopus 로고    scopus 로고
    • Functional similarities among two-component sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction
    • Williams S.B., Stewart V. Functional similarities among two-component sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction. Mol. Microbiol. 1999, 33:1093-1102.
    • (1999) Mol. Microbiol. , vol.33 , pp. 1093-1102
    • Williams, S.B.1    Stewart, V.2
  • 9
    • 0030811371 scopus 로고    scopus 로고
    • Mutational analysis of the linker region of EnvZ, an osmosensor in Escherichia coli
    • Park H., Inouye M. Mutational analysis of the linker region of EnvZ, an osmosensor in Escherichia coli. J. Bacteriol. 1997, 179:4382-4390.
    • (1997) J. Bacteriol. , vol.179 , pp. 4382-4390
    • Park, H.1    Inouye, M.2
  • 10
    • 0037216619 scopus 로고    scopus 로고
    • Mutational analysis of a conserved signal-transducing element: the HAMP linker of the Escherichia coli nitrate sensor NarX
    • Appleman J.A., Stewart V. Mutational analysis of a conserved signal-transducing element: the HAMP linker of the Escherichia coli nitrate sensor NarX. J. Bacteriol. 2003, 185:89-97.
    • (2003) J. Bacteriol. , vol.185 , pp. 89-97
    • Appleman, J.A.1    Stewart, V.2
  • 11
    • 0032766134 scopus 로고    scopus 로고
    • The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins
    • Aravind L., Ponting C.P. The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins. FEMS Microbiol. Lett. 1999, 176:111-116.
    • (1999) FEMS Microbiol. Lett. , vol.176 , pp. 111-116
    • Aravind, L.1    Ponting, C.P.2
  • 12
    • 33748183257 scopus 로고    scopus 로고
    • The HAMP domain structure implies helix rotation in transmembrane signaling
    • Hulko M., Berndt F., Gruber M., Linder J.U., Truffault V., Schultz A., et al. The HAMP domain structure implies helix rotation in transmembrane signaling. Cell 2006, 126:929-940.
    • (2006) Cell , vol.126 , pp. 929-940
    • Hulko, M.1    Berndt, F.2    Gruber, M.3    Linder, J.U.4    Truffault, V.5    Schultz, A.6
  • 13
    • 17444424974 scopus 로고    scopus 로고
    • The structure of alpha-helical coiled coils
    • Lupas A.N., Gruber M. The structure of alpha-helical coiled coils. Adv. Protein Chem. 2005, 70:37-78.
    • (2005) Adv. Protein Chem. , vol.70 , pp. 37-78
    • Lupas, A.N.1    Gruber, M.2
  • 14
    • 0024462539 scopus 로고
    • Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate
    • Utsumi R., Brissette R.E., Rampersaud A., Forst S.A., Oosawa K., Inouye M. Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate. Science 1989, 245:1246-1249.
    • (1989) Science , vol.245 , pp. 1246-1249
    • Utsumi, R.1    Brissette, R.E.2    Rampersaud, A.3    Forst, S.A.4    Oosawa, K.5    Inouye, M.6
  • 15
    • 57649118508 scopus 로고    scopus 로고
    • Salt-driven equilibrium between two conformations in the HAMP domain from Natronomonas pharaonis: the language of signal transfer?
    • Doebber M., Bordignon E., Klare J.P., Holterhues J., Martell S., Mennes N., et al. Salt-driven equilibrium between two conformations in the HAMP domain from Natronomonas pharaonis: the language of signal transfer?. J. Biol. Chem. 2008, 283:28691-28701.
    • (2008) J. Biol. Chem. , vol.283 , pp. 28691-28701
    • Doebber, M.1    Bordignon, E.2    Klare, J.P.3    Holterhues, J.4    Martell, S.5    Mennes, N.6
  • 16
    • 69249240168 scopus 로고    scopus 로고
    • Evolution of prokaryotic two-component systems: insights from comparative genomics
    • Whitworth D.E., Cock P.J. Evolution of prokaryotic two-component systems: insights from comparative genomics. Amino Acids 2009, 37:459-466.
    • (2009) Amino Acids , vol.37 , pp. 459-466
    • Whitworth, D.E.1    Cock, P.J.2
  • 17
    • 0035019043 scopus 로고    scopus 로고
    • Genomic analysis of the histidine kinase family in bacteria and archaea
    • Kim D., Forst S. Genomic analysis of the histidine kinase family in bacteria and archaea. Microbiology (Reading, UK) 2001, 147:1197-1212.
    • (2001) Microbiology (Reading, UK) , vol.147 , pp. 1197-1212
    • Kim, D.1    Forst, S.2
  • 19
    • 0033277340 scopus 로고    scopus 로고
    • The histidine protein kinase superfamily
    • Grebe T.W., Stock J.B. The histidine protein kinase superfamily. Adv. Microb. Physiol. 1999, 41:139-227.
    • (1999) Adv. Microb. Physiol. , vol.41 , pp. 139-227
    • Grebe, T.W.1    Stock, J.B.2
  • 20
    • 0028955458 scopus 로고
    • Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution
    • Pao G.M., Saier M.H. Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. J. Mol. Evol. 1995, 40:136-154.
    • (1995) J. Mol. Evol. , vol.40 , pp. 136-154
    • Pao, G.M.1    Saier, M.H.2
  • 21
    • 0142122328 scopus 로고    scopus 로고
    • The class III adenylyl cyclases: multi-purpose signalling modules
    • Linder J.U., Schultz J.E. The class III adenylyl cyclases: multi-purpose signalling modules. Cell Signalling 2003, 15:1081-1089.
    • (2003) Cell Signalling , vol.15 , pp. 1081-1089
    • Linder, J.U.1    Schultz, J.E.2
  • 22
    • 0030909737 scopus 로고    scopus 로고
    • Nonplastid eukaryotic response regulators have a monophyletic origin and evolved from their bacterial precursors in parallel with their cognate sensor kinases
    • Pao G.M., Saier M.H. Nonplastid eukaryotic response regulators have a monophyletic origin and evolved from their bacterial precursors in parallel with their cognate sensor kinases. J. Mol. Evol. 1997, 44:605-613.
    • (1997) J. Mol. Evol. , vol.44 , pp. 605-613
    • Pao, G.M.1    Saier, M.H.2
  • 23
    • 33747843430 scopus 로고    scopus 로고
    • HHsenser: exhaustive transitive profile search using HMM-HMM comparison
    • Söding J., Remmert M., Biegert A., Lupas A.N. HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Res. 2006, 34:W374-W378.
    • (2006) Nucleic Acids Res. , vol.34
    • Söding, J.1    Remmert, M.2    Biegert, A.3    Lupas, A.N.4
  • 25
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Söding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33:W244-W248.
    • (2005) Nucleic Acids Res. , vol.33
    • Söding, J.1    Biegert, A.2    Lupas, A.N.3
  • 26
    • 10044222704 scopus 로고    scopus 로고
    • CLANS: a Java application for visualizing protein families based on pairwise similarity
    • Frickey T., Lupas A. CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 2004, 20:3702-3704.
    • (2004) Bioinformatics , vol.20 , pp. 3702-3704
    • Frickey, T.1    Lupas, A.2
  • 27
    • 0037589946 scopus 로고    scopus 로고
    • Analysis of the role of the EnvZ linker region in signal transduction using a chimeric Tar/EnvZ receptor protein, Tez1
    • Zhu Y., Inouye M. Analysis of the role of the EnvZ linker region in signal transduction using a chimeric Tar/EnvZ receptor protein, Tez1. J. Biol. Chem. 2003, 278:22812-22819.
    • (2003) J. Biol. Chem. , vol.278 , pp. 22812-22819
    • Zhu, Y.1    Inouye, M.2
  • 28
    • 0042561788 scopus 로고    scopus 로고
    • Probing conservation of HAMP linker structure and signal transduction mechanism through analysis of hybrid sensor kinases
    • Appleman J.A., Chen L.L., Stewart V. Probing conservation of HAMP linker structure and signal transduction mechanism through analysis of hybrid sensor kinases. J. Bacteriol. 2003, 185:4872-4882.
    • (2003) J. Bacteriol. , vol.185 , pp. 4872-4882
    • Appleman, J.A.1    Chen, L.L.2    Stewart, V.3
  • 29
    • 0028115617 scopus 로고
    • Transmembrane signalling by a hybrid protein: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to the kinase/phosphatase domain of osmosensor EnvZ
    • Baumgartner J.W., Kim C., Brissette R.E., Inouye M., Park C., Hazelbauer G.L. Transmembrane signalling by a hybrid protein: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to the kinase/phosphatase domain of osmosensor EnvZ. J. Bacteriol. 1994, 176:1157-1163.
    • (1994) J. Bacteriol. , vol.176 , pp. 1157-1163
    • Baumgartner, J.W.1    Kim, C.2    Brissette, R.E.3    Inouye, M.4    Park, C.5    Hazelbauer, G.L.6
  • 30
    • 0036289324 scopus 로고    scopus 로고
    • Exploring the role of alanine in the structure of the Lac repressor tetramerization domain, a ferritin-like Alacoil
    • Solan A., Ratia K., Fairman R. Exploring the role of alanine in the structure of the Lac repressor tetramerization domain, a ferritin-like Alacoil. J. Mol. Biol. 2002, 317:601-612.
    • (2002) J. Mol. Biol. , vol.317 , pp. 601-612
    • Solan, A.1    Ratia, K.2    Fairman, R.3
  • 33
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B., Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA 2000, 97:10383-10388.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 34
    • 77950501101 scopus 로고    scopus 로고
    • Prediction of Coiled-Coil Proteins. PhD Dissertation, University of Tübingen, Germany.
    • Gruber, M. (2006). Prediction of Coiled-Coil Proteins. PhD Dissertation, University of Tübingen, Germany.
    • (2006)
    • Gruber, M.1
  • 35
    • 33744457709 scopus 로고    scopus 로고
    • A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses
    • Fares M.A., Travers S.A. A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics 2006, 173:9-23.
    • (2006) Genetics , vol.173 , pp. 9-23
    • Fares, M.A.1    Travers, S.A.2
  • 36
    • 18544362952 scopus 로고    scopus 로고
    • Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions
    • Gloor G.B., Martin L.C., Wahl L.M., Dunn S.D. Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry 2005, 44:7156-7165.
    • (2005) Biochemistry , vol.44 , pp. 7156-7165
    • Gloor, G.B.1    Martin, L.C.2    Wahl, L.M.3    Dunn, S.D.4
  • 37
    • 0033977832 scopus 로고    scopus 로고
    • Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis
    • Atchley W.R., Wollenberg K.R., Fitch W.M., Terhalle W., Dress A.W. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol. Biol. Evol. 2000, 17:164-178.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 164-178
    • Atchley, W.R.1    Wollenberg, K.R.2    Fitch, W.M.3    Terhalle, W.4    Dress, A.W.5
  • 38
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless S.W., Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999, 286:295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 39
    • 3042842115 scopus 로고    scopus 로고
    • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
    • Fodor A.A., Aldrich R.W. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 2004, 56:211-221.
    • (2004) Proteins , vol.56 , pp. 211-221
    • Fodor, A.A.1    Aldrich, R.W.2
  • 41
    • 58149479212 scopus 로고    scopus 로고
    • Conserved residues in the HAMP domain define a new family of proposed bipartite energy taxis receptors
    • Elliott K.T., Zhulin I.B., Stuckey J.A., DiRita V.J. Conserved residues in the HAMP domain define a new family of proposed bipartite energy taxis receptors. J. Bacteriol. 2009, 191:375-387.
    • (2009) J. Bacteriol. , vol.191 , pp. 375-387
    • Elliott, K.T.1    Zhulin, I.B.2    Stuckey, J.A.3    DiRita, V.J.4
  • 42
    • 6044254952 scopus 로고    scopus 로고
    • Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer
    • Watts K.J., Ma Q., Johnson M.S., Taylor B.L. Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer. J. Bacteriol. 2004, 186:7440-7449.
    • (2004) J. Bacteriol. , vol.186 , pp. 7440-7449
    • Watts, K.J.1    Ma, Q.2    Johnson, M.S.3    Taylor, B.L.4
  • 43
    • 33644771099 scopus 로고    scopus 로고
    • Development of the signal in sensory rhodopsin and its transfer to the cognate transducer
    • Moukhametzianov R., Klare J.P., Efremov R., Baeken C., Göppner A., Labahn J., et al. Development of the signal in sensory rhodopsin and its transfer to the cognate transducer. Nature 2006, 440:115-119.
    • (2006) Nature , vol.440 , pp. 115-119
    • Moukhametzianov, R.1    Klare, J.P.2    Efremov, R.3    Baeken, C.4    Göppner, A.5    Labahn, J.6
  • 44
    • 74249104499 scopus 로고    scopus 로고
    • Fast and accurate automatic structure prediction with HHpred
    • Hildebrand A., Remmert M., Biegert A., Söding J. Fast and accurate automatic structure prediction with HHpred. Proteins 2009, 77:128-132.
    • (2009) Proteins , vol.77 , pp. 128-132
    • Hildebrand, A.1    Remmert, M.2    Biegert, A.3    Söding, J.4
  • 46
    • 3042579686 scopus 로고    scopus 로고
    • Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
    • Viklund H., Elofsson A. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci. 2004, 13:1908-1917.
    • (2004) Protein Sci. , vol.13 , pp. 1908-1917
    • Viklund, H.1    Elofsson, A.2
  • 47
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 48
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982, 157:105-132.
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 49
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: calculation of positional conservation in a protein sequence alignment
    • Pei J., Grishin N.V. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 2001, 17:700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 51
    • 12344256786 scopus 로고    scopus 로고
    • PCOAT: positional correlation analysis using multiple methods
    • Qi Y., Grishin N.V. PCOAT: positional correlation analysis using multiple methods. Bioinformatics 2004, 20:3697-3699.
    • (2004) Bioinformatics , vol.20 , pp. 3697-3699
    • Qi, Y.1    Grishin, N.V.2


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