-
1
-
-
0037569526
-
Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria
-
Casadio R., et al. Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria. Protein Sci. 12 (2003) 1158-1168
-
(2003)
Protein Sci.
, vol.12
, pp. 1158-1168
-
-
Casadio, R.1
-
2
-
-
25444484398
-
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
-
Garrow A.G., et al. TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics 6 (2005) 56
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 56
-
-
Garrow, A.G.1
-
3
-
-
0036147641
-
Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures
-
Wimley W.C. Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures. Protein Sci. 11 (2002) 301-312
-
(2002)
Protein Sci.
, vol.11
, pp. 301-312
-
-
Wimley, W.C.1
-
4
-
-
0036708003
-
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes
-
Zhai Y., and Saier Jr. M.H. The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci. 11 (2002) 2196-2207
-
(2002)
Protein Sci.
, vol.11
, pp. 2196-2207
-
-
Zhai, Y.1
Saier Jr., M.H.2
-
5
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
-
Krogh A., et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 (2001) 567-580
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
-
6
-
-
0041341888
-
Prediction of lipoprotein signal peptides in Gram-negative bacteria
-
Juncker A.S., et al. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. 12 (2003) 1652-1662
-
(2003)
Protein Sci.
, vol.12
, pp. 1652-1662
-
-
Juncker, A.S.1
-
7
-
-
10944249586
-
Hiding behind hydrophobicity. Transmembrane segments in mass spectrometry
-
Eichacker L.A., et al. Hiding behind hydrophobicity. Transmembrane segments in mass spectrometry. J. Biol. Chem 279 (2004) 50915-50922
-
(2004)
J. Biol. Chem
, vol.279
, pp. 50915-50922
-
-
Eichacker, L.A.1
-
8
-
-
13244295436
-
The membrane proteome of Halobacterium salinarum
-
Klein C., et al. The membrane proteome of Halobacterium salinarum. Proteomics 5 (2005) 180-197
-
(2005)
Proteomics
, vol.5
, pp. 180-197
-
-
Klein, C.1
-
9
-
-
0034630358
-
Two-dimensional electrophoresis of membrane proteins using immobilized pH gradients
-
Molloy M.P. Two-dimensional electrophoresis of membrane proteins using immobilized pH gradients. Anal. Biochem. 280 (2000) 1-10
-
(2000)
Anal. Biochem.
, vol.280
, pp. 1-10
-
-
Molloy, M.P.1
-
10
-
-
0034066471
-
Membrane proteins and proteomics: un amour impossible?
-
Santoni V., et al. Membrane proteins and proteomics: un amour impossible?. Electrophoresis 21 (2000) 1054-1070
-
(2000)
Electrophoresis
, vol.21
, pp. 1054-1070
-
-
Santoni, V.1
-
11
-
-
70349350617
-
Exploring membrane proteomes
-
Hagen V. (Ed), Wiley-VCH
-
Stenberg F., and Daley D.O. Exploring membrane proteomes. In: Hagen V. (Ed). Proteomics Sample Preparation (2008), Wiley-VCH 303-312
-
(2008)
Proteomics Sample Preparation
, pp. 303-312
-
-
Stenberg, F.1
Daley, D.O.2
-
12
-
-
50049135906
-
Proteome of the Escherichia coli envelope and technological challenges in membrane proteome analysis
-
Weiner J.H., and Li L. Proteome of the Escherichia coli envelope and technological challenges in membrane proteome analysis. Biochim. Biophys. Acta 1778 (2008) 1698-1713
-
(2008)
Biochim. Biophys. Acta
, vol.1778
, pp. 1698-1713
-
-
Weiner, J.H.1
Li, L.2
-
13
-
-
57549088143
-
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome
-
Diaz-Mejia J.J., et al. Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. FEMS Microbiol. Rev. 33 (2009) 66-97
-
(2009)
FEMS Microbiol. Rev.
, vol.33
, pp. 66-97
-
-
Diaz-Mejia, J.J.1
-
14
-
-
33745127048
-
The Escherichia coli proteome: past, present, and future prospects
-
Han M.J., and Lee S.Y. The Escherichia coli proteome: past, present, and future prospects. Microbiol. Mol. Biol. Rev. 70 (2006) 362-439
-
(2006)
Microbiol. Mol. Biol. Rev.
, vol.70
, pp. 362-439
-
-
Han, M.J.1
Lee, S.Y.2
-
15
-
-
33745160404
-
Large-scale identification of protein-protein interaction of Escherichia coli K-12
-
Arifuzzaman M., et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 (2006) 686-691
-
(2006)
Genome Res.
, vol.16
, pp. 686-691
-
-
Arifuzzaman, M.1
-
16
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
Butland G., et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 (2005) 531-537
-
(2005)
Nature
, vol.433
, pp. 531-537
-
-
Butland, G.1
-
17
-
-
34547228693
-
Membrane proteome in Escherichia coli probed by MS3 mass spectrometry: a preliminary report
-
Cirulli C., et al. Membrane proteome in Escherichia coli probed by MS3 mass spectrometry: a preliminary report. Rapid Commun. Mass Spectrom 21 (2007) 2389-2397
-
(2007)
Rapid Commun. Mass Spectrom
, vol.21
, pp. 2389-2397
-
-
Cirulli, C.1
-
18
-
-
0041923788
-
Toward a protein profile of Escherichia coli: comparison to its transcription profile
-
Corbin R.W., et al. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 9232-9237
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 9232-9237
-
-
Corbin, R.W.1
-
19
-
-
0037354386
-
Proteomic analysis of the cell envelope fraction of Escherichia coli
-
Fountoulakis M., and Gasser R. Proteomic analysis of the cell envelope fraction of Escherichia coli. Amino Acids 24 (2003) 19-41
-
(2003)
Amino Acids
, vol.24
, pp. 19-41
-
-
Fountoulakis, M.1
Gasser, R.2
-
20
-
-
0038271634
-
Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins
-
Gevaert K., et al. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol. Cell. Proteomics 1 (2002) 896-903
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 896-903
-
-
Gevaert, K.1
-
21
-
-
33750112261
-
Effect of 2MEGA labeling on membrane proteome analysis using LC-ESI QTOF MS
-
Ji C., et al. Effect of 2MEGA labeling on membrane proteome analysis using LC-ESI QTOF MS. J. Proteome Res. 5 (2006) 2567-2576
-
(2006)
J. Proteome Res.
, vol.5
, pp. 2567-2576
-
-
Ji, C.1
-
22
-
-
33748346853
-
A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis
-
Lasserre J.P., et al. A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 (2006) 3306-3321
-
(2006)
Electrophoresis
, vol.27
, pp. 3306-3321
-
-
Lasserre, J.P.1
-
23
-
-
24044496176
-
Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth
-
Lopez-Campistrous A., et al. Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol. Cell. Proteomics 4 (2005) 1205-1209
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1205-1209
-
-
Lopez-Campistrous, A.1
-
24
-
-
23344450195
-
Detection and identification of stable oligomeric protein complexes in Escherichia coli inner membranes: a proteomics approach
-
Spelbrink R.E., et al. Detection and identification of stable oligomeric protein complexes in Escherichia coli inner membranes: a proteomics approach. J. Biol. Chem. 280 (2005) 28742-28748
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 28742-28748
-
-
Spelbrink, R.E.1
-
25
-
-
27144431766
-
Protein complexes of the Escherichia coli cell envelope
-
Stenberg F., et al. Protein complexes of the Escherichia coli cell envelope. J. Biol. Chem. 280 (2005) 34409-34419
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 34409-34419
-
-
Stenberg, F.1
-
26
-
-
34848823739
-
Consequences of membrane protein overexpression in Escherichia coli
-
Wagner S., et al. Consequences of membrane protein overexpression in Escherichia coli. Mol. Cell. Proteomics 6 (2007) 1527-1550
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 1527-1550
-
-
Wagner, S.1
-
27
-
-
0036907867
-
Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli
-
Yan J.X., et al. Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2 (2002) 1682-1698
-
(2002)
Proteomics
, vol.2
, pp. 1682-1698
-
-
Yan, J.X.1
-
28
-
-
33847681015
-
Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS
-
Zhang N., et al. Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics 7 (2007) 484-493
-
(2007)
Proteomics
, vol.7
, pp. 484-493
-
-
Zhang, N.1
-
29
-
-
44449083478
-
Prediction of membrane-protein topology from first principles
-
Bernsel A., et al. Prediction of membrane-protein topology from first principles. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 7177-7181
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 7177-7181
-
-
Bernsel, A.1
-
30
-
-
38549140094
-
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
-
Gama-Castro S., et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36 (2008) D120-D124
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Gama-Castro, S.1
-
31
-
-
0026716643
-
Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
-
von Heijne G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol 225 (1992) 487-494
-
(1992)
J. Mol. Biol
, vol.225
, pp. 487-494
-
-
von Heijne, G.1
-
32
-
-
33846413528
-
Proteomics of Synechocystis sp. PCC 6803. Identification of novel integral plasma membrane proteins
-
Pisareva T., et al. Proteomics of Synechocystis sp. PCC 6803. Identification of novel integral plasma membrane proteins. FEBS J 274 (2007) 791-804
-
(2007)
FEBS J
, vol.274
, pp. 791-804
-
-
Pisareva, T.1
-
33
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
-
Washburn M.P., et al. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19 (2001) 242-247
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
-
34
-
-
51649102828
-
A shotgun proteomic method for the identification of membrane-embedded proteins and peptides
-
Blackler A.R., et al. A shotgun proteomic method for the identification of membrane-embedded proteins and peptides. J. Proteome Res. 7 (2008) 3028-3034
-
(2008)
J. Proteome Res.
, vol.7
, pp. 3028-3034
-
-
Blackler, A.R.1
-
35
-
-
33646557331
-
Protein cleavage strategies for an improved analysis of the membrane proteome
-
Fischer F., and Poetsch A. Protein cleavage strategies for an improved analysis of the membrane proteome. Proteome Sci. 4 (2006) 2
-
(2006)
Proteome Sci.
, vol.4
, pp. 2
-
-
Fischer, F.1
Poetsch, A.2
-
36
-
-
39749139655
-
Membrane protein identification: N-terminal labeling of nontryptic membrane protein peptides facilitates database searching
-
Jansson M., et al. Membrane protein identification: N-terminal labeling of nontryptic membrane protein peptides facilitates database searching. J. Proteome Res. 7 (2008) 659-665
-
(2008)
J. Proteome Res.
, vol.7
, pp. 659-665
-
-
Jansson, M.1
-
37
-
-
3042521098
-
Improved prediction of signal peptides: SignalP 3.0
-
Bendtsen J.D., et al. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol 340 (2004) 783-795
-
(2004)
J. Mol. Biol
, vol.340
, pp. 783-795
-
-
Bendtsen, J.D.1
-
38
-
-
33748878164
-
Methods for predicting bacterial protein subcellular localization
-
Gardy J.L., and Brinkman F.S. Methods for predicting bacterial protein subcellular localization. Nat. Rev. Microbiol. 4 (2006) 741-751
-
(2006)
Nat. Rev. Microbiol.
, vol.4
, pp. 741-751
-
-
Gardy, J.L.1
Brinkman, F.S.2
-
39
-
-
37249037182
-
Molecular code for transmembrane-helix recognition by the Sec61 translocon
-
Hessa T., et al. Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450 (2007) 1026-1030
-
(2007)
Nature
, vol.450
, pp. 1026-1030
-
-
Hessa, T.1
-
40
-
-
2142657817
-
A combined transmembrane topology and signal peptide prediction method
-
Kall L., et al. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 338 (2004) 1027-1036
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 1027-1036
-
-
Kall, L.1
|