Experts and Doctors on escherichia coli in Cambridge, Massachusetts, United States


Locale: Cambridge, Massachusetts, United States
Topic: escherichia coli

Top Publications

  1. Griffiths S, Cooney C. Relationship between protein structure and methionine oxidation in recombinant human alpha 1-antitrypsin. Biochemistry. 2002;41:6245-52 pubmed
    ..In sum, this work provides a detailed analysis of methionine oxidation in alpha 1-antitrypsin and offers new insights into the protein's solution structure. ..
  2. Schreiter E, Sintchak M, Guo Y, Chivers P, Sauer R, Drennan C. Crystal structure of the nickel-responsive transcription factor NikR. Nat Struct Biol. 2003;10:794-9 pubmed publisher
    ..The regulatory domain of NikR contains four nickel-binding sites at the tetramer interface, each exhibiting a novel square-planar coordination by three histidines and one cysteine side chain...
  3. Jennings L, Bohon J, Chance M, Licht S. The ClpP N-terminus coordinates substrate access with protease active site reactivity. Biochemistry. 2008;47:11031-40 pubmed publisher
  4. Puthenveetil S, Liu D, White K, Thompson S, Ting A. Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase. J Am Chem Soc. 2009;131:16430-8 pubmed publisher
    ..The kinetic improvement over LAP1 allowed us to rapidly label cell surface peptide-fused receptors with quantum dots. ..
  5. Knudsen S, von Muhlen M, Schauer D, Manalis S. Determination of bacterial antibiotic resistance based on osmotic shock response. Anal Chem. 2009;81:7087-90 pubmed publisher
  6. Phillips C, Schreiter E, Stultz C, Drennan C. Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli. Biochemistry. 2010;49:7830-8 pubmed publisher
  7. Martin C, Dhamankar H, Tseng H, Sheppard M, Reisch C, Prather K. A platform pathway for production of 3-hydroxyacids provides a biosynthetic route to 3-hydroxy-?-butyrolactone. Nat Commun. 2013;4:1414 pubmed publisher
    ..We also unexpectedly observe the condensation reaction resulting in the production of the 2,3-dihydroxybutyric acid isomer, a potential value-added monomer. ..
  8. Blair D, Kim D, Berg H. Mutant MotB proteins in Escherichia coli. J Bacteriol. 1991;173:4049-55 pubmed
    ..These results support the hypothesis that MotB is a linker. ..
  9. Barthel T, Zhang J, Walker G. ATPase-defective derivatives of Escherichia coli DnaK that behave differently with respect to ATP-induced conformational change and peptide release. J Bacteriol. 2001;183:5482-90 pubmed

More Information

Publications183 found, 100 shown here

  1. Gross C, Parsons J, Grossman T, Charifson P, Bellon S, Jernee J, et al. Active-site residues of Escherichia coli DNA gyrase required in coupling ATP hydrolysis to DNA supercoiling and amino acid substitutions leading to novobiocin resistance. Antimicrob Agents Chemother. 2003;47:1037-46 pubmed
    ..Four new residues (D73, G77, I78, and T165) that, when changed to the appropriate amino acid, result in both significant levels of novobiocin resistance and maintain in vivo function were identified in E. coli. ..
  2. Huang J, Lipscomb W. T-state active site of aspartate transcarbamylase: crystal structure of the carbamyl phosphate and L-alanosine ligated enzyme. Biochemistry. 2006;45:346-52 pubmed
    ..Moreover, the alanosine position in this T-state is somewhat displaced from that expected for its analogue, aspartate, from the R-state position. The relations of these structural aspects to the kinetics are presented...
  3. Cheng C, Shipps G, Yang Z, Sun B, Kawahata N, Soucy K, et al. Discovery and optimization of antibacterial AccC inhibitors. Bioorg Med Chem Lett. 2009;19:6507-14 pubmed publisher
    ..This compound is a potent and selective inhibitor of bacterial AccC with an IC(50) of 20 nM and a MIC of 0.8 microg/mL against a sensitized strain of Escherichia coli (HS294 E. coli). ..
  4. Grueneberg D, Henry R, Brauer A, Novina C, Cheriyath V, Roy A, et al. A multifunctional DNA-binding protein that promotes the formation of serum response factor/homeodomain complexes: identity to TFII-I. Genes Dev. 1997;11:2482-93 pubmed
    ..We propose that this multifunctional protein coordinates the formation of an active promoter complex at the c-fos gene, including the linkage of specific signal responsive activator complexes to the general transcription machinery. ..
  5. Sun L, Yim C, Verdine G. Chemical communication across the zinc tetrathiolate cluster in Escherichia coli Ada, a metalloactivated DNA repair protein. Biochemistry. 2001;40:11596-603 pubmed
    ..These findings demonstrate that the three "spectator" Cys ligands communicate chemically with Cys 69 through the bound metal ion. ..
  6. Thattai M, Shraiman B. Metabolic switching in the sugar phosphotransferase system of Escherichia coli. Biophys J. 2003;85:744-54 pubmed
  7. Delaney S, Delaney J, Essigmann J. Chemical-biological fingerprinting: probing the properties of DNA lesions formed by peroxynitrite. Chem Res Toxicol. 2007;20:1718-29 pubmed
    ..Therefore, while 8-oxoGua itself is nontoxic and only mildly mutagenic in repair-proficient cells, peroxynitrite reveals the promutagenic potential and triggers the covert nature of this DNA lesion. ..
  8. Köster S, Evilevitch A, Jeembaeva M, Weitz D. Influence of internal capsid pressure on viral infection by phage lambda. Biophys J. 2009;97:1525-9 pubmed publisher
    ..The lysis probability decreases markedly with decreased capsid pressure. Of interest, the average lysis times remain the same but the distribution is broadened as the pressure is lowered. ..
  9. Zheng T, Bullock J, Nolan E. Siderophore-mediated cargo delivery to the cytoplasm of Escherichia coli and Pseudomonas aeruginosa: syntheses of monofunctionalized enterobactin scaffolds and evaluation of enterobactin-cargo conjugate uptake. J Am Chem Soc. 2012;134:18388-400 pubmed publisher
    ..Enterobactin may be utilized for delivering molecular cargos via its transport machinery to the cytoplasm of E. coli and P. aeruginosa thereby providing a means to overcome the Gram-negative outer membrane permeability barrier. ..
  10. Minnihan E, Nocera D, Stubbe J. Reversible, long-range radical transfer in E. coli class Ia ribonucleotide reductase. Acc Chem Res. 2013;46:2524-35 pubmed publisher
    ..The rate constant of one of the PCET steps is ∼10(5) s(-1), as measured in photoinitiated experiments. ..
  11. Kellner S, DeMott M, Cheng C, Russell B, Cao B, You D, et al. Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability. Nat Chem Biol. 2017;13:888-894 pubmed publisher
    ..The genotoxicity of HOCl in PT-containing bacteria suggests reduced fitness in competition with HOCl-producing organisms and during infections in humans. ..
  12. Seyedsayamdost M, Yee C, Reece S, Nocera D, Stubbe J. pH Rate profiles of FnY356-R2s (n = 2, 3, 4) in Escherichia coli ribonucleotide reductase: evidence that Y356 is a redox-active amino acid along the radical propagation pathway. J Am Chem Soc. 2006;128:1562-8 pubmed
  13. Seyedsayamdost M, Stubbe J. Forward and reverse electron transfer with the Y356DOPA-beta2 heterodimer of E. coli ribonucleotide reductase. J Am Chem Soc. 2007;129:2226-7 pubmed
  14. Wang J, Caron P, Kim R. The role of DNA topoisomerases in recombination and genome stability: a double-edged sword?. Cell. 1990;62:403-6 pubmed
  15. Lin C, Jao C, Ting A. Genetically encoded fluorescent reporters of histone methylation in living cells. J Am Chem Soc. 2004;126:5982-3 pubmed
    ..These reporters should be useful for studying gene silencing and X-chromosome inactivation with high spatial and temporal resolution in intact cells and may also aid in the search for conjectured histone demethylase activity. ..
  16. Behan R, Lippard S. The aging-associated enzyme CLK-1 is a member of the carboxylate-bridged diiron family of proteins. Biochemistry. 2010;49:9679-81 pubmed publisher
    ..The direct reaction of NADH with a diiron-containing oxidase enzyme has not previously been encountered for any member of the protein superfamily. ..
  17. Artavanis Tsakonas K, Kasperkovitz P, Papa E, Cardenas M, Khan N, van der Veen A, et al. The tetraspanin CD82 is specifically recruited to fungal and bacterial phagosomes prior to acidification. Infect Immun. 2011;79:1098-106 pubmed publisher
    ..Together, these data show that the CD82 tetraspanin is specifically recruited to pathogen-containing phagosomes prior to fusion with lysosomes. ..
  18. Lu M, Kleckner N. Molecular cloning and characterization of the pgm gene encoding phosphoglucomutase of Escherichia coli. J Bacteriol. 1994;176:5847-51 pubmed
    ..The predicted amino acid sequence of the pgm gene is highly conserved in E. coli, Acetobacter xylinum, Saccharomyces cerevisiae, rabbits, and humans. pgm deletion mutant strains are deficient in phosphoglucomutase activity. ..
  19. Carroll S, Marx C. Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology. PLoS Genet. 2013;9:e1003427 pubmed publisher
  20. Uttamapinant C, Sánchez M, Liu D, Yao J, Ting A. Site-specific protein labeling using PRIME and chelation-assisted click chemistry. Nat Protoc. 2013;8:1620-34 pubmed publisher
    ..Reagent preparations, including synthesis of pAz probes and expression of LplA, take 12 d, whereas the procedure for performing site-specific pAz ligation and CuAAC on cells or on purified proteins takes 40 min-3 h. ..
  21. Margolis P, Driks A, Losick R. Sporulation gene spoIIB from Bacillus subtilis. J Bacteriol. 1993;175:528-40 pubmed
    ..The nature of the spoIIB spoVG mutant phenotype is discussed in terms of the events involved in the maturation of the sporulation septum and in the activation of sporulation transcription factors sigma F and sigma E. ..
  22. Esra Demircioglu F, Cruz V, Schwartz T. Purification and Structural Analysis of SUN and KASH Domain Proteins. Methods Enzymol. 2016;569:63-78 pubmed publisher
    ..Protocols used to study the biochemical and structural characteristics of core elements of SUN-KASH complexes are described here to facilitate further studies in this new field of cell biology. ..
  23. Abdi K, Chen T, Klein B, Tai A, Coursen J, Liu X, et al. Mechanisms by which Porphyromonas gingivalis evades innate immunity. PLoS ONE. 2017;12:e0182164 pubmed publisher
    ..Taken together, our results suggest that P. gingivalis has evolved potent mechanisms to modulate its virulence factors and dampen the innate immune response by selectively inactivating most proinflammatory cytokines...
  24. Deng H, Lee J, Goldstein L, Branton D. Drosophila development requires spectrin network formation. J Cell Biol. 1995;128:71-9 pubmed
    ..Our results show that spectrin's capacity to form a network is a crucial aspect of its function in nonerythroid cells. ..
  25. Aldovini A, Husson R, Young R. The uraA locus and homologous recombination in Mycobacterium bovis BCG. J Bacteriol. 1993;175:7282-9 pubmed
    ..These results have implications for understanding the role of mycobacterial genes in disease pathogenesis and for the genetic engineering of improved mycobacterial vaccines. ..
  26. Berg H, Turner L. Torque generated by the flagellar motor of Escherichia coli. Biophys J. 1993;65:2201-16 pubmed
    ..These results are consistent with a tightly coupled ratchet mechanism, provided that elastic deformation of force-generating elements is limited by a stop and that mechanical components yield at high applied torques. ..
  27. Delaney J, Essigmann J. Effect of sequence context on O(6)-methylguanine repair and replication in vivo. Biochemistry. 2001;40:14968-75 pubmed
  28. Bellon S, Parsons J, Wei Y, Hayakawa K, Swenson L, Charifson P, et al. Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase. Antimicrob Agents Chemother. 2004;48:1856-64 pubmed
    ..These data demonstrate that the ParE M74 and GyrB I78 side chains impart opposite effects on the enzyme's substrate affinity and catalytic efficiency. ..
  29. LaMarche M, Leeds J, Dzink Fox J, Gangl E, Krastel P, Neckermann G, et al. Antibiotic optimization and chemical structure stabilization of thiomuracin A. J Med Chem. 2012;55:6934-41 pubmed publisher
  30. Douglas S, Chubiz L, Harcombe W, Marx C. Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation. PLoS ONE. 2017;12:e0174345 pubmed publisher
    ..This work highlights that where biosynthesis of metabolites involves multiple layers of regulation, significant secretion of those metabolites may require multiple mutations, thereby constraining the evolution of cooperation. ..
  31. Chen L, Frankel A, Harder J, Fawell S, Barsoum J, Pepinsky B. Increased cellular uptake of the human immunodeficiency virus-1 Tat protein after modification with biotin. Anal Biochem. 1995;227:168-75 pubmed
    ..The increased uptake of Tat and Tat conjugates by addition of hydrophobic groups may significantly enhance the usefulness of Tat as a delivery vehicle, and the approach may be applicable to other systems. ..
  32. Bauer B, Rafie Kolpin M, Lu L, Han A, Chen J. Multiple autophosphorylation is essential for the formation of the active and stable homodimer of heme-regulated eIF2alpha kinase. Biochemistry. 2001;40:11543-51 pubmed
    ..Additional multiple autophosphorylation in the second stage is required for the formation of stable dimeric HRI (species II) with eIF2alpha kinase activity that is regulated by heme. ..
  33. Min W, Lu S, Chong S, Roy R, Holtom G, Xie X. Imaging chromophores with undetectable fluorescence by stimulated emission microscopy. Nature. 2009;461:1105-9 pubmed publisher
    ..For all these applications, sensitivity is orders of magnitude higher than for spontaneous emission or absorption contrast, permitting nonfluorescent reporters for molecular imaging. ..
  34. Jin L, Pandey P, Babine R, Gorga J, Seidl K, Gelfand E, et al. Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions. J Biol Chem. 2005;280:4704-12 pubmed
    ..These structures provide us with an understanding of substrate binding interactions of FXIa, the structural information essential for the structure-based design of FXIa-selective inhibitors. ..
  35. Wang K, Oakes E, Sauer R, Baker T. Tuning the strength of a bacterial N-end rule degradation signal. J Biol Chem. 2008;283:24600-7 pubmed publisher
    ..Together, these data define in vitro the sequence and structural requirements for the function of bacterial N-end signals. ..
  36. Hassan A, Wang Y, Plate L, Stubbe J. Methodology to probe subunit interactions in ribonucleotide reductases. Biochemistry. 2008;47:13046-55 pubmed publisher
    ..4 microM for subunit interaction. Disruption of the interaction of the alpha2-DAN-beta2 complex is accompanied by a decrease in fluorescence intensity and can serve as a high-throughput screen for inhibitors of subunit interactions. ..
  37. Ravichandran K, Liang L, Stubbe J, Tommos C. Formal reduction potential of 3,5-difluorotyrosine in a structured protein: insight into multistep radical transfer. Biochemistry. 2013;52:8907-15 pubmed publisher
    ..The findings in this paper are discussed relative to recent mechanistic studies of the multistep radical-transfer process in Escherichia coli ribonucleotide reductase site-specifically labeled with unnatural tyrosine residues. ..
  38. Thorens B, Sarkar H, Kaback H, Lodish H. Cloning and functional expression in bacteria of a novel glucose transporter present in liver, intestine, kidney, and beta-pancreatic islet cells. Cell. 1988;55:281-90 pubmed
    ..Insulinoma cells express, inappropriately, the erythrocyte glucose transporter, and we suggest that this may be related to their inability to secrete insulin in response to elevations in glucose. ..
  39. Spek E, Wright T, Stitt M, Taghizadeh N, Tannenbaum S, Marinus M, et al. Recombinational repair is critical for survival of Escherichia coli exposed to nitric oxide. J Bacteriol. 2001;183:131-8 pubmed
    ..can induce. Furthermore, the importance of recombinational repair for cellular survival of NO(.) exposure reveals a potential susceptibility factor for invading microbes. ..
  40. Moon T, Lou C, Tamsir A, Stanton B, Voigt C. Genetic programs constructed from layered logic gates in single cells. Nature. 2012;491:249-53 pubmed publisher
    ..This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells. ..
  41. Li D, Fedeles B, Shrivastav N, Delaney J, Yang X, Wong C, et al. Removal of N-alkyl modifications from N(2)-alkylguanine and N(4)-alkylcytosine in DNA by the adaptive response protein AlkB. Chem Res Toxicol. 2013;26:1182-7 pubmed publisher
  42. Kim Y, Levchenko I, Fraczkowska K, Woodruff R, Sauer R, Baker T. Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase. Nat Struct Biol. 2001;8:230-3 pubmed
    ..Mapping of the IGF loop onto a homolog of known structure suggests a model for ClpX-ClpP docking. ..
  43. Ge J, Yu G, Ator M, Stubbe J. Pre-steady-state and steady-state kinetic analysis of E. coli class I ribonucleotide reductase. Biochemistry. 2003;42:10071-83 pubmed
  44. Foote S, Denny C. Construction of YAC libraries with large inserts. Curr Protoc Hum Genet. 2002;Chapter 5:Unit5.2 pubmed publisher
    ..Additional support protocols detail two methods for partial digestion of genomic DNA: EcoRI restriction endonuclease-EcoRI methylase competition and the partial digestion of genomic DNA by use of limiting amounts of Mg2+, respectively...
  45. Boes M, Prodeus A, Schmidt T, Carroll M, Chen J. A critical role of natural immunoglobulin M in immediate defense against systemic bacterial infection. J Exp Med. 1998;188:2381-6 pubmed
    ..These findings demonstrate a critical role of natural IgM in the immediate defense against severe bacterial infection. ..
  46. Schwartz R, Ting C, King J. Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. Genome Res. 2001;11:703-9 pubmed
    ..Our analyses also suggest that the proportions of proteomes consisting of membrane-associated proteins may be currently underestimated. ..
  47. Wang Y, Lynch A, Chen S, Wang J. On the molecular basis of the thermal sensitivity of an Escherichia coli topA mutant. J Biol Chem. 2002;277:1203-9 pubmed
    ..Our results thus implicate an indispensable role of DNA topoisomerase I in E. coli cells grown in media of any osmolarity. ..
  48. Simmons L, Goranov A, Kobayashi H, Davies B, Yuan D, Grossman A, et al. Comparison of responses to double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS induction. J Bacteriol. 2009;191:1152-61 pubmed publisher
    ..Thus, we found that the contribution of SOS induction to double-strand break repair differs substantially between E. coli and B. subtilis. ..
  49. Little M, Steel B, Bai F, Sowa Y, Bilyard T, Mueller D, et al. Steps and bumps: precision extraction of discrete states of molecular machines. Biophys J. 2011;101:477-85 pubmed publisher
    ..Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided. ..
  50. Chen Y, Liu P, Nielsen A, Brophy J, Clancy K, Peterson T, et al. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods. 2013;10:659-64 pubmed publisher
    ..The availability of many terminators of varying strength, as well as an understanding of the sequence dependence of their properties, will extend their usability in the forward design of synthetic cistrons. ..
  51. Boyd E, Hill C, Rich S, Hartl D. Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics. 1996;143:1091-100 pubmed
    ..The relatively high rate of recombination in F-plasmid genes suggests that conjugational gene transfer may play a greater role in bacterial population structure than previously appreciated...
  52. Feijó Delgado F, Cermak N, Hecht V, Son S, Li Y, Knudsen S, et al. Intracellular water exchange for measuring the dry mass, water mass and changes in chemical composition of living cells. PLoS ONE. 2013;8:e67590 pubmed publisher
    ..For mammalian cells, changes in growth conditions cause substantial shifts in dry density, suggesting concurrent changes in the protein, nucleic acid and lipid content of the cell. ..
  53. Iverson S, Haddock T, Beal J, Densmore D. CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology. ACS Synth Biol. 2016;5:99-103 pubmed publisher
    ..Optimized protocols reduce reaction time and cost by >80% from that of previously published protocols. ..
  54. Fernandez Rodriguez J, Moser F, Song M, Voigt C. Engineering RGB color vision into Escherichia coli. Nat Chem Biol. 2017;13:706-708 pubmed publisher
    ..We use this system to produce 'color photographs' on bacterial culture plates by controlling pigment production and to redirect metabolic flux by expressing CRISPRi guide RNAs. ..
  55. Cai L, Friedman N, Xie X. Stochastic protein expression in individual cells at the single molecule level. Nature. 2006;440:358-62 pubmed
    ..This microfluidic single cell assay opens up possibilities for system-wide characterization of the expression of these low copy number proteins. ..
  56. Levin P, Losick R. Characterization of a cell division gene from Bacillus subtilis that is required for vegetative and sporulation septum formation. J Bacteriol. 1994;176:1451-9 pubmed
  57. Chivers P, Sauer R. Regulation of high affinity nickel uptake in bacteria. Ni2+-Dependent interaction of NikR with wild-type and mutant operator sites. J Biol Chem. 2000;275:19735-41 pubmed
    ..In addition to both GTATGA sites and nickel, high affinity operator binding also requires the C-terminal domain of NikR. ..
  58. Yokoyama K, Uhlin U, Stubbe J. Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-active tyrosines in ribonucleotide reductase. J Am Chem Soc. 2010;132:8385-97 pubmed publisher
  59. Levin J, Johnson A, Demple B. Homogeneous Escherichia coli endonuclease IV. Characterization of an enzyme that recognizes oxidative damage in DNA. J Biol Chem. 1988;263:8066-71 pubmed
    ..Endonuclease IV also activated H2O2-damaged DNA for repair synthesis by DNA polymerase I. Thus, endonuclease IV can act on a variety of oxidative damages in DNA, consistent with a role for the enzyme in combating free-radical toxicity. ..
  60. Nicholas R, Strominger J. Relations between beta-lactamases and penicillin-binding proteins: beta-lactamase activity of penicillin-binding protein 5 from Escherichia coli. Rev Infect Dis. 1988;10:733-8 pubmed
    ..The crystals of sPBP5' diffract to greater than 3 A resolution and are suitable for detailed crystallographic analysis. ..
  61. Moreau K, King J. Hydrophobic core mutations associated with cataract development in mice destabilize human gammaD-crystallin. J Biol Chem. 2009;284:33285-95 pubmed publisher
    ..These results support models of cataract formation in which generation of partially unfolded species are precursors to the aggregated cataractous states responsible for light scattering. ..
  62. Freinkman E, Okuda S, Ruiz N, Kahne D. Regulated assembly of the transenvelope protein complex required for lipopolysaccharide export. Biochemistry. 2012;51:4800-6 pubmed publisher
    ..This ordered sequence of events may ensure that LPS is never transported to the OM if it cannot be translocated across it to the cell surface...
  63. Wakasugi K, Quinn C, Tao N, Schimmel P. Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant. EMBO J. 1998;17:297-305 pubmed
    ..Thus, functionally important co-adaptations of a synthetase to its tRNA act as small modular units that can be moved across taxonomic domains and thereby preserve the universality of the code. ..
  64. Elbaz J, Yin P, Voigt C. Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nat Commun. 2016;7:11179 pubmed publisher
    ..Genetically encoding DNA nanostructures provides a route for their production as well as applications in living cells. ..
  65. Zhou X, Taghizadeh K, Dedon P. Chemical and biological evidence for base propenals as the major source of the endogenous M1dG adduct in cellular DNA. J Biol Chem. 2005;280:25377-82 pubmed
    ..Parallel studies with gamma-radiation revealed levels of MDA similar to those produced by ONOO- but no detectable M1dG. These results are consistent with base propenals as the major source of M1dG in this model cell system. ..
  66. Seyedsayamdost M, Xie J, Chan C, Schultz P, Stubbe J. Site-specific insertion of 3-aminotyrosine into subunit alpha2 of E. coli ribonucleotide reductase: direct evidence for involvement of Y730 and Y731 in radical propagation. J Am Chem Soc. 2007;129:15060-71 pubmed
    ..The observed NH2Y. may constitute the first detection of an amino acid radical intermediate in the proposed radical propagation pathway during turnover. ..
  67. Kosman R, Gouaux J, Lipscomb W. Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for ATCase mutants and the mechanism of negative cooperativity. Proteins. 1993;15:147-76 pubmed
    ..Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase. ..
  68. Roche E, Sauer R. Identification of endogenous SsrA-tagged proteins reveals tagging at positions corresponding to stop codons. J Biol Chem. 2001;276:28509-15 pubmed
    ..These and previous results support a broad role for the SsrA.SmpB system in freeing stalled ribosomes and in directing degradation of the products of these frustrated protein synthesis reactions. ..
  69. Seyedsayamdost M, Argirević T, Minnihan E, Stubbe J, Bennati M. Structural examination of the transient 3-aminotyrosyl radical on the PCET pathway of E. coli ribonucleotide reductase by multifrequency EPR spectroscopy. J Am Chem Soc. 2009;131:15729-38 pubmed publisher
    ..This analysis is an essential first step in using the detailed structure of NH(2)Y(730)* to formulate a model for a PCET mechanism within alpha2 and for use of NH(2)Y in other systems where transient Y*s participate in catalysis. ..
  70. Myers L, Terranova M, Nash H, Markus M, Verdine G. Zinc binding by the methylation signaling domain of the Escherichia coli Ada protein. Biochemistry. 1992;31:4541-7 pubmed
  71. Lauer G, Rudd E, McKay D, Ally A, Ally D, Backman K. Cloning, nucleotide sequence, and engineered expression of Thermus thermophilus DNA ligase, a homolog of Escherichia coli DNA ligase. J Bacteriol. 1991;173:5047-53 pubmed
    ..We have engineered the expression of the T. thermophilus gene in Escherichia coli, and we show that E. coli proteins may be substantially removed from the thermostable ligase by a simple heat precipitation step. ..
  72. Chen J, Peterson R, Schreiber S. Alpha 4 associates with protein phosphatases 2A, 4, and 6. Biochem Biophys Res Commun. 1998;247:827-32 pubmed
    ..By analogy, alpha 4 and its associated phosphatases may participate in the mammalian rapamycin-sensitive pathway mediated by FRAP. ..
  73. Slavoff S, Liu D, Cohen J, Ting A. Imaging protein-protein interactions inside living cells via interaction-dependent fluorophore ligation. J Am Chem Soc. 2011;133:19769-76 pubmed publisher
    ..ID-PRIME provides a powerful and complementary approach to existing methods for visualization of PPIs in living cells with spatial and temporal resolution. ..
  74. Boyd E, Hartl D. Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution. J Bacteriol. 1998;180:1159-65 pubmed
    ..These results suggest that the hly, kps, sfa, and pap pathogenicity determinants may play a role in the evolution of enteric bacteria quite apart from, and perhaps with precedence over, their ability to cause disease. ..
  75. Chen X, Berg H. Torque-speed relationship of the flagellar rotary motor of Escherichia coli. Biophys J. 2000;78:1036-41 pubmed
    ..In the high-speed regime, it decreases markedly at lower temperature. These results are consistent with models in which torque is generated by a powerstroke mechanism (, Biophys. J. 76:580-587). ..
  76. Chowdhury T, Chien P, Ebrahim S, Sauer R, Baker T. Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species. Protein Sci. 2010;19:242-54 pubmed publisher
    ..Our results also reveal highly conserved residues in the XB peptides of both E. coli SspB and C. crescentus SspBalpha that play no detectable role in ClpX-binding or substrate delivery. ..
  77. Chen A, Deng Z, Billings A, Seker U, Lu M, Citorik R, et al. Synthesis and patterning of tunable multiscale materials with engineered cells. Nat Mater. 2014;13:515-23 pubmed publisher
    ..This work lays a foundation for synthesizing, patterning, and controlling functional composite materials with engineered cells. ..
  78. Xue D, Shaham S, Horvitz H. The Caenorhabditis elegans cell-death protein CED-3 is a cysteine protease with substrate specificities similar to those of the human CPP32 protease. Genes Dev. 1996;10:1073-83 pubmed
    ..Our results suggest that different mammalian CED-3/ICE-like proteases may have distinct roles in mammalian apoptosis and that CPP32 is a candidate for being a mammalian functional equivalent of CED-3. ..
  79. McCoy J, La Ville E. Expression and purification of thioredoxin fusion proteins. Curr Protoc Protein Sci. 2001;Chapter 6:Unit 6.7 pubmed publisher
    ..Additional protocols describe E. coli cell lysis and fractionation, osmotic release of thioredoxin fusion proteins from the E. coli cytoplasm, and heat treatment to purify some thioredoxin fusion proteins. ..
  80. Lebar M, Lupoli T, Tsukamoto H, May J, Walker S, Kahne D. Forming cross-linked peptidoglycan from synthetic gram-negative Lipid II. J Am Chem Soc. 2013;135:4632-5 pubmed publisher
    ..This work provides the tools necessary for reconstituting cell wall synthesis, an essential cellular process and major antibiotic target, in a purified system. ..
  81. Zimanyi C, Chen P, Kang G, Funk M, Drennan C. Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli. elife. 2016;5:e07141 pubmed publisher
  82. Yu H, Schreiber S. Cloning, Zn2+ binding, and structural characterization of the guanine nucleotide exchange factor human Mss4. Biochemistry. 1995;34:9103-10 pubmed
    ..Many resonances pertaining to a loop region of the molecule cannot be identified, suggesting that it might be involved in local movements. These studies provide the first structural insights into a protein possessing GEF activity. ..
  83. Ozbudak E, Thattai M, Lim H, Shraiman B, van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature. 2004;427:737-40 pubmed
    ..The phase diagram thus serves as a sensitive probe of molecular interactions and as a powerful tool for rational network design. ..
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