Genomes and Genes
Experts and Doctors on escherichia coli proteins in Philadelphia, Pennsylvania, United States
Locale: Philadelphia, Pennsylvania, United States
Topic: escherichia coli proteins
- Kodali G, Siddiqui S, Stanley R. Charge redistribution in oxidized and semiquinone E. coli DNA photolyase upon photoexcitation: stark spectroscopy reveals a rationale for the position of Trp382. J Am Chem Soc. 2009;131:4795-807 pubmed publisher..The ramifications of vectorial charge redistribution are discussed in the context of the wider class of flavoprotein blue light photoreceptors. ..
- ..Understanding how effector molecules alter the thermodynamic properties of the repressor is essential for establishing a detailed understanding of gene regulation. ..
- Nakamaru Ogiso E, Kao M, Chen H, Sinha S, Yagi T, Ohnishi T. The membrane subunit NuoL(ND5) is involved in the indirect proton pumping mechanism of Escherichia coli complex I. J Biol Chem. 2010;285:39070-8 pubmed publisher..The electron transfer activities were basically unaffected by EIPA in both control and mutants. Taken together, our data strongly indicate that the NuoL subunit is involved in the indirect coupling mechanism. ..
- Cassone M, Vogiatzi P, La Montagna R, de Olivier Inacio V, Cudic P, Wade J, et al. Scope and limitations of the designer proline-rich antibacterial peptide dimer, A3-APO, alone or in synergy with conventional antibiotics. Peptides. 2008;29:1878-86 pubmed publisher..However, the synergy appeared to be individual strain and small molecule drug combination-dependent. ..
- Pimkin M, Pimkina J, Markham G. A regulatory role of the Bateman domain of IMP dehydrogenase in adenylate nucleotide biosynthesis. J Biol Chem. 2009;284:7960-9 pubmed publisher..We conclude that the Bateman domain of IMPDH is a negative trans-regulator of adenylate nucleotide synthesis, and that this role is independent of the catalytic function of IMPDH in the de novo GMP biosynthesis. ..
- Mellata M, Mitchell N, SchÃ¶del F, Curtiss R, Pier G. Novel vaccine antigen combinations elicit protective immune responses against Escherichia coli sepsis. Vaccine. 2016;34:656-662 pubmed publisher..The information and data presented are the first step toward the development of a broadly protective vaccine against sepsis-causing E. coli strains. ..
- Miyashiro T, Goulian M. High stimulus unmasks positive feedback in an autoregulated bacterial signaling circuit. Proc Natl Acad Sci U S A. 2008;105:17457-62 pubmed publisher..Our results demonstrate a simple and general mechanism for regulating the positive feedback associated with autoregulation within a bacterial signaling circuit to boost response range and maintain a relatively uniform and graded output. ..
- Chen H, Schifferli D. Enhanced immune responses to viral epitopes by combining macrophage-inducible expression with multimeric display on a Salmonella vector. Vaccine. 2001;19:3009-18 pubmed..This indicated that the pagC promoter can be used successfully to improve epitope-display by chimeric fimbriae on Salmonella vaccine strains for the induction of a desired immune response. ..
- Westhoff C, Wylie D. Transport characteristics of mammalian Rh and Rh glycoproteins expressed in heterologous systems. Transfus Clin Biol. 2006;13:132-8 pubmed..The relationship of Rh and Rh-glycoproteins to the Amt/Mep ammonium transporters is substantiated with functional transport data and structural modeling. ..
- Christian T, Lahoud G, Liu C, Hou Y. Control of catalytic cycle by a pair of analogous tRNA modification enzymes. J Mol Biol. 2010;400:204-17 pubmed publisher..This parallel suggests that the findings have a fundamental importance for enzymes that catalyze both methyl and aminoacyl transfer to tRNA in the decoding process. ..
- Whittington D, Rusche K, Shin H, Fierke C, Christianson D. Crystal structure of LpxC, a zinc-dependent deacetylase essential for endotoxin biosynthesis. Proc Natl Acad Sci U S A. 2003;100:8146-50 pubmed publisher..Notably, simple inhibitors designed to target interactions in the hydrophobic tunnel bind with micromolar affinity, thereby representing a step toward the structure-based design of a potent, broad-spectrum antibacterial drug...
- Miyashiro T, Goulian M. Stimulus-dependent differential regulation in the Escherichia coli PhoQ PhoP system. Proc Natl Acad Sci U S A. 2007;104:16305-10 pubmed
- Liu H, Pan D, Pech M, Cooperman B. Interrupted catalysis: the EF4 (LepA) effect on back-translocation. J Mol Biol. 2010;396:1043-52 pubmed publisher..The delay in polypeptide elongation resulting from transient accumulation of I(3) is likely to be important for optimizing functional protein biosynthesis. ..
- ..A historical perspective that illustrates the role these two repressor molecules played and their contribution to our understanding of gene regulation is presented. ..
- Wagner M, Khanna P, Jorns M. Structure of the flavocoenzyme of two homologous amine oxidases: monomeric sarcosine oxidase and N-methyltryptophan oxidase. Biochemistry. 1999;38:5588-95 pubmed..There is only one conserved cysteine found among these enzymes, suggesting that Cys308 is the covalent flavin attachment site in MTOX. ..
- Fu Y, Wand A. Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure. J Biomol NMR. 2013;56:353-7 pubmed publisher..However, DMPC/DHPC bicelles and collagen gel are found to be unsuitable. Evidence is presented to demonstrate that pressure-induced structural changes can be identified using the residual dipolar coupling. ..
- Shitivelband S, Hou Y. Breaking the stereo barrier of amino acid attachment to tRNA by a single nucleotide. J Mol Biol. 2005;348:513-21 pubmed..Thus, the single nucleotide U73 of tRNA has the ability to break the stereo barrier of amino acid attachment to tRNA, by mobilizing the 2' and 3'-hydroxyl groups of A76 in flexible geometry with respect to the tRNA acceptor stem. ..
- Sun W, Pertzev A, Nicholson A. Catalytic mechanism of Escherichia coli ribonuclease III: kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis. Nucleic Acids Res. 2005;33:807-15 pubmed..A preliminary model is presented for functional roles of two divalent metal ions in the RNase III catalytic mechanism. ..
- Balasubramanian K, Stitt B. Evidence for amino acid roles in the chemistry of ATP hydrolysis in Escherichia coli Rho. J Mol Biol. 2010;404:587-99 pubmed publisher..All four mutant proteins behaved as expected for Rhos lacking the proposed mechanistic roles. The results provide firm biochemical evidence in support of the proposed model for hydrolysis chemistry. ..
- Freeman N, Zurawski D, Chowrashi P, Ayoob J, Huang L, Mittal B, et al. Interaction of the enteropathogenic Escherichia coli protein, translocated intimin receptor (Tir), with focal adhesion proteins. Cell Motil Cytoskeleton. 2000;47:307-18 pubmed..Since pedestals also contain villin, tropomyosin and myosin II [Sanger et al., 1996: Cell Motil. Cytoskeleton 34:279-287], the pedestals appear to be a novel structure sharing properties of both focal adhesions and microvilli. ..
- Stitt B, Xiao H. Conformation changes in E. coli Rho monitored by hydrogen/deuterium exchange and mass spectrometry: response to ligand binding. J Mol Biol. 2010;402:813-24 pubmed publisher..Overall, the results show changes in a few protein segments rather than a different overall conformation. ..
- Sun W, Li G, Nicholson A. Mutational analysis of the nuclease domain of Escherichia coli ribonuclease III. Identification of conserved acidic residues that are important for catalytic function in vitro. Biochemistry. 2004;43:13054-62 pubmed..RNase III[D45E] activity is partially rescued by Mn(2+). The potential functions of the conserved acidic residues are discussed in the context of the crystallographic data and proposed catalytic mechanisms. ..
- Zeng P, Rane N, Du W, Chintapalli J, Prendergast G. Role for RhoB and PRK in the suppression of epithelial cell transformation by farnesyltransferase inhibitors. Oncogene. 2003;22:1124-34 pubmed
- Khanna P, Schuman Jorns M. Characterization of the FAD-containing N-methyltryptophan oxidase from Escherichia coli. Biochemistry. 2001;40:1441-50 pubmed..Charge-transfer complexes are formed with 3-indoleacrylate, pyrrole-2-carboxylate, and CH(3)XCH(2)CO(2)(-) (X = S, Se, Te). ..
- Correnti J, Munster V, Chan T, Woude M. Dam-dependent phase variation of Ag43 in Escherichia coli is altered in a seqA mutant. Mol Microbiol. 2002;44:521-32 pubmed..In isolates with a mutant seqA allele, agn43 phase variation rates were altered and resulted in a bias to the OFF phase. In part, this can be attributed to the observed decrease in the level of DNA methylation in the seqA mutant. ..
- Pham J, Sakaguchi R, Yeoh L, De Silva N, McFadden G, Hou Y, et al. A dual-targeted aminoacyl-tRNA synthetase in Plasmodium falciparum charges cytosolic and apicoplast tRNACys. Biochem J. 2014;458:513-23 pubmed publisher..Inhibitors of the Plasmodium dual-targeted CysRS would potentially offer a therapy capable of the desirable immediate effects on parasite growth as well as the irreversibility of inhibitors that disrupt apicoplast inheritance...
- Desantis M, Leung E, Sweeny E, Jackrel M, Cushman Nick M, Neuhaus Follini A, et al. Operational plasticity enables hsp104 to disaggregate diverse amyloid and nonamyloid clients. Cell. 2012;151:778-793 pubmed publisher..Thus, operational plasticity enables Hsp104 to robustly dissolve amyloid and nonamyloid clients, which impose distinct mechanical demands. ..
- Dupasquier M, Kim S, Halkidis K, Gamper H, Hou Y. tRNA integrity is a prerequisite for rapid CCA addition: implication for quality control. J Mol Biol. 2008;379:579-88 pubmed publisher..These results suggest a kinetic quality control provided by the CCA enzyme to inspect the integrity of the tRNA molecule and to discriminate against nicked or damaged species from further maturation. ..
- Pascal J. DNA and RNA ligases: structural variations and shared mechanisms. Curr Opin Struct Biol. 2008;18:96-105 pubmed publisher..Together with unliganded crystal structures of DNA and RNA ligases, a more comprehensive and dynamic understanding of the multi-step ligation reaction mechanism has emerged. ..
- Coskun Ari F, Skokotas A, Moe G, Hill T. Biophysical characteristics of Tus, the replication arrest protein of Escherichia coli. J Biol Chem. 1994;269:4027-34 pubmed..In addition, partial proteolytic digests of free Tus protein did not produce a subfragment of Tus that retained DNA binding activity, but did demonstrate that Tus was resistant to proteolysis when complexed with a Ter site. ..
- Muppirala U, Desensi S, Lybrand T, Hazelbauer G, Li Z. Molecular modeling of flexible arm-mediated interactions between bacterial chemoreceptors and their modification enzyme. Protein Sci. 2009;18:1702-14 pubmed publisher..Our analysis introduces the notion that physiologically relevant adaptational assistance could occur even if only a subset of sites on a particular receptor are within reach. ..
- Thiele G, Friedman C, Tsai K, Beld J, Londergan C, Charkoudian L. Acyl Carrier Protein Cyanylation Delivers a Ketoacyl Synthase-Carrier Protein Cross-Link. Biochemistry. 2017;56:2533-2536 pubmed publisher..This represents a practical and generalizable method for obtaining and visualizing ACP-protein complexes relevant to biocatalysis and will be valuable in future structural and engineering studies...
- Khanna P, Jorns M. Tautomeric rearrangement of a dihydroflavin bound to monomeric sarcosine oxidase or N-methyltryptophan oxidase. Biochemistry. 2003;42:864-9 pubmed..The observed tautomeric rearrangement of 3,4-dihydroflavin may provide insight regarding a related flavin tautomerization reaction that has been proposed as a key step in the biosynthesis of covalent flavin linkages. ..
- Ugulava N, Frederick K, Jarrett J. Control of adenosylmethionine-dependent radical generation in biotin synthase: a kinetic and thermodynamic analysis of substrate binding to active and inactive forms of BioB. Biochemistry. 2003;42:2708-19 pubmed..Cooperative binding of AdoMet and DTB may be an important mechanism for limiting the production of 5'-deoxyadenosyl radicals in the absence of the correct substrate. ..
- Skokotas A, Hiasa H, Marians K, O DONNELL L, Hill T. Mutations in the Escherichia coli Tus protein define a domain positioned close to the DNA in the Tus-Ter complex. J Biol Chem. 1995;270:30941-8 pubmed..Finally, the half-lives of the mutant protein-DNA complexes suggested that the domain of Tus where these mutations are located is positioned close to the DNA in the Tus-Ter complex. ..
- Wallecha A, Munster V, Correnti J, Chan T, van der Woude M. Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation. J Bacteriol. 2002;184:3338-47 pubmed..Deletion analyses of the regulatory region showed that a 101-nucleotide region of the agn43 regulatory region containing the promoter and this OxyR binding region was sufficient for Dam- and OxyR-dependent phase variation ..
- Sliozberg Y, Abrams C. Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations. Biophys J. 2007;93:1906-16 pubmed..Finally, we propose a novel mechanism for inter-ring cooperativity in ATP binding inspired by the observation of spontaneous insertion of the side chain of Ala(480) into the empty nucleotide pocket. ..
- Mazurek A, Berardini M, Fishel R. Activation of human MutS homologs by 8-oxo-guanine DNA damage. J Biol Chem. 2002;277:8260-6 pubmed..These results suggest that only hMSH2-hMSH6 is activated by recognition of 8-oxo-G lesions. Our data are consistent with the notion that post-replication MMR only participates in the repair of mismatched 8-oxo-G lesions. ..
- Bell C, Lewis M. A closer view of the conformation of the Lac repressor bound to operator. Nat Struct Biol. 2000;7:209-14 pubmed..An extensive network of interactions between the DNA-binding and core domains of the repressor suggests a possible mechanism for the allosteric transition. ..
- Browne R, Stitt B. Active site occupancy required for catalytic cooperativity by Escherichia coli transcription termination factor Rho. J Biol Chem. 2005;280:13300-3 pubmed..They further suggest that, once the enzyme is saturated with ATP, a V(max) enzyme conformation is achieved that is stable for at least three catalytic cycles. ..
- Lewis M. The lac repressor. C R Biol. 2005;328:521-48 pubmed..The structures of lac repressor, bound to its operator and inducer, have also been invaluable for interpreting a plethora of biochemical and genetic data. ..
- Christian T, Hou Y. Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases. J Mol Biol. 2007;373:623-32 pubmed..Our results also shed new light onto the significance of the m1G37 modification in the controversial quadruplet-pairing model of tRNA frameshift suppressors...
- Sharma B, Hill T. TerF, the sixth identified replication arrest site in Escherichia coli, is located within the rcsC gene. J Bacteriol. 1992;174:7854-8 pubmed
- Lamoureux G, Klein M, Berneche S. A stable water chain in the hydrophobic pore of the AmtB ammonium transporter. Biophys J. 2007;92:L82-4 pubmed..The probable presence of water molecules in the pore would influence the relative stability of NH(3) and NH(4)(+), and thus calls for a reassessment of the overall permeation mechanism in ammonium transporters. ..
- Batchelor E, Walthers D, Kenney L, Goulian M. The Escherichia coli CpxA-CpxR envelope stress response system regulates expression of the porins ompF and ompC. J Bacteriol. 2005;187:5723-31 pubmed..However, at least for the classical porins OmpF and OmpC, our results show that the Cpx envelope stress response system plays a role in regulating their expression. ..
- Pertzev A, Nicholson A. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III. Nucleic Acids Res. 2006;34:3708-21 pubmed..The base pair sequence control of reactivity is discussed within the context of new structural information on a post-catalytic complex of a bacterial RNase III bound to the cleaved minimal substrate. ..
- Khanna P, Schuman Jorns M. N-methyltryptophan oxidase from Escherichia coli: reaction kinetics with N-methyl amino acid and carbinolamine substrates. Biochemistry. 2001;40:1451-9 pubmed..The basis for the apparent stability of the MTOX.oxygen complex (K(d) = 72 microM) is unknown. ..
- Lautenbach E, Metlay J, Mao X, Han X, Fishman N, Bilker W, et al. The prevalence of fluoroquinolone resistance mechanisms in colonizing Escherichia coli isolates recovered from hospitalized patients. Clin Infect Dis. 2010;51:280-5 pubmed publisher..Significant temporal changes occurred in the proportion of isolates exhibiting various resistance mechanisms. ..
- Narayanan M, Sakyiama J, Elguindy M, Nakamaru Ogiso E. Roles of subunit NuoL in the proton pumping coupling mechanism of NADH:ubiquinone oxidoreductase (complex I) from Escherichia coli. J Biochem. 2016;160:205-215 pubmed
- Hirokawa G, Nijman R, Raj V, Kaji H, Igarashi K, Kaji A. The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits. RNA. 2005;11:1317-28 pubmed..The three-factor-dependent stable dissociation of ribosomes into subunits completes the ribosome cycle and the resulting subunits are ready for the next round of translation. ..
- Siryaporn A, Goulian M. Cross-talk suppression between the CpxA-CpxR and EnvZ-OmpR two-component systems in E. coli. Mol Microbiol. 2008;70:494-506 pubmed publisher..e. it masks the effects of mutations that would otherwise lead to increased cross-talk. The mechanisms that provide insulation against interference described here may be applicable to many other two-component systems. ..
- Towles K, Beausang J, Garcia H, Phillips R, Nelson P. First-principles calculation of DNA looping in tethered particle experiments. Phys Biol. 2009;6:025001 pubmed publisher..We also show that it is unlikely to be the result of a hypothetical 'open' conformation of the LacI tetramer. ..
- Qin H, Grigoriadou C, Cooperman B. Interaction of IF2 with the ribosomal GTPase-associated center during 70S initiation complex formation. Biochemistry. 2009;48:4699-706 pubmed publisher..coli 70SIC, relative reactivities toward dipeptide formation of 70SICs formed with the two IF2s suggest that the Bst-IF2.GDP complex is more difficult to displace from the GAC than the E. coli IF2.GDP complex. ..
- Wang M, Church G. A whole genome approach to in vivo DNA-protein interactions in E. coli. Nature. 1992;360:606-10 pubmed..The in vivo protection at the Dam site upstream of the car operon was correlated with a downregulation of car expression, as expected of a feedback repressor-binding model...
- Bell C, Barry J, Matthews K, Lewis M. Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator. J Mol Biol. 2001;313:99-109 pubmed
- Lightfoot R, Shuman D, Ischiropoulos H. Oxygen-insensitive nitroreductases of Escherichia coli do not reduce 3-nitrotyrosine. Free Radic Biol Med. 2000;28:1132-6 pubmed..The degree of 3-nitrotyrosine immunoreactivity over the 2-h postexposure period did not differ between mutant and wild-type strains. These results indicate that the nfsA and nfsB enzymes do not reduce 3-nitrotyrosine. ..
- Liu H, Chen C, Zhang H, Kaur J, Goldman Y, Cooperman B. The conserved protein EF4 (LepA) modulates the elongation cycle of protein synthesis. Proc Natl Acad Sci U S A. 2011;108:16223-8 pubmed publisher..Our present results strongly suggest that PRE complex is the principal target of EF4 action on translation, rather than POST complex as had been previously supposed. ..
- Gottlieb P, Wu S, Zhang X, Tecklenburg M, Kuempel P, Hill T. Equilibrium, kinetic, and footprinting studies of the Tus-Ter protein-DNA interaction. J Biol Chem. 1992;267:7434-43 pubmed..The distribution of contacts along the TerB sequence was consistent with the functional polarity of the Tus-Ter complex and suggested possible mechanisms for the impediment of protein translocation along DNA. ..
- Skokotas A, Wrobleski M, Hill T. Isolation and characterization of mutants of Tus, the replication arrest protein of Escherichia coli. J Biol Chem. 1994;269:20446-55 pubmed..We concluded from these observations that the standard in vitro helicase assay was inadequate for measuring Tus activity. ..
- Zhao K, Chai X, Marmorstein R. Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli. J Mol Biol. 2004;337:731-41 pubmed..Together, these studies suggest that substrate-specific binding by sirtuin proteins involves contributions from the zinc-binding domain of the enzyme and substrate regions distal to the acetyl-lysine-binding site. ..
- Guerrette S, Acharya S, Fishel R. The interaction of the human MutL homologues in hereditary nonpolyposis colon cancer. J Biol Chem. 1999;274:6336-41 pubmed
- Shaver A, Sniegowski P. Spontaneously arising mutL mutators in evolving Escherichia coli populations are the result of changes in repeat length. J Bacteriol. 2003;185:6076-82 pubmed..The similarity of the two mutator mutations (despite the independent evolutionary histories of the populations that gave rise to them) leads to a discussion of the potential adaptive role of DNA repeats. ..
- Bell C, Lewis M. Crystallographic analysis of Lac repressor bound to natural operator O1. J Mol Biol. 2001;312:921-6 pubmed
- Wallecha A, Correnti J, Munster V, van der Woude M. Phase variation of Ag43 is independent of the oxidation state of OxyR. J Bacteriol. 2003;185:2203-9 pubmed
- Haagmans W, van der Woude M. Phase variation of Ag43 in Escherichia coli: Dam-dependent methylation abrogates OxyR binding and OxyR-mediated repression of transcription. Mol Microbiol. 2000;35:877-87 pubmed..These results show that Dam-dependent phase variation in E. coli is not limited to the previously identified regulatory system of the family of pap-like fimbrial operons. ..
- Anandan S, Uram J. Genetic selection scheme for isolation of signal transduction pathway mutants. Appl Environ Microbiol. 2004;70:967-72 pubmed..The selection scheme presented here extends the molecular tools available for the genetic dissection of signal transduction pathways. ..
- Fishel R, Wilson T. MutS homologs in mammalian cells. Curr Opin Genet Dev. 1997;7:105-13 pubmed..The redundant functions of MSH3 and MSH6 explain the greater prevalence of hmsh2 mutations in HNPCC families. ..
- Acharya S, Foster P, Brooks P, Fishel R. The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair. Mol Cell. 2003;12:233-46 pubmed..Additionally, MutL promotes ATP binding-independent turnover of idle MutS sliding clamps. These results support a model of MMR that relies on two dynamic and redundant ATP-regulated molecular switches. ..
- Honarvar S, Choi B, Schifferli D. Phase variation of the 987P-like CS18 fimbriae of human enterotoxigenic Escherichia coli is regulated by site-specific recombinases. Mol Microbiol. 2003;48:157-71 pubmed..Acquisition of a phase variation module to regulate fimbrial genes is proposed to be beneficial for the adaptation and transmission of pathogens. ..
- Hirokawa G, Kaji H, Kaji A. Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin. Antimicrob Agents Chemother. 2007;51:175-80 pubmed..These results indicate that the stabilization of 70S ribosomes by paromomycin may in part be responsible for its inhibitory effects on translocation and ribosome recycling. ..