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Volumn 81, Issue 1, 2011, Pages 56-68

Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; GAS VESICLE PROTEIN A; MEMBRANE PROTEIN; MUTANT PROTEIN; PROTEINASE; UNCLASSIFIED DRUG;

EID: 79959562522     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2011.07669.x     Document Type: Article
Times cited : (36)

References (50)
  • 2
    • 0037031128 scopus 로고    scopus 로고
    • The sequence of the major gas vesicle protein, GvpA, influences width and strength of halobacterial gas vesicles
    • Beard, S., Hayes, P., Pfeifer, F., and Walsby, A.E. (2002) The sequence of the major gas vesicle protein, GvpA, influences width and strength of halobacterial gas vesicles. FEMS Microbiol Lett 213: 149-157.
    • (2002) FEMS Microbiol Lett , vol.213 , pp. 149-157
    • Beard, S.1    Hayes, P.2    Pfeifer, F.3    Walsby, A.E.4
  • 3
    • 0346057921 scopus 로고    scopus 로고
    • Subunit structure of gas vesicles: a MALDI-TOF mass spectrometry study
    • Belenky, M., Meyers, R., and Herzfeld, J. (2004) Subunit structure of gas vesicles: a MALDI-TOF mass spectrometry study. Biophys J 86: 499-505.
    • (2004) Biophys J , vol.86 , pp. 499-505
    • Belenky, M.1    Meyers, R.2    Herzfeld, J.3
  • 4
    • 79959553743 scopus 로고
    • Crystalline structure of gas vesicle wall from Anabaena flos-aquae
    • Blaurock, A., and Walsby, A.E. (1976) Crystalline structure of gas vesicle wall from Anabaena flos-aquae. J Mol Biol 16: 871-888.
    • (1976) J Mol Biol , vol.16 , pp. 871-888
    • Blaurock, A.1    Walsby, A.E.2
  • 5
    • 0017142818 scopus 로고
    • Structure of the wall of Halobacterium halobium gas vesicles
    • Blaurock, A., and Wober, W. (1976) Structure of the wall of Halobacterium halobium gas vesicles. J Mol Biol 106: 871-888.
    • (1976) J Mol Biol , vol.106 , pp. 871-888
    • Blaurock, A.1    Wober, W.2
  • 8
    • 0027155201 scopus 로고
    • Analysis of gas vesicle gene expression in Haloferax mediterranei reveals that GvpA and GvpC are both gas vesicle structural proteins
    • Englert, C., and Pfeifer, F. (1993) Analysis of gas vesicle gene expression in Haloferax mediterranei reveals that GvpA and GvpC are both gas vesicle structural proteins. J Biol Chem 268: 9329-9336.
    • (1993) J Biol Chem , vol.268 , pp. 9329-9336
    • Englert, C.1    Pfeifer, F.2
  • 9
    • 0026714661 scopus 로고
    • Three different but related gene clusters encoding gas vesicles in halophilic Archaea
    • Englert, C., Krüger, K., Offner, S., and Pfeifer, F. (1992a) Three different but related gene clusters encoding gas vesicles in halophilic Archaea. J Mol Biol 227: 586-592.
    • (1992) J Mol Biol , vol.227 , pp. 586-592
    • Englert, C.1    Krüger, K.2    Offner, S.3    Pfeifer, F.4
  • 10
    • 0026677546 scopus 로고
    • Functional analysis of the gas vesicle gene cluster of the halophilic archaeon Haloferax mediterranei defines the vac-region boundary and suggests a regulatory role for the gvpD gene or its product
    • Englert, C., Wanner, G., and Pfeifer, F. (1992b) Functional analysis of the gas vesicle gene cluster of the halophilic archaeon Haloferax mediterranei defines the vac-region boundary and suggests a regulatory role for the gvpD gene or its product. Mol Microbiol 6: 3543-3550.
    • (1992) Mol Microbiol , vol.6 , pp. 3543-3550
    • Englert, C.1    Wanner, G.2    Pfeifer, F.3
  • 11
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: a simple approach to improve protein structure predictions
    • Ginalski, K., Elofsson, A., Fischer, D., and Rychlewski, L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19: 1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 12
    • 33646196840 scopus 로고    scopus 로고
    • Evaluation of the information content in infrared spectra for protein secondary structure determination
    • Goormaghtigh, E., Ruysschaert, J.M., and Raussens, V. (2006) Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys J 90: 2946-2957.
    • (2006) Biophys J , vol.90 , pp. 2946-2957
    • Goormaghtigh, E.1    Ruysschaert, J.M.2    Raussens, V.3
  • 13
    • 70349472977 scopus 로고    scopus 로고
    • Template-free protein structure prediction and quality assessment with an all-atom free-energy model
    • Gopal, S.M., Verma, A., and Wenzel, W. (2009) Template-free protein structure prediction and quality assessment with an all-atom free-energy model. Proteins 77: 330-341.
    • (2009) Proteins , vol.77 , pp. 330-341
    • Gopal, S.M.1    Verma, A.2    Wenzel, W.3
  • 14
    • 49049087284 scopus 로고    scopus 로고
    • Relating sequence evolution of HIV1-protease to its underlying molecular mechanics
    • Hamacher, K. (2008) Relating sequence evolution of HIV1-protease to its underlying molecular mechanics. Gene 422: 30-36.
    • (2008) Gene , vol.422 , pp. 30-36
    • Hamacher, K.1
  • 15
    • 33846247964 scopus 로고    scopus 로고
    • Computing the amino acid specificity of fluctuations in biomolecular systems
    • Hamacher, K., and McCammon, J.A. (2006) Computing the amino acid specificity of fluctuations in biomolecular systems. J Chem Theor Comput 2: 873.
    • (2006) J Chem Theor Comput , vol.2 , pp. 873
    • Hamacher, K.1    McCammon, J.A.2
  • 16
    • 0023049694 scopus 로고
    • Complete amino acid sequence of cyanobacterial gas-vesicle protein indicates a 70-residue molecule that corresponds in size to the crystallographic unit cell
    • Hayes, P., Walsby, A., and Walker, J. (1986) Complete amino acid sequence of cyanobacterial gas-vesicle protein indicates a 70-residue molecule that corresponds in size to the crystallographic unit cell. Biochem J 236: 31-36.
    • (1986) Biochem J , vol.236 , pp. 31-36
    • Hayes, P.1    Walsby, A.2    Walker, J.3
  • 17
    • 58149125398 scopus 로고    scopus 로고
    • Anaerobiosis inhibits gas vesicle formation in halophilic Archaea
    • Hechler, T., and Pfeifer, F. (2009) Anaerobiosis inhibits gas vesicle formation in halophilic Archaea. Mol Microbiol 71: 132-145.
    • (2009) Mol Microbiol , vol.71 , pp. 132-145
    • Hechler, T.1    Pfeifer, F.2
  • 18
    • 3142767630 scopus 로고    scopus 로고
    • GvpE- and GvpD-mediated transcription regulation of the p-gvp genes encoding gas vesicles in Halobacterium salinarum
    • Hofacker, A., Schmitz, K., Cichonczyk, A., Sartorius-Neef, S., and Pfeifer, F. (2004) GvpE- and GvpD-mediated transcription regulation of the p-gvp genes encoding gas vesicles in Halobacterium salinarum. Microbiology 150: 1829-1838.
    • (2004) Microbiology , vol.150 , pp. 1829-1838
    • Hofacker, A.1    Schmitz, K.2    Cichonczyk, A.3    Sartorius-Neef, S.4    Pfeifer, F.5
  • 19
    • 77951065786 scopus 로고    scopus 로고
    • BioPhysConnectoR: connecting sequence information and biophysical models
    • Hoffgaard, F., Weil, P., and Hamacher, K. (2010) BioPhysConnectoR: connecting sequence information and biophysical models. BMC Bioinformatics 11: 199.
    • (2010) BMC Bioinformatics , vol.11 , pp. 199
    • Hoffgaard, F.1    Weil, P.2    Hamacher, K.3
  • 20
  • 21
    • 0029018548 scopus 로고
    • The use and misuse of FTIR spectroscopy in the determination of protein structure
    • Jackson, M., and Mantsch, H.H. (1995) The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit Rev Biochem Mol Biol 30: 95-120.
    • (1995) Crit Rev Biochem Mol Biol , vol.30 , pp. 95-120
    • Jackson, M.1    Mantsch, H.H.2
  • 22
    • 0242362161 scopus 로고    scopus 로고
    • Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
    • Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M., and Hughey, R. (2003) Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 53 (Suppl. 6): 491-496.
    • (2003) Proteins , vol.53 , Issue.6 SUPPL. , pp. 491-496
    • Karplus, K.1    Karchin, R.2    Draper, J.3    Casper, J.4    Mandel-Gutfreund, Y.5    Diekhans, M.6    Hughey, R.7
  • 23
    • 54949103617 scopus 로고    scopus 로고
    • PREDICT-2ND: a tool for generalized protein local structure prediction
    • Katzman, S., Barrett, C., Thiltgen, G., Karchin, R., and Karplus, K. (2008) PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics 24: 2453-2459.
    • (2008) Bioinformatics , vol.24 , pp. 2453-2459
    • Katzman, S.1    Barrett, C.2    Thiltgen, G.3    Karchin, R.4    Karplus, K.5
  • 24
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: a case study using the PHYRE server
    • Kelley, L.A., and Sternberg, M.J.E. (2009) Protein structure prediction on the Web: a case study using the PHYRE server. Nat Protoc 4: 363-371.
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 25
    • 0029042511 scopus 로고
    • Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4Å resolution
    • Löwe, J., Stock, D., Jap, B., Zwickl, P., Baumeister, W., and Huber, R. (1995) Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4Å resolution. Science 268: 533-539.
    • (1995) Science , vol.268 , pp. 533-539
    • Löwe, J.1    Stock, D.2    Jap, B.3    Zwickl, P.4    Baumeister, W.5    Huber, R.6
  • 26
    • 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, A.D., Feig, M., and Brooks, C.L., III (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, A.D.1    Feig, M.2    Brooks III, C.L.3
  • 27
    • 0029862834 scopus 로고    scopus 로고
    • Direct observation of protein secondary structure in gas vesicles by atomic force microscopy
    • McMaster, T., Niles, M., and Walsby, A.E. (1996) Direct observation of protein secondary structure in gas vesicles by atomic force microscopy. Biophys J 70: 2431-2436.
    • (1996) Biophys J , vol.70 , pp. 2431-2436
    • McMaster, T.1    Niles, M.2    Walsby, A.E.3
  • 28
    • 0033623952 scopus 로고    scopus 로고
    • Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea
    • Offner, S., Hofacker, A., Wanner, G., and Pfeifer, F. (2000) Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea. J Bacteriol 182: 4328-4336.
    • (2000) J Bacteriol , vol.182 , pp. 4328-4336
    • Offner, S.1    Hofacker, A.2    Wanner, G.3    Pfeifer, F.4
  • 29
    • 0027207837 scopus 로고
    • Plasmid pHH1 of Halobacterium salinarum: characterization of the replicon region, the gas vesicle gene cluster and insertion elements
    • Pfeifer, F., and Ghahraman, P. (1993) Plasmid pHH1 of Halobacterium salinarum: characterization of the replicon region, the gas vesicle gene cluster and insertion elements. Mol Gen Genet 238: 193-200.
    • (1993) Mol Gen Genet , vol.238 , pp. 193-200
    • Pfeifer, F.1    Ghahraman, P.2
  • 30
    • 0035157178 scopus 로고    scopus 로고
    • A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei
    • Pfeifer, F., Zotzel, J., Kurenbach, B., Röder, R., and Zimmermann, P. (2001) A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei. Microbiology 147: 63-73.
    • (2001) Microbiology , vol.147 , pp. 63-73
    • Pfeifer, F.1    Zotzel, J.2    Kurenbach, B.3    Röder, R.4    Zimmermann, P.5
  • 33
    • 49749084731 scopus 로고    scopus 로고
    • Regulation of gvp genes encoding gas vesicle proteins in halophilic archaea
    • Scheuch, S., Marschaus, L., Sartorius-Neef, S., and Pfeifer, F. (2008) Regulation of gvp genes encoding gas vesicle proteins in halophilic archaea. Arch Microbiol 190: 333-340.
    • (2008) Arch Microbiol , vol.190 , pp. 333-340
    • Scheuch, S.1    Marschaus, L.2    Sartorius-Neef, S.3    Pfeifer, F.4
  • 34
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi, J., Blundell, T.L., and Mizuguchi, K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310: 243-257.
    • (2001) J Mol Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 35
    • 2342660728 scopus 로고    scopus 로고
    • Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins
    • Shukla, H.D., and DasSarma, S. (2004) Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. J Bacteriol 186: 3182-3186.
    • (2004) J Bacteriol , vol.186 , pp. 3182-3186
    • Shukla, H.D.1    DasSarma, S.2
  • 36
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: an automated measure for the assessment of protein structure prediction quality
    • Siew, N., Elofsson, A., Rychlewski, L., and Fischer, D. (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 16: 776-785.
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4
  • 37
    • 62649156736 scopus 로고    scopus 로고
    • Solid-state NMR evidence for inequal GvpA subunits in gas vesicles
    • Sivertsen, A., Bayro, M., Belenky, M., Griffin, R., and Herzfeld, J. (2009) Solid-state NMR evidence for inequal GvpA subunits in gas vesicles. J Mol Biol 387: 1032-1039.
    • (2009) J Mol Biol , vol.387 , pp. 1032-1039
    • Sivertsen, A.1    Bayro, M.2    Belenky, M.3    Griffin, R.4    Herzfeld, J.5
  • 38
    • 77957340600 scopus 로고    scopus 로고
    • Solid-state NMR characterization of gas vesicle structure
    • Sivertsen, A., Bayro, M., Belenky, M., Griffin, R., and Herzfeld, J. (2010) Solid-state NMR characterization of gas vesicle structure. Biophys J 99: 1932-1939.
    • (2010) Biophys J , vol.99 , pp. 1932-1939
    • Sivertsen, A.1    Bayro, M.2    Belenky, M.3    Griffin, R.4    Herzfeld, J.5
  • 39
    • 0014322650 scopus 로고
    • Further characterization of particulate fractions from lysed cell envelopes of Halobacterium halobium and isolation of gas vacuole membranes
    • Stoeckenius, W., and Kunau, W. (1968) Further characterization of particulate fractions from lysed cell envelopes of Halobacterium halobium and isolation of gas vacuole membranes. J Cell Biol 38: 337-357.
    • (1968) J Cell Biol , vol.38 , pp. 337-357
    • Stoeckenius, W.1    Kunau, W.2
  • 40
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • Tsai, J., Bonneau, R., Morozov, A.V., Kuhlman, B., Rohl, C.A., and Baker, D. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53: 76-87.
    • (2003) Proteins , vol.53 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Morozov, A.V.3    Kuhlman, B.4    Rohl, C.A.5    Baker, D.6
  • 42
    • 0028514996 scopus 로고
    • Linearly scalable computation of smooth molecular surfaces
    • Varshney, A., Brooks, F.P., and Wright, W.V. (1994) Linearly scalable computation of smooth molecular surfaces. IEEE Comput Graph Appl 14: 19-25.
    • (1994) IEEE Comput Graph Appl , vol.14 , pp. 19-25
    • Varshney, A.1    Brooks, F.P.2    Wright, W.V.3
  • 43
    • 67650354848 scopus 로고    scopus 로고
    • A free-energy approach for all-atom protein simulation
    • Verma, A., and Wenzel, W. (2009) A free-energy approach for all-atom protein simulation. Biophys J 96: 3483-3494.
    • (2009) Biophys J , vol.96 , pp. 3483-3494
    • Verma, A.1    Wenzel, W.2
  • 44
    • 33749665952 scopus 로고    scopus 로고
    • Basin hopping simulations for all-atom protein folding
    • Verma, A., Schug, A., Lee, K.H., and Wenzel, W. (2006) Basin hopping simulations for all-atom protein folding. J Chem Phys 124: 044515.
    • (2006) J Chem Phys , vol.124 , pp. 044515
    • Verma, A.1    Schug, A.2    Lee, K.H.3    Wenzel, W.4
  • 45
    • 0028261412 scopus 로고
    • Gas vesicles
    • Walsby, A.E. (1994) Gas vesicles. Microbiol Rev 58: 94-144.
    • (1994) Microbiol Rev , vol.58 , pp. 94-144
    • Walsby, A.E.1
  • 46
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • Wang, C., Bradley, P., and Baker, D. (2007) Protein-protein docking with backbone flexibility. J Mol Biol 373: 503-519.
    • (2007) J Mol Biol , vol.373 , pp. 503-519
    • Wang, C.1    Bradley, P.2    Baker, D.3
  • 47
    • 9344243513 scopus 로고    scopus 로고
    • FTIR reveals structural differences between native β-sheet proteins and amyloid fibrils
    • Zandomeneghi, G., Krebs, M.R.H., McCammon, M.G., and Fändrich, M. (2004) FTIR reveals structural differences between native β-sheet proteins and amyloid fibrils. Protein Sci 13: 3314-3321.
    • (2004) Protein Sci , vol.13 , pp. 3314-3321
    • Zandomeneghi, G.1    Krebs, M.R.H.2    McCammon, M.G.3    Fändrich, M.4
  • 48
    • 0032128128 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray crystallographic studies of the native and chemically modified anion-selective porin from Comamonas acidovorans
    • Zeth, K., Schnaible, V., Przyblyski, M., Welte, W., Diederichs, K., and Engelhardt, H. (1998) Crystallization and preliminary X-ray crystallographic studies of the native and chemically modified anion-selective porin from Comamonas acidovorans. Acta Cryst D54: 650-653.
    • (1998) Acta Cryst , vol.D54 , pp. 650-653
    • Zeth, K.1    Schnaible, V.2    Przyblyski, M.3    Welte, W.4    Diederichs, K.5    Engelhardt, H.6
  • 49
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Zhang, Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9: 40.
    • (2008) BMC Bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1
  • 50
    • 0026467097 scopus 로고
    • Expression of functional Thermoplasma acidophilum proteasomes in Escherichia coli
    • Zwickl, P., Lottspeich, F., and Baumeister, W. (1992) Expression of functional Thermoplasma acidophilum proteasomes in Escherichia coli. FEBS Lett 312: 157-160.
    • (1992) FEBS Lett , vol.312 , pp. 157-160
    • Zwickl, P.1    Lottspeich, F.2    Baumeister, W.3


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