PortEco logo


From EcoliWiki
Jump to: navigation, search

Star gold.png

Expert Annotator

You have been awarded the gold star of annotation for being an Expert Annotator and completing 500+ annotations.

Awared by Daniel May, 2009.


About Me

My name is Brenley McIntosh and I am a post-doc in Jim's lab. I have 3 major projects in the lab:

  1. Designing CACAO 0.1 - a course to teach undergraduates to annotate scientific literature using GO terminology!
  2. Annotating genes in E. coli and its phages.
  3. Coding and uploading content, including more phage genomes.

Contact Info Email Snail Mail

Brenley Kathleen McIntosh


Dept. of Biochemistry and Biophysics Texas A&M University College Station, Texas 77843-2128

About the wiki and me

I have a background in phage genetics, but I would love to hear about your project! Please feel free to contact me about content you would like to see on the wiki.

About the pictures

I am a runner at heart (ok, jogger) and these are from my marathon in 2005. I have finished the Houston Marathon and Half Marathon, Calgary Stampede Half Marathon and too many 5km and 10km races to count.


[1] [2] [3] [4] [5] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [15] [16] [17] [18] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [28] [29] [30] [31] [32] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [50] [51] [52] [53] [54] [55] [55] [56] [57] [58] [59] [60] [61] [62] [63] [63] [64] [65] [66] [67] [68] [69] [70] [70] [71] [72] [73] [74] [75] [76] [77] [77] [78] [79] [80] [80] [80] [81] [82] [83] [84] [84] [85] [86] [87] [88] [89] [90] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [99] [100] [101] [102] [103] [104] [104] [105] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [168] [169] [170] [171] [172] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [181] [182] [183] [184] [185] [185] [186] [187] [188] [189] [190] [191] [191] [191] [191] [191]

  1. Song, J et al. (2010) Nuclear magnetic resonance evidence for the role of the flexible regions of the E1 component of the pyruvate dehydrogenase complex from gram-negative bacteria. J. Biol. Chem. 285 4680-94 PubMed EcoliWiki page
  2. Salsbury, FR Jr (2010) Effects of Cisplatin binding to DNA on the dynamics of the E. Coli MutS dimer. Protein Pept. Lett. 17 744-50 PubMed EcoliWiki page
  3. Srivastava, D et al. (2010) The structure of the proline utilization a proline dehydrogenase domain inactivated by N-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction. Biochemistry 49 560-9 PubMed EcoliWiki page
  4. Eng, K et al. (2010) Selective inhibition of DNA replicase assembly by a non-natural nucleotide: exploiting the structural diversity of ATP-binding sites. ACS Chem. Biol. 5 183-94 PubMed EcoliWiki page
  5. 5.0 5.1 Jackson, AP et al. (2009) Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC Genomics 10 584 PubMed EcoliWiki page
  6. Zhang, J et al. (2010) Role of the RNA polymerase trigger loop in catalysis and pausing. Nat. Struct. Mol. Biol. 17 99-104 PubMed EcoliWiki page
  7. Ito, T et al. (2009) The implication of YggT of Escherichia coli in osmotic regulation. Biosci. Biotechnol. Biochem. 73 2698-704 PubMed EcoliWiki page
  8. Miyake, K & Kakita, S (2009) A novel catalytic ability of gamma-glutamylcysteine synthetase of Escherichia coli and its application in theanine production. Biosci. Biotechnol. Biochem. 73 2677-83 PubMed EcoliWiki page
  9. Stewart, V & Chen, LL (2010) The S helix mediates signal transmission as a HAMP domain coiled-coil extension in the NarX nitrate sensor from Escherichia coli K-12. J. Bacteriol. 192 734-45 PubMed EcoliWiki page
  10. Meades, G Jr et al. (2010) A tale of two functions: enzymatic activity and translational repression by carboxyltransferase. Nucleic Acids Res. 38 1217-27 PubMed EcoliWiki page
  11. Kimura, S & Suzuki, T (2010) Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res. 38 1341-52 PubMed EcoliWiki page
  12. Edwards, MJ et al. (2009) A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase. Science 326 1415-8 PubMed EcoliWiki page
  13. Depuydt, M et al. (2009) A periplasmic reducing system protects single cysteine residues from oxidation. Science 326 1109-11 PubMed EcoliWiki page
  14. Vrentas, CE et al. (2010) An improved procedure for the purification of the Escherichia coli RNA polymerase omega subunit. Protein Expr. Purif. 71 190-4 PubMed EcoliWiki page
  15. 15.0 15.1 Kim, HK et al. (2010) 5S rRNA-assisted DnaK refolding. Biochem. Biophys. Res. Commun. 391 1177-81 PubMed EcoliWiki page
  16. Nagy, M et al. (2010) Synergistic cooperation between two ClpB isoforms in aggregate reactivation. J. Mol. Biol. 396 697-707 PubMed EcoliWiki page
  17. Price, CE & Driessen, AJ (2010) Conserved negative charges in the transmembrane segments of subunit K of the NADH:ubiquinone oxidoreductase determine its dependence on YidC for membrane insertion. J. Biol. Chem. 285 3575-81 PubMed EcoliWiki page
  18. 18.0 18.1 Tucker, NP et al. (2010) Essential roles of three enhancer sites in sigma54-dependent transcription by the nitric oxide sensing regulatory protein NorR. Nucleic Acids Res. 38 1182-94 PubMed EcoliWiki page
  19. Acharya, S & Patterson, K (2010) Mutations in the conserved glycine and serine of the MutS ABC signature motif affect nucleotide exchange, kinetics of sliding clamp release of mismatch and mismatch repair. Mutat. Res. 684 56-65 PubMed EcoliWiki page
  20. Jarosz, DF et al. (2009) A DinB variant reveals diverse physiological consequences of incomplete TLS extension by a Y-family DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 106 21137-42 PubMed EcoliWiki page
  21. Burgos Zepeda, MY et al. (2010) C-terminal domain of the Uup ATP-binding cassette ATPase is an essential folding domain that binds to DNA. Biochim. Biophys. Acta 1804 755-61 PubMed EcoliWiki page
  22. Zhang, W et al. (2010) IscS functions as a primary sulfur-donating enzyme by interacting specifically with MoeB and MoaD in the biosynthesis of molybdopterin in Escherichia coli. J. Biol. Chem. 285 2302-8 PubMed EcoliWiki page
  23. Maciag, M et al. (2010) ppGpp inhibits the activity of Escherichia coli DnaG primase. Plasmid 63 61-7 PubMed EcoliWiki page
  24. Jourdan, SS et al. (2010) The sequence of sites recognised by a member of the RNase E/G family can control the maximal rate of cleavage, while a 5'-monophosphorylated end appears to function cooperatively in mediating RNA binding. Biochem. Biophys. Res. Commun. 391 879-83 PubMed EcoliWiki page
  25. Suzuki, T & Miyauchi, K (2010) Discovery and characterization of tRNAIle lysidine synthetase (TilS). FEBS Lett. 584 272-7 PubMed EcoliWiki page
  26. Christensen-Dalsgaard, M et al. (2010) Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses. Mol. Microbiol. 75 333-48 PubMed EcoliWiki page
  27. Sim, SH et al. (2010) Escherichia coli ribonuclease III activity is downregulated by osmotic stress: consequences for the degradation of bdm mRNA in biofilm formation. Mol. Microbiol. 75 413-25 PubMed EcoliWiki page
  28. 28.0 28.1 Strömqvist, J et al. (2010) Estimating Z-ring radius and contraction in dividing Escherichia coli. Mol. Microbiol. 76 151-8 PubMed EcoliWiki page
  29. Korshunov, S & Imlay, JA (2010) Two sources of endogenous hydrogen peroxide in Escherichia coli. Mol. Microbiol. 75 1389-401 PubMed EcoliWiki page
  30. Schneider, S et al. (2010) Redesigning the active site of transaldolase TalB from Escherichia coli: new variants with improved affinity towards nonphosphorylated substrates. Chembiochem 11 681-90 PubMed EcoliWiki page
  31. Cox, J & Putonti, C (2010) Mechanisms responsible for a PhiX174 mutant's ability to infect Escherichia coli by phosphorylation. J. Virol. 84 4860-3 PubMed EcoliWiki page
  32. 32.0 32.1 Su, PT et al. (2010) Factors affecting daughter cells' arrangement during the early bacterial divisions. PLoS ONE 5 e9147 PubMed EcoliWiki page
  33. Yosef, I et al. (2010) Membrane protein biogenesis in Ffh- or FtsY-depleted Escherichia coli. PLoS ONE 5 e9130 PubMed EcoliWiki page
  34. Bissonnette, SA et al. (2010) The IbpA and IbpB small heat-shock proteins are substrates of the AAA+ Lon protease. Mol. Microbiol. 75 1539-49 PubMed EcoliWiki page
  35. Katayama, T et al. (2010) Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Nat. Rev. Microbiol. 8 163-70 PubMed EcoliWiki page
  36. Teramoto, J et al. (2010) A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions. Nucleic Acids Res. 38 3605-18 PubMed EcoliWiki page
  37. Tolla, DA & Savageau, MA (2010) Regulation of aerobic-to-anaerobic transitions by the FNR cycle in Escherichia coli. J. Mol. Biol. 397 893-905 PubMed EcoliWiki page
  38. Szymanski, MR et al. (2010) Interactions of the Escherichia coli primosomal PriB protein with the single-stranded DNA. Stoichiometries, intrinsic affinities, cooperativities, and base specificities. J. Mol. Biol. 398 8-25 PubMed EcoliWiki page
  39. Zhang, X et al. (2010) Fermentation of glycerol to succinate by metabolically engineered strains of Escherichia coli. Appl. Environ. Microbiol. 76 2397-401 PubMed EcoliWiki page
  40. Li, H et al. (2010) DmsD, a Tat system specific chaperone, interacts with other general chaperones and proteins involved in the molybdenum cofactor biosynthesis. Biochim. Biophys. Acta 1804 1301-9 PubMed EcoliWiki page
  41. Heermann, R & Jung, K (2010) The complexity of the 'simple' two-component system KdpD/KdpE in Escherichia coli. FEMS Microbiol. Lett. 304 97-106 PubMed EcoliWiki page
  42. Bechtluft, P et al. (2010) Tight hydrophobic contacts with the SecB chaperone prevent folding of substrate proteins. Biochemistry 49 2380-8 PubMed EcoliWiki page
  43. Reinau, ME et al. (2010) The diversity of FtsY-lipid interactions. Biopolymers 93 595-606 PubMed EcoliWiki page
  44. Lloyd, GS et al. (2010) Targets for the MalI repressor at the divergent Escherichia coli K-12 malX-malI promoters. FEMS Microbiol. Lett. 305 28-34 PubMed EcoliWiki page
  45. MacPhee, DG & Ambrose, M (2010) Catabolite repression of SOS-dependent and SOS-independent spontaneous mutagenesis in stationary-phase Escherichia coli. Mutat. Res. 686 84-9 PubMed EcoliWiki page
  46. Vine, CE et al. (2010) Detection by whole genome microarrays of a spontaneous 126-gene deletion during construction of a ytfE mutant: confirmation that a ytfE mutation results in loss of repair of iron-sulfur centres in proteins damaged by oxidative or nitrosative stress. J. Microbiol. Methods 81 77-9 PubMed EcoliWiki page
  47. Chiancone, E & Ceci, P (2010) The multifaceted capacity of Dps proteins to combat bacterial stress conditions: Detoxification of iron and hydrogen peroxide and DNA binding. Biochim. Biophys. Acta 1800 798-805 PubMed EcoliWiki page
  48. Maheshwari, A et al. (2010) Equilibrium and kinetics of the unfolding and refolding of Escherichia coli Malate Synthase G monitored by circular dichroism and fluorescence spectroscopy. Biochimie 92 491-8 PubMed EcoliWiki page
  49. Fonville, NC et al. (2010) RecQ-dependent death-by-recombination in cells lacking RecG and UvrD. DNA Repair (Amst.) 9 403-13 PubMed EcoliWiki page
  50. 50.0 50.1 Zhou, H et al. (2010) Enhanced l-phenylalanine biosynthesis by co-expression of pheA(fbr) and aroF(wt). Bioresour. Technol. 101 4151-6 PubMed EcoliWiki page
  51. Hernick, M et al. (2010) Activation of Escherichia coli UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase by Fe2+ yields a more efficient enzyme with altered ligand affinity. Biochemistry 49 2246-55 PubMed EcoliWiki page
  52. Cámara, B et al. (2010) T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site. Proc. Natl. Acad. Sci. U.S.A. 107 2247-52 PubMed EcoliWiki page
  53. Chayot, R et al. (2010) An end-joining repair mechanism in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 107 2141-6 PubMed EcoliWiki page
  54. Rhodius, VA & Mutalik, VK (2010) Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc. Natl. Acad. Sci. U.S.A. 107 2854-9 PubMed EcoliWiki page
  55. 55.0 55.1 Hoffmann, A et al. (2010) Structure and function of the molecular chaperone Trigger Factor. Biochim. Biophys. Acta 1803 650-61 PubMed EcoliWiki page
  56. Sangurdekar, DP et al. (2010) Thymineless death is associated with loss of essential genetic information from the replication origin. Mol. Microbiol. 75 1455-67 PubMed EcoliWiki page
  57. Pul, U et al. (2010) Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol. Microbiol. 75 1495-512 PubMed EcoliWiki page
  58. Nakamura, K & Katayama, T (2010) Novel essential residues of Hda for interaction with DnaA in the regulatory inactivation of DnaA: unique roles for Hda AAA Box VI and VII motifs. Mol. Microbiol. 76 302-17 PubMed EcoliWiki page
  59. Tobin, C et al. (2010) Ribosomes lacking protein S20 are defective in mRNA binding and subunit association. J. Mol. Biol. 397 767-76 PubMed EcoliWiki page
  60. Shen, B & Lutkenhaus, J (2010) Examination of the interaction between FtsZ and MinCN in E. coli suggests how MinC disrupts Z rings. Mol. Microbiol. 75 1285-98 PubMed EcoliWiki page
  61. Thomas, J et al. (2010) Utilization of positional isotope exchange experiments to evaluate reversibility of ATP hydrolysis catalyzed by Escherichia coli Lon protease. Biochem. Cell Biol. 88 119-28 PubMed EcoliWiki page
  62. Makowska-Grzyska, M & Kaguni, JM (2010) Primase directs the release of DnaC from DnaB. Mol. Cell 37 90-101 PubMed EcoliWiki page
  63. 63.0 63.1 Giuliodori, AM et al. (2010) The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA. Mol. Cell 37 21-33 PubMed EcoliWiki page
  64. Han, X et al. (2010) Escherichia coli genes that reduce the lethal effects of stress. BMC Microbiol. 10 35 PubMed EcoliWiki page
  65. Dyszel, JL et al. (2010) E. coli K-12 and EHEC genes regulated by SdiA. PLoS ONE 5 e8946 PubMed EcoliWiki page
  66. Kthiri, F et al. (2010) Protein aggregation in a mutant deficient in yajL, the bacterial homolog of the Parkinsonism-associated protein DJ-1. J. Biol. Chem. 285 10328-36 PubMed EcoliWiki page
  67. Wang, Q et al. (2010) Metabolic flux control at the pyruvate node in an anaerobic Escherichia coli strain with an active pyruvate dehydrogenase. Appl. Environ. Microbiol. 76 2107-14 PubMed EcoliWiki page
  68. Kozmin, SG et al. (2010) Role for CysJ flavin reductase in molybdenum cofactor-dependent resistance of Escherichia coli to 6-N-hydroxylaminopurine. J. Bacteriol. 192 2026-33 PubMed EcoliWiki page
  69. Kaminska, R & van der Woude, MW (2010) Establishing and maintaining sequestration of Dam target sites for phase variation of agn43 in Escherichia coli. J. Bacteriol. 192 1937-45 PubMed EcoliWiki page
  70. 70.0 70.1 Ford, B et al. (2010) Structural homology between the C-terminal domain of the PapC usher and its plug. J. Bacteriol. 192 1824-31 PubMed EcoliWiki page
  71. Eydallin, G et al. (2010) Genome-wide screening of genes whose enhanced expression affects glycogen accumulation in Escherichia coli. DNA Res. 17 61-71 PubMed EcoliWiki page
  72. Fernández-Ramírez, F et al. (2010) Nucleic acid and protein factors involved in Escherichia coli polynucleotide phosphorylase function on RNA. Biochimie 92 445-54 PubMed EcoliWiki page
  73. Pomerantz, RT & O'Donnell, M (2010) Direct restart of a replication fork stalled by a head-on RNA polymerase. Science 327 590-2 PubMed EcoliWiki page
  74. Nemeria, NS et al. (2010) Communication between thiamin cofactors in the Escherichia coli pyruvate dehydrogenase complex E1 component active centers: evidence for a "direct pathway" between the 4'-aminopyrimidine N1' atoms. J. Biol. Chem. 285 11197-209 PubMed EcoliWiki page
  75. Górna, MW et al. (2010) The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA 16 553-62 PubMed EcoliWiki page
  76. Barrick, JE et al. (2010) Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol. Biol. Evol. 27 1338-47 PubMed EcoliWiki page
  77. 77.0 77.1 Kumar, R & Shimizu, K (2010) Metabolic regulation of Escherichia coli and its gdhA, glnL, gltB, D mutants under different carbon and nitrogen limitations in the continuous culture. Microb. Cell Fact. 9 8 PubMed EcoliWiki page
  78. Kim, Y et al. (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ. Microbiol. 12 1105-21 PubMed EcoliWiki page
  79. Banik, SD & Nandi, N (2010) Aminoacylation reaction in the histidyl-tRNA synthetase: fidelity mechanism of the activation step. J Phys Chem B 114 2301-11 PubMed EcoliWiki page
  80. 80.0 80.1 80.2 Sánchez-Romero, MA et al. (2010) Correlation between ribonucleoside-diphosphate reductase and three replication proteins in Escherichia coli. BMC Mol. Biol. 11 11 PubMed EcoliWiki page
  81. Severi, E et al. (2010) Characterization of a novel sialic acid transporter of the sodium solute symporter (SSS) family and in vivo comparison with known bacterial sialic acid transporters. FEMS Microbiol. Lett. 304 47-54 PubMed EcoliWiki page
  82. Luan, Q et al. (2010) Hairpin DNA probe based surface plasmon resonance biosensor used for the activity assay of E. coli DNA ligase. Analyst 135 414-8 PubMed EcoliWiki page
  83. Del Re, B et al. (2009) Extremely low frequency magnetic field exposure affects DnaK and GroEL expression in E. coli cells with impaired heat shock response. Gen. Physiol. Biophys. 28 420-4 PubMed EcoliWiki page
  84. 84.0 84.1 Doi, A et al. (2010) Comparison of the molecular influences of NO-induced lesions in DNA strands on the reactivity of polynucleotide kinases, DNA ligases and DNA polymerases. J. Biochem. 147 697-703 PubMed EcoliWiki page
  85. Nishiyama, S et al. (2010) Thermosensing function of the Escherichia coli redox sensor Aer. J. Bacteriol. 192 1740-3 PubMed EcoliWiki page
  86. Peña-Sandoval, GR & Georgellis, D (2010) The ArcB sensor kinase of Escherichia coli autophosphorylates by an intramolecular reaction. J. Bacteriol. 192 1735-9 PubMed EcoliWiki page
  87. Zhang, Z et al. (2010) Precise excision of IS5 from the intergenic region between the fucPIK and the fucAO operons and mutational control of fucPIK operon expression in Escherichia coli. J. Bacteriol. 192 2013-9 PubMed EcoliWiki page
  88. Picas, L et al. (2010) Preferential insertion of lactose permease in phospholipid domains: AFM observations. Biochim. Biophys. Acta 1798 1014-9 PubMed EcoliWiki page
  89. Weiss, SA et al. (2010) A study of cytochrome bo3 in a tethered bilayer lipid membrane. Biochim. Biophys. Acta 1797 1917-23 PubMed EcoliWiki page
  90. 90.0 90.1 Köhler, SD et al. (2010) The proline-rich domain of TonB possesses an extended polyproline II-like conformation of sufficient length to span the periplasm of Gram-negative bacteria. Protein Sci. 19 625-30 PubMed EcoliWiki page
  91. Rudolph, CJ et al. (2010) Is RecG a general guardian of the bacterial genome? DNA Repair (Amst.) 9 210-23 PubMed EcoliWiki page
  92. Gao, X et al. (2010) Mechanism of substrate recognition and transport by an amino acid antiporter. Nature 463 828-32 PubMed EcoliWiki page
  93. Szymanski, MR et al. (2010) The Escherichia coli PriA helicase specifically recognizes gapped DNA substrates: effect of the two nucleotide-binding sites of the enzyme on the recognition process. J. Biol. Chem. 285 9683-96 PubMed EcoliWiki page
  94. Fujiwara, K et al. (2010) Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. J. Biol. Chem. 285 9971-80 PubMed EcoliWiki page
  95. Djoko, KY et al. (2010) Reaction mechanisms of the multicopper oxidase CueO from Escherichia coli support its functional role as a cuprous oxidase. J. Am. Chem. Soc. 132 2005-15 PubMed EcoliWiki page
  96. Wang, SC et al. (2010) Potassium is critical for the Ni(II)-responsive DNA-binding activity of Escherichia coli NikR. J. Am. Chem. Soc. 132 1506-7 PubMed EcoliWiki page
  97. Warnecke, T & Hurst, LD (2010) GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution. Mol. Syst. Biol. 6 340 PubMed EcoliWiki page
  98. Mahendran, KR et al. (2010) Permeation of antibiotics through Escherichia coli OmpF and OmpC porins: screening for influx on a single-molecule level. J Biomol Screen 15 302-7 PubMed EcoliWiki page
  99. 99.0 99.1 Liao, JH et al. (2010) Binding and cleavage of E. coli HUbeta by the E. coli Lon protease. Biophys. J. 98 129-37 PubMed EcoliWiki page
  100. Holland, PJ & Hollis, T (2010) Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching. PLoS ONE 5 e8680 PubMed EcoliWiki page
  101. Volkmann, G et al. (2010) Intein-mediated cyclization of bacterial acyl carrier protein stabilizes its folded conformation but does not abolish function. J. Biol. Chem. 285 8605-14 PubMed EcoliWiki page
  102. Perla-Kajan, J et al. (2010) Properties of Escherichia coli EF-Tu mutants designed for fluorescence resonance energy transfer from tRNA molecules. Protein Eng. Des. Sel. 23 129-36 PubMed EcoliWiki page
  103. Hunke, C et al. (2010) The effect of NBD-Cl in nucleotide-binding of the major subunit alpha and B of the motor proteins F1FO ATP synthase and A1AO ATP synthase. J. Bioenerg. Biomembr. 42 1-10 PubMed EcoliWiki page
  104. 104.0 104.1 Mendillo, ML et al. (2009) A conserved MutS homolog connector domain interface interacts with MutL homologs. Proc. Natl. Acad. Sci. U.S.A. 106 22223-8 PubMed EcoliWiki page
  105. 105.0 105.1 Etson, CM et al. (2010) Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA. Proc. Natl. Acad. Sci. U.S.A. 107 1900-5 PubMed EcoliWiki page
  106. Loh, E et al. (2010) Optimization of DNA polymerase mutation rates during bacterial evolution. Proc. Natl. Acad. Sci. U.S.A. 107 1154-9 PubMed EcoliWiki page
  107. Boehr, DD et al. (2010) Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands. Proc. Natl. Acad. Sci. U.S.A. 107 1373-8 PubMed EcoliWiki page
  108. Sridharan, S et al. (2010) Crystal structure of Escherichia coli enterobactin-specific isochorismate synthase (EntC) bound to its reaction product isochorismate: implications for the enzyme mechanism and differential activity of chorismate-utilizing enzymes. J. Mol. Biol. 397 290-300 PubMed EcoliWiki page
  109. Clarke, DJ et al. (2010) Subdivision of the bacterioferritin comigratory protein family of bacterial peroxiredoxins based on catalytic activity. Biochemistry 49 1319-30 PubMed EcoliWiki page
  110. Epshtein, V et al. (2010) An allosteric mechanism of Rho-dependent transcription termination. Nature 463 245-9 PubMed EcoliWiki page
  111. Mauldin, RV & Lee, AL (2010) Nuclear magnetic resonance study of the role of M42 in the solution dynamics of Escherichia coli dihydrofolate reductase. Biochemistry 49 1606-15 PubMed EcoliWiki page
  112. Cotruvo, JA Jr & Stubbe, J (2010) An active dimanganese(III)-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase. Biochemistry 49 1297-309 PubMed EcoliWiki page
  113. Krylov, AA et al. (2010) Conditional silencing of the Escherichia coli pykF gene results from artificial convergent transcription protected from Rho-dependent termination. J. Mol. Microbiol. Biotechnol. 18 1-13 PubMed EcoliWiki page
  114. Persaud, C et al. (2010) Mutagenesis of the modified bases, m(5)U1939 and psi2504, in Escherichia coli 23S rRNA. Biochem. Biophys. Res. Commun. 392 223-7 PubMed EcoliWiki page
  115. Hayashi, M et al. (2010) Effect of multidrug-efflux transporter genes on dipeptide resistance and overproduction in Escherichia coli. FEMS Microbiol. Lett. 304 12-9 PubMed EcoliWiki page
  116. 116.0 116.1 Noda-García, L et al. (2010) Identification and analysis of residues contained on beta --> alpha loops of the dual-substrate (beta alpha)8 phosphoribosyl isomerase A specific for its phosphoribosyl anthranilate isomerase activity. Protein Sci. 19 535-43 PubMed EcoliWiki page
  117. Wang, F & Yang, W (2009) Structural insight into translesion synthesis by DNA Pol II. Cell 139 1279-89 PubMed EcoliWiki page
  118. Guymer, D et al. (2010) Intrinsic GTPase activity of a bacterial twin-arginine translocation proofreading chaperone induced by domain swapping. FEBS J. 277 511-25 PubMed EcoliWiki page
  119. Chang, JR et al. (2010) Assembly of bacteriophage P2 capsids from capsid protein fused to internal scaffolding protein. Virus Genes 40 298-306 PubMed EcoliWiki page
  120. Wang, P et al. (2010) Global change of gene expression and cell physiology in YidC-depleted Escherichia coli. J. Bacteriol. 192 2193-209 PubMed EcoliWiki page
  121. Cardozo, MJ et al. (2010) Disruption of Chemoreceptor Signaling Arrays by High Level of CheW, the Receptor-Kinase Coupling Protein. Mol. Microbiol. PubMed EcoliWiki page
  122. Chakrabarti, KS et al. (2010) X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate. FEBS J. 277 697-712 PubMed EcoliWiki page
  123. Kidd, PB & Wingreen, NS (2010) Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism. Phys Biol 7 016006 PubMed EcoliWiki page
  124. Bharti, SK & Varshney, U (2010) Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli. Nucleic Acids Res. 38 2291-301 PubMed EcoliWiki page
  125. Trotter, V et al. (2009) The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein. Mol. Microbiol. 74 1527-42 PubMed EcoliWiki page
  126. Rothery, RA et al. (2010) Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation. J. Biol. Chem. 285 8801-7 PubMed EcoliWiki page
  127. Montgomery, MG et al. (2010) Assembly of a 20-nm protein cage by Escherichia coli 2-hydroxypentadienoic acid hydratase. J. Mol. Biol. 396 1379-91 PubMed EcoliWiki page
  128. Smith, MA et al. (2010) Exploring the roles of the metal ions in Escherichia coli copper amine oxidase. Biochemistry 49 1268-80 PubMed EcoliWiki page
  129. Koutsioulis, D et al. (2010) Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases. Protein Sci. 19 75-84 PubMed EcoliWiki page
  130. 130.0 130.1 Mircheva, M et al. (2009) Predominant membrane localization is an essential feature of the bacterial signal recognition particle receptor. BMC Biol. 7 76 PubMed EcoliWiki page
  131. Florio, R et al. (2009) Structural stability of the cofactor binding site in Escherichia coli serine hydroxymethyltransferase--the role of evolutionarily conserved hydrophobic contacts. FEBS J. 276 7319-28 PubMed EcoliWiki page
  132. Li, Q et al. (2009) Bolaamphiphile-class surfactants can stabilize and support the function of solubilized integral membrane proteins. Biochemistry 48 11606-8 PubMed EcoliWiki page
  133. Zhang, X et al. (2009) Metabolic evolution of energy-conserving pathways for succinate production in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 106 20180-5 PubMed EcoliWiki page
  134. Minnihan, EC et al. (2009) Use of 3-aminotyrosine to examine the pathway dependence of radical propagation in Escherichia coli ribonucleotide reductase. Biochemistry 48 12125-32 PubMed EcoliWiki page
  135. McCrudden, MT et al. (2009) The contribution of key hydrophobic residues in ecotin to enzyme-inhibitor complex stability. J Enzyme Inhib Med Chem 24 1207-10 PubMed EcoliWiki page
  136. Britt, RL et al. (2010) Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange. J. Biol. Chem. 285 3211-26 PubMed EcoliWiki page
  137. Kim, Y & Wood, TK (2010) Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem. Biophys. Res. Commun. 391 209-13 PubMed EcoliWiki page
  138. Schwartz, JJ & Quake, SR (2009) Single molecule measurement of the "speed limit" of DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 106 20294-9 PubMed EcoliWiki page
  139. Mohanty, BK & Kushner, SR (2010) Processing of the Escherichia coli leuX tRNA transcript, encoding tRNA(Leu5), requires either the 3'-->5' exoribonuclease polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator. Nucleic Acids Res. 38 597-607 PubMed EcoliWiki page
  140. Overgaard, M et al. (2009) Modulating the bacterial surface with small RNAs: a new twist on PhoP/Q-mediated lipopolysaccharide modification. Mol. Microbiol. 74 1289-94 PubMed EcoliWiki page
  141. Peeters, E et al. (2009) Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP. Mol. Microbiol. 74 1513-26 PubMed EcoliWiki page
  142. Guan, W et al. (2009) Enzymatic synthesis of UDP-GlcNAc/UDP-GalNAc analogs using N-acetylglucosamine 1-phosphate uridyltransferase (GlmU). Chem. Commun. (Camb.) 6976-8 PubMed EcoliWiki page
  143. Hudson, BP et al. (2009) Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc. Natl. Acad. Sci. U.S.A. 106 19830-5 PubMed EcoliWiki page
  144. Calmat, S et al. (2009) Dissociation kinetics of the GroEL-gp31 chaperonin complex studied with Förster resonance energy transfer. Biochemistry 48 11692-8 PubMed EcoliWiki page
  145. Link, TM et al. (2009) Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proc. Natl. Acad. Sci. U.S.A. 106 19292-7 PubMed EcoliWiki page
  146. Cheng, CC et al. (2009) Discovery and optimization of antibacterial AccC inhibitors. Bioorg. Med. Chem. Lett. 19 6507-14 PubMed EcoliWiki page
  147. Maciejewska, AM et al. (2010) Chloroacetaldehyde-induced mutagenesis in Escherichia coli: the role of AlkB protein in repair of 3,N(4)-ethenocytosine and 3,N(4)-alpha-hydroxyethanocytosine. Mutat. Res. 684 24-34 PubMed EcoliWiki page
  148. Tan, M et al. (2010) tRNA-dependent pre-transfer editing by prokaryotic leucyl-tRNA synthetase. J. Biol. Chem. 285 3235-44 PubMed EcoliWiki page
  149. 149.0 149.1 Feng, Y et al. (2009) Disassembly intermediates of RbsD protein remain oligomeric despite the loss of an intact secondary structure. Sci. China, C, Life Sci. 52 997-1002 PubMed EcoliWiki page
  150. Bekker, M et al. (2010) The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool. J. Bacteriol. 192 746-54 PubMed EcoliWiki page
  151. Domain, F & Levy, SB (2010) GyrA interacts with MarR to reduce repression of the marRAB operon in Escherichia coli. J. Bacteriol. 192 942-8 PubMed EcoliWiki page
  152. Dhakshnamoorthy, B et al. (2010) Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction. J. Mol. Biol. 396 293-300 PubMed EcoliWiki page
  153. Shoji, S et al. (2010) Translation factor LepA contributes to tellurite resistance in Escherichia coli but plays no apparent role in the fidelity of protein synthesis. Biochimie 92 157-63 PubMed EcoliWiki page
  154. Andreoni, F et al. (2010) Overexpression of the single-stranded DNA-binding protein (SSB) stabilises CAG*CTG triplet repeats in an orientation dependent manner. FEBS Lett. 584 153-8 PubMed EcoliWiki page
  155. Burton, RL et al. (2009) Transient kinetic analysis of the interaction of L-serine with Escherichia coli D-3-phosphoglycerate dehydrogenase reveals the mechanism of V-type regulation and the order of effector binding. Biochemistry 48 12242-51 PubMed EcoliWiki page
  156. Su, L & Cukier, RI (2009) Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK. J Phys Chem B 113 16197-208 PubMed EcoliWiki page
  157. Herz, K et al. (2010) Transmembrane segment II of NhaA Na+/H+ antiporter lines the cation passage, and Asp65 is critical for pH activation of the antiporter. J. Biol. Chem. 285 2211-20 PubMed EcoliWiki page
  158. Challand, MR et al. (2010) Catalytic activity of the anaerobic tyrosine lyase required for thiamine biosynthesis in Escherichia coli. J. Biol. Chem. 285 5240-8 PubMed EcoliWiki page
  159. Kanchan, K et al. (2010) Transmembrane signaling in chimeras of the Escherichia coli aspartate and serine chemotaxis receptors and bacterial class III adenylyl cyclases. J. Biol. Chem. 285 2090-9 PubMed EcoliWiki page
  160. Berg, AK et al. (2010) Solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase. Biochim. Biophys. Acta 1804 704-13 PubMed EcoliWiki page
  161. White, GF et al. (2010) Subunit organization in the TatA complex of the twin arginine protein translocase: a site-directed EPR spin labeling study. J. Biol. Chem. 285 2294-301 PubMed EcoliWiki page
  162. Jakes, KS & Finkelstein, A (2010) The colicin Ia receptor, Cir, is also the translocator for colicin Ia. Mol. Microbiol. 75 567-78 PubMed EcoliWiki page
  163. Mikoulinskaia, GV et al. (2009) Identification and characterization of the metal ion-dependent L-alanoyl-D-glutamate peptidase encoded by bacteriophage T5. FEBS J. 276 7329-42 PubMed EcoliWiki page
  164. Erez, E & Bibi, E (2009) Cleavage of a multispanning membrane protein by an intramembrane serine protease. Biochemistry 48 12314-22 PubMed EcoliWiki page
  165. Li, N et al. (2010) Multiple Escherichia coli RecQ helicase monomers cooperate to unwind long DNA substrates: a fluorescence cross-correlation spectroscopy study. J. Biol. Chem. 285 6922-36 PubMed EcoliWiki page
  166. Sarkar, SK et al. (2010) Deletion of penicillin-binding protein 5 (PBP5) sensitises Escherichia coli cells to beta-lactam agents. Int. J. Antimicrob. Agents 35 244-9 PubMed EcoliWiki page
  167. Loveridge, EJ et al. (2010) Solvent effects on catalysis by Escherichia coli dihydrofolate reductase. J. Am. Chem. Soc. 132 1137-43 PubMed EcoliWiki page
  168. 168.0 168.1 Horiuchi, Y et al. (2010) Coupling effects of distal loops on structural stability and enzymatic activity of Escherichia coli dihydrofolate reductase revealed by deletion mutants. Biochim. Biophys. Acta 1804 846-55 PubMed EcoliWiki page
  169. Liu, Z et al. (2010) Helix dynamics in LacY: helices II and IV. J. Mol. Biol. 396 617-26 PubMed EcoliWiki page
  170. Yokota, A et al. (2010) Probing the roles of conserved arginine-44 of Escherichia coli dihydrofolate reductase in its function and stability by systematic sequence perturbation analysis. Biochem. Biophys. Res. Commun. 391 1703-7 PubMed EcoliWiki page
  171. Brown, BL et al. (2009) Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties. PLoS Pathog. 5 e1000706 PubMed EcoliWiki page
  172. 172.0 172.1 Lescat, M et al. (2009) aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species. BMC Microbiol. 9 273 PubMed EcoliWiki page
  173. Elkins, CA et al. (2010) Single nucleotide polymorphism analysis of the major tripartite multidrug efflux pump of Escherichia coli: functional conservation in disparate animal reservoirs despite exposure to antimicrobial chemotherapy. Antimicrob. Agents Chemother. 54 1007-15 PubMed EcoliWiki page
  174. Kim, HS et al. (2010) Multidrug efflux pump MdtBC of Escherichia coli is active only as a B2C heterotrimer. J. Bacteriol. 192 1377-86 PubMed EcoliWiki page
  175. Gutgsell, NS & Jain, C (2010) Coordinated regulation of 23S rRNA maturation in Escherichia coli. J. Bacteriol. 192 1405-9 PubMed EcoliWiki page
  176. Bay, DC et al. (2010) Multimeric forms of the small multidrug resistance protein EmrE in anionic detergent. Biochim. Biophys. Acta 1798 526-35 PubMed EcoliWiki page
  177. Cohen, SE & Walker, GC (2010) The transcription elongation factor NusA is required for stress-induced mutagenesis in Escherichia coli. Curr. Biol. 20 80-5 PubMed EcoliWiki page
  178. Mari, SA et al. (2010) pH-induced conformational change of the beta-barrel-forming protein OmpG reconstituted into native E. coli lipids. J. Mol. Biol. 396 610-6 PubMed EcoliWiki page
  179. Kerff, F et al. (2010) Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family. J. Mol. Biol. 397 249-59 PubMed EcoliWiki page
  180. Nakamura, A et al. (2010) Crystal structure of a thermophilic GrpE protein: insight into thermosensing function for the DnaK chaperone system. J. Mol. Biol. 396 1000-11 PubMed EcoliWiki page
  181. 181.0 181.1 Zhou, Y et al. (2010) Functional analyses of Escherichia coli MutS-beta clamp interaction in vitro and in vivo. Curr. Microbiol. 60 466-70 PubMed EcoliWiki page
  182. Dubarry, N & Barre, FX (2010) Fully efficient chromosome dimer resolution in Escherichia coli cells lacking the integral membrane domain of FtsK. EMBO J. 29 597-605 PubMed EcoliWiki page
  183. Wurm, R et al. () 6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products. Biol. Chem. 391 187-96 PubMed EcoliWiki page
  184. Kunzelmann, S et al. (2010) Mechanism of interaction between single-stranded DNA binding protein and DNA. Biochemistry 49 843-52 PubMed EcoliWiki page
  185. 185.0 185.1 Xu, Y et al. (2010) Structure of the adenylylation domain of E. coli glutamine synthetase adenylyl transferase: evidence for gene duplication and evolution of a new active site. J. Mol. Biol. 396 773-84 PubMed EcoliWiki page
  186. Hsieh, CW et al. (2010) Direct MinE-membrane interaction contributes to the proper localization of MinDE in E. coli. Mol. Microbiol. 75 499-512 PubMed EcoliWiki page
  187. Auclair, SM et al. (2010) Mapping of the signal peptide-binding domain of Escherichia coli SecA using Förster resonance energy transfer. Biochemistry 49 782-92 PubMed EcoliWiki page
  188. Zhou, X et al. (2010) The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket. J. Struct. Biol. 169 277-85 PubMed EcoliWiki page
  189. Cui, TZ et al. (2010) A subunit of decaprenyl diphosphate synthase stabilizes octaprenyl diphosphate synthase in Escherichia coli by forming a high-molecular weight complex. FEBS Lett. 584 652-6 PubMed EcoliWiki page
  190. Taylor, PL et al. (2010) Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli. Biochemistry 49 1033-41 PubMed EcoliWiki page
  191. 191.0 191.1 191.2 191.3 191.4 Wang, L et al. (2010) Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB). Biochemistry 49 1072-81 PubMed EcoliWiki page