RegulonDB RegulonDB 10.7: Gene Form

ompF gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

asnS aspC ompF CpxR CpxR OmpR IHF CRP IHF CpxR RstA CRP OmpR OmpR CpxR IHF CRP OmpR MicF TSS_1232 TSS_1232 TSS_1231 TSS_1231 ompFp ompFp TSS_1229 TSS_1229 TSS_1228 TSS_1228 TSS_1227 TSS_1227 TSS_1226 (cluster) TSS_1226 (cluster) TSS_1225 (cluster) TSS_1225 (cluster) TSS_1224 TSS_1224 TSS_1223 TSS_1223 TSS_1222 TSS_1222 TSS_1221 TSS_1221 TSS_1220 TSS_1220 TSS_1219 (cluster) TSS_1219 (cluster) TSS_1218 TSS_1218 TSS_1217 TSS_1217 TSS_1216 TSS_1216 TSS_1215 (cluster) TSS_1215 (cluster) TSS_1214 TSS_1214 TSS_1213 TSS_1213 TSS_1212 TSS_1212 aspCp aspCp TSS_1211 TSS_1211 TSS_1210 TSS_1210 TSS_1209 TSS_1209 TSS_1208 TSS_1208 TSS_1207 (cluster) TSS_1207 (cluster)

Name: ompF    Texpresso search in the literature
Synonym(s): ECK0920, EG10671, b0929, cmlB, cry, nfxB, tolF
Genome position(nucleotides): 985894 <-- 986982 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
Reference(s): [1] Inokuchi K., et al., 1982
External database links:  
M3D: ompF
PortEco: b0929

Name: outer membrane porin F
Synonym(s): CmlB, Cry, NfxB, OmpF, TolF, colB, outer membrane protein 0-9, outer membrane protein 1a, outer membrane protein 4, outer membrane protein A1, outer membrane protein F, outer membrane protein b
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 39.333
Isoelectric point: 4.533
Type Positions Sequence
141 -> 141 G
172 -> 181 GLNFAVQYLG
307 -> 307 G
23 -> 28 AEIYNK


Multifun Terms (GenProtEC)  
  4 - transport --> 4.1 - Channel-type Transporters --> 4.1.B - Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0016020 - membrane
GO:0016021 - integral component of membrane
GO:0034702 - ion channel complex
GO:0046930 - pore complex
molecular_function GO:0047485 - protein N-terminus binding
GO:0097718 - disordered domain specific binding
GO:0005515 - protein binding
GO:0015075 - ion transmembrane transporter activity
GO:0015288 - porin activity
GO:0005216 - ion channel activity
GO:0008289 - lipid binding
GO:0042802 - identical protein binding
GO:0001530 - lipopolysaccharide binding
GO:0042912 - colicin transmembrane transporter activity
biological_process GO:0006811 - ion transport
GO:0043213 - bacteriocin transport
GO:0034220 - ion transmembrane transport
GO:0042908 - xenobiotic transport
GO:0070207 - protein homotrimerization
Note(s): Note(s): ...[more].
Reference(s): [2] Aguilella-Arzo M., et al., 2007
[3] Alcaraz A., et al., 2009
[4] Baars L., et al., 2006
[5] Bainbridge G., et al., 1998
[6] Bajaj H., et al., 2017
[7] Basle A., et al., 2001
[8] Benson SA., et al., 1985
[9] Biro I., et al., 2010
[10] Bredin J., et al., 2003
[11] Buehler LK., et al., 1993
[12] Burgess NK., et al., 2008
[13] Castillo-Keller M., et al., 2006
[14] Chong ZS., et al., 2015
[15] Danelon C., et al., 2003
[16] Darcan C., et al., 2003
[17] Diedrich DL., et al., 1990
[18] Duval V., et al., 2009
[19] Faraudo J., et al., 2010
[20] Fourel D., et al., 1994
[21] Fourel D., et al., 1992
[22] Garcia-Gimenez E., et al., 2012
[23] Garcia-Gimenez E., et al., 2011
[24] Gehring KB., et al., 1989
[25] Henning U., et al., 1975
[26] Ho D., et al., 2006
[27] Housden NG., et al., 2018
[28] Im W., et al., 2002
[29] Im W., et al., 2002
[30] Im W., et al., 2000
[31] Ionescu SA., et al., 2017
[32] Jahn LJ., et al., 2017
[33] Jeanteur D., et al., 1991
[34] Jin M., et al., 2018
[35] Jo YL., et al., 1986
[36] Koga-Ban Y., et al., 1983
[37] Kreir M., et al., 2008
[38] Kumar A., et al., 2010
[39] Law CJ., et al., 2003
[40] Lin M., et al., 2017
[41] Lupi N., et al., 1989
[42] Ma H., et al., 2018
[43] Miedema H., et al., 2006
[44] Miedema H., et al., 2006
[45] Mizuno T., et al., 1988
[46] Mutoh N., et al., 1981
[47] Nara F., et al., 1984
[48] Nara F., et al., 1986
[49] Nikaido H., et al., 1985
[50] Niramitranon J., et al., 2016
[51] Norioka S., et al., 1986
[52] Osborn MJ., et al., 1980
[53] Ozawa Y., et al., 1983
[54] Pages JM., et al., null
[55] Pages JM., et al., 1988
[56] Phale PS., et al., 2001
[57] Phan K., et al., 2017
[58] Pu Y., et al., 2016
[59] Pugsley AP., et al., 1978
[60] Queralt-Martin M., et al., 2011
[61] Ried G., et al., 1990
[62] Rosenbusch JP. 1974
[63] Schabert FA., et al., 1995
[64] Schmitt EK., et al., 2006
[65] Sen K., et al., 1991
[66] Silverman JA., et al., 1987
[67] Spector J., et al., 2010
[68] Takayanagi K., et al., 1992
[69] Tieleman DP., et al., 1998
[70] Tommassen J., et al., 1981
[71] Varma S., et al., 2006
[72] Varma S., et al., 2004
[73] Visudtiphole V., et al., 2005
[74] Vrouenraets M., et al., 2010
[75] Zakharov SD., et al., 2008
[76] Zhang DF., et al., 2018
[77] Zhang E., et al., 1999
[78] Zhao Z., et al., 2015
[79] Zhu Y., et al., 2009
External database links:  

Name: ompF         
Operon arrangement:
Transcription unit        Promoter

Transcriptional Regulation      
Display Regulation             
Activated by: CRP, Fur, OmpR, IHF, PhoB, EnvY
Repressed by: CpxR, OmpR, IHF, RstA

Regulation by small RNA    
  Display Regulation
small RNA micF, ipeX

Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1207 (cluster) 984970 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [80]
  promoter TSS_1208 985039 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1209 985236 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1210 985360 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1211 985652 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1212 985744 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1213 985982 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1214 985984 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1215 (cluster) 985988 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [80]
  promoter TSS_1216 986008 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1217 986010 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1218 986077 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1219 (cluster) 986081 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [80]
  promoter TSS_1220 986084 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1221 986119 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1222 986124 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1223 986314 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1224 986647 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1225 (cluster) 986768 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [80]
  promoter TSS_1226 (cluster) 986786 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [80]
  promoter TSS_1227 986788 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1228 986897 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1229 986969 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1231 988306 reverse nd [RS-EPT-CBR] [80]
  promoter TSS_1232 988310 reverse nd [RS-EPT-CBR] [80]


 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


 [1] Inokuchi K., Mutoh N., Matsuyama S., Mizushima S., 1982, Primary structure of the ompF gene that codes for a major outer membrane protein of Escherichia coli K-12., Nucleic Acids Res 10(21):6957-68

 [2] Aguilella-Arzo M., Garcia-Celma JJ., Cervera J., Alcaraz A., Aguilella VM., 2007, Electrostatic properties and macroscopic electrodiffusion in OmpF porin and mutants., Bioelectrochemistry 70(2):320-7

 [3] Alcaraz A., Nestorovich EM., Lopez ML., Garcia-Gimenez E., Bezrukov SM., Aguilella VM., 2009, Diffusion, exclusion, and specific binding in a large channel: a study of OmpF selectivity inversion., Biophys J 96(1):56-66

 [4] Baars L., Ytterberg AJ., Drew D., Wagner S., Thilo C., van Wijk KJ., de Gier JW., 2006, Defining the role of the Escherichia coli chaperone SecB using comparative proteomics., J Biol Chem 281(15):10024-34

 [5] Bainbridge G., Mobasheri H., Armstrong GA., Lea EJ., Lakey JH., 1998, Voltage-gating of Escherichia coli porin: a cystine-scanning mutagenesis study of loop 3., J Mol Biol 275(2):171-6

 [6] Bajaj H., Acosta Gutierrez S., Bodrenko I., Malloci G., Scorciapino MA., Winterhalter M., Ceccarelli M., 2017, Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules., ACS Nano 11(6):5465-5473

 [7] Basle A., Delcour AH., 2001, Effect of two polyamine toxins on the bacterial porin OmpF., Biochem Biophys Res Commun 285(2):550-4

 [8] Benson SA., Decloux A., 1985, Isolation and characterization of outer membrane permeability mutants in Escherichia coli K-12., J Bacteriol 161(1):361-7

 [9] Biro I., Pezeshki S., Weingart H., Winterhalter M., Kleinekathofer U., 2010, Comparing the temperature-dependent conductance of the two structurally similar E. coli porins OmpC and OmpF., Biophys J 98(9):1830-9

 [10] Bredin J., Simonet V., Iyer R., Delcour AH., Pages JM., 2003, Colicins, spermine and cephalosporins: a competitive interaction with the OmpF eyelet., Biochem J 376(Pt 1):245-52

 [11] Buehler LK., Rosenbusch JP., 1993, Single channel behavior of matrix porin of Escherichia coli., Biochem Biophys Res Commun 190(2):624-9

 [12] Burgess NK., Dao TP., Stanley AM., Fleming KG., 2008, Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro., J Biol Chem 283(39):26748-58

 [13] Castillo-Keller M., Vuong P., Misra R., 2006, Novel mechanism of Escherichia coli porin regulation., J Bacteriol 188(2):576-86

 [14] Chong ZS., Woo WF., Chng SS., 2015, Osmoporin OmpC forms a complex with MlaA to maintain outer membrane lipid asymmetry in Escherichia coli., Mol Microbiol 98(6):1133-46

 [15] Danelon C., Suenaga A., Winterhalter M., Yamato I., 2003, Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation., Biophys Chem 104(3):591-603

 [16] Darcan C., Ozkanca R., Flint KP., 2003, Survival of nonspecific porin-deficient mutants of Escherichia coli in black sea water., Lett Appl Microbiol 37(5):380-5

 [17] Diedrich DL., Stein MA., Schnaitman CA., 1990, Associations of Escherichia coli K-12 OmpF trimers with rough and smooth lipopolysaccharides., J Bacteriol 172(9):5307-11

 [18] Duval V., Nicoloff H., Levy SB., 2009, Combined inactivation of lon and ycgE decreases multidrug susceptibility by reducing the amount of OmpF porin in Escherichia coli., Antimicrob Agents Chemother 53(11):4944-8

 [19] Faraudo J., Calero C., Aguilella-Arzo M., 2010, Ionic partition and transport in multi-ionic channels: a molecular dynamics simulation study of the OmpF bacterial porin., Biophys J 99(7):2107-15

 [20] Fourel D., Bernadac A., Pages JM., 1994, Involvement of exposed polypeptide loops in trimeric stability and membrane insertion of Escherichia coli OmpF porin., Eur J Biochem 222(2):625-30

 [21] Fourel D., Mizushima S., Pages JM., 1992, Dynamics of the exposure of epitopes on OmpF, an outer membrane protein of Escherichia coli., Eur J Biochem 206(1):109-14

 [22] Garcia-Gimenez E., Alcaraz A., Aguilella VM., 2012, Divalent Metal Ion Transport across Large Biological Ion Channels and Their Effect on Conductance and Selectivity., Biochem Res Int 245786

 [23] Garcia-Gimenez E., Lopez ML., Aguilella VM., Alcaraz A., 2011, Linearity, saturation and blocking in a large multiionic channel: divalent cation modulation of the OmpF porin conductance., Biochem Biophys Res Commun 404(1):330-4

 [24] Gehring KB., Nikaido H., 1989, Existence and purification of porin heterotrimers of Escherichia coli K12 OmpC, OmpF, and PhoE proteins., J Biol Chem 264(5):2810-5

 [25] Henning U., Haller I., 1975, Mutants of Escherichia coli K12 lacking all 'major' proteins of the outer cell envelope membrane., FEBS Lett 55(1):161-4

 [26] Ho D., Chang S., Montemagno CD., 2006, Fabrication of biofunctional nanomaterials via Escherichia coli OmpF protein air/water interface insertion/integration with copolymeric amphiphiles., Nanomedicine 2(2):103-12

 [27] Housden NG., Rassam P., Lee S., Samsudin F., Kaminska R., Sharp C., Goult JD., Francis ML., Khalid S., Bayley H., Kleanthous C., 2018, Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm., Biochemistry 57(29):4374-4381

 [28] Im W., Roux B., 2002, Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution., J Mol Biol 319(5):1177-97

 [29] Im W., Roux B., 2002, Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory., J Mol Biol 322(4):851-69

 [30] Im W., Seefeld S., Roux B., 2000, A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels., Biophys J 79(2):788-801

 [31] Ionescu SA., Lee S., Housden NG., Kaminska R., Kleanthous C., Bayley H., 2017, Orientation of the OmpF Porin in Planar Lipid Bilayers., Chembiochem 18(6):554-562

 [32] Jahn LJ., Munck C., Ellabaan MMH., Sommer MOA., 2017, Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes., Front Microbiol 8:816

 [33] Jeanteur D., Lakey JH., Pattus F., 1991, The bacterial porin superfamily: sequence alignment and structure prediction., Mol Microbiol 5(9):2153-64

 [34] Jin M., Lu J., Chen Z., Nguyen SH., Mao L., Li J., Yuan Z., Guo J., 2018, Antidepressant fluoxetine induces multiple antibiotics resistance in Escherichia coli via ROS-mediated mutagenesis., Environ Int 120:421-430

 [35] Jo YL., Nara F., Ichihara S., Mizuno T., Mizushima S., 1986, Purification and characterization of the OmpR protein, a positive regulator involved in osmoregulatory expression of the ompF and ompC genes in Escherichia coli., J Biol Chem 261(32):15253-6

 [36] Koga-Ban Y., Mutoh N., Inokuchi K., Mizushima S., 1983, Mutation causing overproduction of outer membrane protein OmpF and suppression of OmpC synthesis in Escherichia coli., J Bacteriol 155(3):1110-5

 [37] Kreir M., Farre C., Beckler M., George M., Fertig N., 2008, Rapid screening of membrane protein activity: electrophysiological analysis of OmpF reconstituted in proteoliposomes., Lab Chip 8(4):587-95

 [38] Kumar A., Hajjar E., Ruggerone P., Ceccarelli M., 2010, Molecular Simulations Reveal the Mechanism and the Determinants for Ampicillin Translocation through OmpF., J Phys Chem B 114(29):9608-16

 [39] Law CJ., Penfold CN., Walker DC., Moore GR., James R., Kleanthous C., 2003, OmpF enhances the ability of BtuB to protect susceptible Escherichia coli cells from colicin E9 cytotoxicity., FEBS Lett 545(2-3):127-32

 [40] Lin M., Zhang G., Fahie M., Morgan LK., Chen M., Keiderling TA., Kenney LJ., Liang J., 2017, Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif., Biochim Biophys Acta Biomembr 1859(7):1180-1189

 [41] Lupi N., Bourgois A., Bernadac A., Laboucarie S., Pages JM., 1989, Immunological analysis of porin polymorphism in Escherichia coli B and K-12., Mol Immunol 26(11):1027-36

 [42] Ma H., Khan A., Nangia S., 2018, Dynamics of OmpF Trimer Formation in the Bacterial Outer Membrane of Escherichia coli., Langmuir 34(19):5623-5634

 [43] Miedema H., Vrouenraets M., Wierenga J., Eisenberg B., Schirmer T., Basle A., Meijberg W., 2006, Conductance and selectivity fluctuations in D127 mutants of the bacterial porin OmpF., Eur Biophys J 36(1):13-22

 [44] Miedema H., Vrouenraets M., Wierenga J., Gillespie D., Eisenberg B., Meijberg W., Nonner W., 2006, Ca2+ selectivity of a chemically modified OmpF with reduced pore volume., Biophys J 91(12):4392-400

 [45] Mizuno T., Kato M., Jo YL., Mizushima S., 1988, Interaction of OmpR, a positive regulator, with the osmoregulated ompC and ompF genes of Escherichia coli. Studies with wild-type and mutant OmpR proteins., J Biol Chem 263(2):1008-12

 [46] Mutoh N., Nagasawa T., Mizushima S., 1981, Specialized transducing bacteriophage lambda carrying the structural gene for a major outer membrane matrix protein of Escherichia coli K-12., J Bacteriol 145(2):1085-90

 [47] Nara F., Inokuchi K., Matsuyama S., Mizushima S., 1984, Mutation causing reverse osmoregulation of synthesis of OmpF, a major outer membrane protein of Escherichia coli., J Bacteriol 159(2):688-92

 [48] Nara F., Mizuno T., Mizushima S., 1986, Complementation analysis of the wild-type and mutant ompR genes exhibiting different phenotypes of osmoregulation of the ompF and ompC genes of Escherichia coli., Mol Gen Genet 205(1):51-5

 [49] Nikaido H., Vaara M., 1985, Molecular basis of bacterial outer membrane permeability., Microbiol Rev 49(1):1-32

 [50] Niramitranon J., Sansom MS., Pongprayoon P., 2016, Why do the outer membrane proteins OmpF from E. coli and OprP from P. aeruginosa prefer trimers? Simulation studies., J Mol Graph Model 65:1-7

 [51] Norioka S., Ramakrishnan G., Ikenaka K., Inouye M., 1986, Interaction of a transcriptional activator, OmpR, with reciprocally osmoregulated genes, ompF and ompC, of Escherichia coli., J Biol Chem 261(36):17113-9

 [52] Osborn MJ., Wu HC., 1980, Proteins of the outer membrane of gram-negative bacteria., Annu Rev Microbiol 34:369-422

 [53] Ozawa Y., Mizushima S., 1983, Regulation of outer membrane porin protein synthesis in Escherichia coli K-12: ompF regulates the expression of ompC., J Bacteriol 154(2):669-75

 [54] Pages JM., Bolla JM., Bernadac A., Fourel D., null, Immunological approach of assembly and topology of OmpF, an outer membrane protein of Escherichia coli., Biochimie 72(2-3):169-76

 [55] Pages JM., Pages C., Bernadac A., Prince P., 1988, Immunological evidence for differences in the exposed regions of OmpF porins from Escherichia coli B and K-12., Mol Immunol 25(6):555-63

 [56] Phale PS., Philippsen A., Widmer C., Phale VP., Rosenbusch JP., Schirmer T., 2001, Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation., Biochemistry 40(21):6319-25

 [57] Phan K., Ferenci T., 2017, The fitness costs and trade-off shapes associated with the exclusion of nine antibiotics by OmpF porin channels., ISME J 11(6):1472-1482

 [58] Pu Y., Zhao Z., Li Y., Zou J., Ma Q., Zhao Y., Ke Y., Zhu Y., Chen H., Baker MAB., Ge H., Sun Y., Xie XS., Bai F., 2016, Enhanced Efflux Activity Facilitates Drug Tolerance in Dormant Bacterial Cells., Mol Cell 62(2):284-294

 [59] Pugsley AP., Schnaitman CA., 1978, Identification of three genes controlling production of new outer membrane pore proteins in Escherichia coli K-12., J Bacteriol 135(3):1118-29

 [60] Queralt-Martin M., Garcia-Gimenez E., Mafe S., Alcaraz A., 2011, Divalent cations reduce the pH sensitivity of OmpF channel inducing the pK(a) shift of key acidic residues., Phys Chem Chem Phys 13(2):563-9

 [61] Ried G., Hindennach I., Henning U., 1990, Role of lipopolysaccharide in assembly of Escherichia coli outer membrane proteins OmpA, OmpC, and OmpF., J Bacteriol 172(10):6048-53

 [62] Rosenbusch JP., 1974, Characterization of the major envelope protein from Escherichia coli. Regular arrangement on the peptidoglycan and unusual dodecyl sulfate binding., J Biol Chem 249(24):8019-29

 [63] Schabert FA., Henn C., Engel A., 1995, Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy., Science 268(5207):92-4

 [64] Schmitt EK., Vrouenraets M., Steinem C., 2006, Channel activity of OmpF monitored in nano-BLMs., Biophys J 91(6):2163-71

 [65] Sen K., Nikaido H., 1991, Trimerization of an in vitro synthesized OmpF porin of Escherichia coli outer membrane., J Biol Chem 266(17):11295-300

 [66] Silverman JA., Benson SA., 1987, Bacteriophage K20 requires both the OmpF porin and lipopolysaccharide for receptor function., J Bacteriol 169(10):4830-3

 [67] Spector J., Zakharov S., Lill Y., Sharma O., Cramer WA., Ritchie K., 2010, Mobility of BtuB and OmpF in the Escherichia coli outer membrane: implications for dynamic formation of a translocon complex., Biophys J 99(12):3880-6

 [68] Takayanagi K., Mizuno T., 1992, Activation of the osmoregulated ompF and ompC genes by the OmpR protein in Escherichia coli: a study involving chimeric promoters., J Biochem 112(1):1-6

 [69] Tieleman DP., Berendsen HJ., 1998, A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer., Biophys J 74(6):2786-801

 [70] Tommassen J., van der Ley P., Lugtenberg B., 1981, Genetic and biochemical characterization of an Escherichia coli K-12 mutant with an altered outer membrane protein., Antonie Van Leeuwenhoek 47(4):325-37

 [71] Varma S., Chiu SW., Jakobsson E., 2006, The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF., Biophys J 90(1):112-23

 [72] Varma S., Jakobsson E., 2004, Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues., Biophys J 86(2):690-704

 [73] Visudtiphole V., Thomas MB., Chalton DA., Lakey JH., 2005, Refolding of Escherichia coli outer membrane protein F in detergent creates LPS-free trimers and asymmetric dimers., Biochem J 392(Pt 2):375-81

 [74] Vrouenraets M., Miedema H., 2010, The ionization state of D37 in E. coli porin OmpF and the nature of conductance fluctuations in D37 mutants., Eur Biophys J 39(12):1563-71

 [75] Zakharov SD., Sharma O., Zhalnina MV., Cramer WA., 2008, Primary events in the colicin translocon: FRET analysis of colicin unfolding initiated by binding to BtuB and OmpF., Biochemistry 47(48):12802-9

 [76] Zhang DF., Ye JZ., Dai HH., Lin XM., Li H., Peng XX., 2018, Identification of ethanol tolerant outer membrane proteome reveals OmpC-dependent mechanism in a manner of EnvZ/OmpR regulation in Escherichia coli., J Proteomics 179:92-99

 [77] Zhang E., Ferenci T., 1999, OmpF changes and the complexity of Escherichia coli adaptation to prolonged lactose limitation., FEMS Microbiol Lett 176(2):395-401

 [78] Zhao Z., Eberhart LJ., Orfe LH., Lu SY., Besser TE., Call DR., 2015, Genome-Wide Screening Identifies Six Genes That Are Associated with Susceptibility to Escherichia coli Microcin PDI., Appl Environ Microbiol 81(20):6953-63

 [79] Zhu Y., Guo T., Park JE., Li X., Meng W., Datta A., Bern M., Lim SK., Sze SK., 2009, Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting., Mol Cell Proteomics

 [80] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.