Genomes and Genes
Experts and Doctors on amino acid sequence in Urbana, Illinois, United States
Locale: Urbana, Illinois, United States
Topic: amino acid sequence
Publications329 found, 100 shown here
- Fang J, Han Q, Li J. Isolation, characterization, and functional expression of kynurenine aminotransferase cDNA from the yellow fever mosquito, Aedes aegypti(1). Insect Biochem Mol Biol. 2002;32:943-50 pubmed..Results indicate that a specific KAT is present in mosquitoes and the enzyme may play an important physiological role in A. aegypti...
- Larson J, Rebeiz M, Stiening C, Windish R, Beever J, Lewin H. MHC class I-like genes in cattle, MHCLA, with similarity to genes encoding NK cell stimulatory ligands. Immunogenetics. 2003;55:16-22 pubmed
- Naidu S, Moose S, AL Shoaibi A, Raines C, Long S. Cold tolerance of C4 photosynthesis in Miscanthus x giganteus: adaptation in amounts and sequence of C4 photosynthetic enzymes. Plant Physiol. 2003;132:1688-97 pubmed..The maintenance of PPDK and Rubisco large subunit amounts in M. x giganteus is consistent with the hypothesis that these proteins are critical to maintaining high rates of C(4) photosynthesis at low temperature. ..
- Gerlt J, Babbitt P, Rayment I. Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys. 2005;433:59-70 pubmed..In this minireview, our current understanding of structure/function relationships in the divergent members of the superfamily is reviewed, and the use of this knowledge for our future studies is proposed. ..
- Lutz C, Robinson G. Activity-dependent gene expression in honey bee mushroom bodies in response to orientation flight. J Exp Biol. 2013;216:2031-8 pubmed publisher..Our results implicate the mushroom bodies in spatial learning and emphasize the deep conservation of Egr-related pathways in experience-dependent plasticity. ..
- Wu S, Lu Q, Kriz A, Harper J. Identification of cDNA clones corresponding to two inducible nitrate reductase genes in soybean: analysis in wild-type and nr1 mutant. Plant Mol Biol. 1995;29:491-506 pubmed..Based on the Eco RI and Hae III restriction enzyme digestion patterns observed in Southern blot analysis of soybean DNA, it is concluded that in soybean iNR1 is encoded by a small multiple gene family and iNR2 is a single gene. ..
- Srinivasan V, Schnitzlein W, Tripathy D. Fowlpox virus encodes a novel DNA repair enzyme, CPD-photolyase, that restores infectivity of UV light-damaged virus. J Virol. 2001;75:1681-8 pubmed..Although expression of a homologous protein has been predicted for some chordopoxviruses, this report is the first to demonstrate that a poxvirus can utilize light to repair damage to its genome...
- Li L, Floyd P, Rubakhin S, Romanova E, Jing J, Alexeeva V, et al. Cerebrin prohormone processing, distribution and action in Aplysia californica. J Neurochem. 2001;77:1569-80 pubmed..Cerebrin-like immunoreactivity is also present in Lymnaea stagnalis suggesting that cerebrin-like peptides may be widespread throughout gastropoda...
- Campbell J, Morgan Kiss R, Cronan J. A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic beta-oxidation pathway. Mol Microbiol. 2003;47:793-805 pubmed..These three genes are conserved in the available genome sequences of pathogenic E. coli, Shigella and Salmonella strains. ..
- Roper R, McAllister R, Biggins J, Michael S, Min S, Tung K, et al. Aod1 controlling day 3 thymectomy-induced autoimmune ovarian dysgenesis in mice encompasses two linked quantitative trait loci with opposing allelic effects on disease susceptibility. J Immunol. 2003;170:5886-91 pubmed
- Okeley N, Paul M, Stasser J, Blackburn N, van der Donk W. SpaC and NisC, the cyclases involved in subtilin and nisin biosynthesis, are zinc proteins. Biochemistry. 2003;42:13613-24 pubmed..The metal may function to activate the cysteine thiol of the peptide substrate toward intramolecular Michael addition to the dehydroalanine and dehydrobutyrine residues in the peptide. ..
- Miao J, Fang S, Bae Y, Kemper J. Functional inhibitory cross-talk between constitutive androstane receptor and hepatic nuclear factor-4 in hepatic lipid/glucose metabolism is mediated by competition for binding to the DR1 motif and to the common coactivators, GRIP-1 and PGC-1alpha. J Biol Chem. 2006;281:14537-46 pubmed
- Hsu S, Yonekura S, Ting C, Robertson H, Iwai Y, Uemura T, et al. Conserved alternative splicing and expression patterns of arthropod N-cadherin. PLoS Genet. 2009;5:e1000441 pubmed publisher..Ectopic muscle expression of either isoform beyond the time it normally ceases leads to paralysis and lethality. Together, our results offer an example of well-conserved alternative splicing increasing cellular diversity in metazoans...
- Butler T, Goldenfeld N, Mathew D, Luthey Schulten Z. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys Rev E Stat Nonlin Soft Matter Phys. 2009;79:060901 pubmed..The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor. ..
- Guan Y, Ranoa D, Jiang S, Mutha S, Li X, Baudry J, et al. Human TLRs 10 and 1 share common mechanisms of innate immune sensing but not signaling. J Immunol. 2010;184:5094-103 pubmed publisher..We conclude that human TLR10 cooperates with TLR2 in the sensing of microbes and fungi but possesses a signaling function distinct from that of other TLR2 subfamily members. ..
- Honda M, Okuno Y, Yoo J, Ha T, Spies M. Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding. EMBO J. 2011;30:3368-82 pubmed publisher..We propose that phosphorylation at Y104 enhances ssDNA annealing activity of RAD52 by attenuating dsDNA binding. Implications of phosphorylation-mediated activation of RAD52 annealing activity are discussed. ..
- Minghetti K, Goswitz V, Gabriel N, Hill J, Barassi C, Georgiou C, et al. Modified, large-scale purification of the cytochrome o complex (bo-type oxidase) of Escherichia coli yields a two heme/one copper terminal oxidase with high specific activity. Biochemistry. 1992;31:6917-24 pubmed..Hence, although subunit II does not contain CuA and does not interact with cytochrome c, it still must have an important function in the bo-type ubiquinol oxidase. ..
- Perera I, Zielinski R. Structure and expression of the Arabidopsis CaM-3 calmodulin gene. Plant Mol Biol. 1992;19:649-64 pubmed..Run-on transcription assays indicated that a portion of the differences in accumulation of ACaM-1, 2, and 3 mRNAs in leaves and siliques was attributable to differences in their net rates of transcription. ..
- Magnuson K, Jackowski S, Rock C, Cronan J. Regulation of fatty acid biosynthesis in Escherichia coli. Microbiol Rev. 1993;57:522-42 pubmed..Pursuing such questions should reveal additional regulatory mechanisms of fatty acid synthesis and, hopefully, the role of fatty acid synthesis and other cellular processes in the global control of cellular growth. ..
- Martinez A, Ostrovsky P, Nunn D. Identification of an additional member of the secretin superfamily of proteins in Pseudomonas aeruginosa that is able to function in type II protein secretion. Mol Microbiol. 1998;28:1235-46 pubmed..aeruginosa. We have also demonstrated that this protein is capable of recognizing all of the exoproteins of P. aeruginosa, arguing against the proposed role of members of the secretin family as determinants of specificity. ..
- Taron C, Wiedman J, Grimme S, Orlean P. Glycosylphosphatidylinositol biosynthesis defects in Gpi11p- and Gpi13p-deficient yeast suggest a branched pathway and implicate gpi13p in phosphoethanolamine transfer to the third mannose. Mol Biol Cell. 2000;11:1611-30 pubmed
- Mukhopadhyay B, Purwantini E, Kreder C, Wolfe R. Oxaloacetate synthesis in the methanarchaeon Methanosarcina barkeri: pyruvate carboxylase genes and a putative Escherichia coli-type bifunctional biotin protein ligase gene (bpl/birA) exhibit a unique organization. J Bacteriol. 2001;183:3804-10 pubmed publisher..We found the element Tyr(Phe)ProX(5)Phe(Tyr) to be fully conserved in biotin-dependent enzymes; it might function as the hinge for their "swinging arms."..
- Montalvetti A, Fernandez A, Sanders J, Ghosh S, Van Brussel E, Oldfield E, et al. Farnesyl pyrophosphate synthase is an essential enzyme in Trypanosoma brucei. In vitro RNA interference and in vivo inhibition studies. J Biol Chem. 2003;278:17075-83 pubmed..These results establish that FPPS is essential for parasite viability and validate this enzyme as a target for drug development. ..
- Li J, Ruyl Kim S, Christensen B, Li J. Purification and primary structural characterization of prophenoloxidases from Aedes aegypti larvae. Insect Biochem Mol Biol. 2005;35:1269-83 pubmed..Results of this study provide a basis for developing a comprehensive understanding of structure/function relationships of individual proPOs in mosquitoes. ..
- Beever J, Smit M, Meyers S, Hadfield T, Bottema C, Albretsen J, et al. A single-base change in the tyrosine kinase II domain of ovine FGFR3 causes hereditary chondrodysplasia in sheep. Anim Genet. 2006;37:66-71 pubmed..In contrast to FGFR3 mutations causing dwarfism in humans, this single-base change is the only known natural mutation of FGFR3 that results in a skeletal overgrowth phenotype in any species. ..
- Belton R, Chen L, Mesquita F, Nowak R. Basigin-2 is a cell surface receptor for soluble basigin ligand. J Biol Chem. 2008;283:17805-14 pubmed publisher..It was concluded that cell surface basigin functions as a membrane receptor for soluble basigin and this homophilic interaction is not dependent upon glycosylation of the basigin ligand. ..
- Wanner K, Robertson H. The gustatory receptor family in the silkworm moth Bombyx mori is characterized by a large expansion of a single lineage of putative bitter receptors. Insect Mol Biol. 2008;17:621-9 pubmed publisher..These Grs might therefore mediate food choice and avoidance as well as oviposition site preference...
- Thekke Veetil T, Hobbs H, Domier L. Sequence diversity of readthrough proteins of Soybean dwarf virus isolates from the Midwestern United States. Arch Virol. 2009;154:861-6 pubmed publisher..Phylogenetic analysis of both amino acid and nucleotide sequences showed three distinct clusters of SbDV isolates. ..
- Li B, Sher D, Kelly L, Shi Y, Huang K, Knerr P, et al. Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Proc Natl Acad Sci U S A. 2010;107:10430-5 pubmed publisher..The extraordinarily efficient pathway for generating structural diversity enables these cyanobacteria to produce as many secondary metabolites as model antibiotic-producing bacteria, but with much smaller genomes. ..
- Park J, Salyers A. Characterization of the Bacteroides CTnDOT regulatory protein RteC. J Bacteriol. 2011;193:91-7 pubmed publisher..Mutational analysis of these half sites showed that both half sites are important for activity. Thus, we have identified the DNA binding portion of RteC and the DNA site to which it binds...
- Chepuri V, Lemieux L, Hill J, Alben J, Gennis R. Recent studies of the cytochrome o terminal oxidase complex of Escherichia coli. Biochim Biophys Acta. 1990;1018:124-7 pubmed..Site-directed mutagenesis is being utilized to define which amino acids are ligands to the heme iron and copper prosthetic groups. ..
- Szurmant H, Bunn M, Cannistraro V, Ordal G. Bacillus subtilis hydrolyzes CheY-P at the location of its action, the flagellar switch. J Biol Chem. 2003;278:48611-6 pubmed..Consequently, we imagine that the duration of enhanced CheY-P levels caused by activation of the CheA kinase upon attractant binding to receptors, is brief due both to adaptational processes and to phosphatase activity of FliY. ..
- Robbins J, Murphy M, White B, Mackie R, Ha T, Cann I. Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI. J Biol Chem. 2004;279:6315-26 pubmed..Although bacterial SSB and eukaryotic RPA have been shown to stimulate DNA synthesis by their cognate DNA polymerases, our findings provide the first in vitro biochemical evidence for the conservation of this property in an archaeon. ..
- Evans B, Ntai I, Chen Y, Robinson S, Kelleher N. Proteomics-based discovery of koranimine, a cyclic imine natural product. J Am Chem Soc. 2011;133:7316-9 pubmed publisher..We also cloned the entire gene cluster and elucidated the biosynthesis of the new compound, which is produced by an unsequenced Bacillus sp. isolated from soil collected in Koran, Louisiana. ..
- Hanlon D, Rosario M, Ordal G, Venema G, van Sinderen D. Identification of TlpC, a novel 62 kDa MCP-like protein from Bacillus subtilis. Microbiology. 1994;140 ( Pt 8):1847-54 pubmed..However, no chemotactic defect was observed for any of the chemoeffectors tested. We suggest that TlpC is similar to an evolutionary intermediate from which the major chemotactic transducers from B. subtilis arose. ..
- Chang Y, Wang A, Cronan J. Expression of Escherichia coli pyruvate oxidase (PoxB) depends on the sigma factor encoded by the rpoS(katF) gene. Mol Microbiol. 1994;11:1019-28 pubmed..However, we found that poxB null mutations had no effect on rpoS(katF) expression. Inactivation of two genes involved in acetate metabolism, ackA and pta, had no effect on either poxB or rpoS(katF) expression. ..
- Reilly T, Baron G, Nano F, Kuhlenschmidt M. Characterization and sequencing of a respiratory burst-inhibiting acid phosphatase from Francisella tularensis. J Biol Chem. 1996;271:10973-83 pubmed..Comparative sequence analyses of AcpA is discussed. To our knowledge, this is the first report describing the cloning and sequencing of a burst-inhibiting acid phosphatase...
- Payton J, Perrin R, Clayton D, George J. Protein-protein interactions of alpha-synuclein in brain homogenates and transfected cells. Brain Res Mol Brain Res. 2001;95:138-45 pubmed..We conclude that alpha-synuclein may interact specifically with heterodimeric tubulin, but not microtubules, in the neuronal cytosol. ..
- Cronan J. Interchangeable enzyme modules. Functional replacement of the essential linker of the biotinylated subunit of acetyl-CoA carboxylase with a linker from the lipoylated subunit of pyruvate dehydrogenase. J Biol Chem. 2002;277:22520-7 pubmed publisher..These data provide new evidence for the functional and structural similarities of biotinylated and lipoylated proteins and strongly support a common evolutionary origin of these enzyme subunits...
- Rajendran R, Nye A, Frasor J, Balsara R, Martini P, Katzenellenbogen B. Regulation of nuclear receptor transcriptional activity by a novel DEAD box RNA helicase (DP97). J Biol Chem. 2003;278:4628-38 pubmed..Our findings add to the growing evidence that RNA helicases can associate with nuclear receptors and function as coregulators to modulate receptor transcriptional activity...
- Jordan S, Cronan J. The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase. J Bacteriol. 2003;185:1582-9 pubmed..A nonhydrolyzable lipoyl-AMP analogue was found to competitively inhibit both ACP-dependent and ATP-dependent reactions of LplA, suggesting that the same active site catalyzes two chemically diverse reactions. ..
- Chen K, Rund L, Beever J, Schook L. Isolation and molecular characterization of the porcine transforming growth factor beta type I receptor (TGFBR1) gene. Gene. 2006;384:62-72 pubmed..The minor allele frequencies of these nucleotide variations varied from 0.13 to 0.5 with an average of 0.26. In addition, seventeen microsatellites were identified throughout the genomic sequence of the porcine TGFBR1 gene. ..
- Hicks L, Moffitt M, Beer L, Moore B, Kelleher N. Structural characterization of in vitro and in vivo intermediates on the loading module of microcystin synthetase. ACS Chem Biol. 2006;1:93-102 pubmed
- Li B, van der Donk W. Identification of essential catalytic residues of the cyclase NisC involved in the biosynthesis of nisin. J Biol Chem. 2007;282:21169-75 pubmed..These findings also argue against an essential role of Arg(280) and Tyr(285) as an active site general acid/base in the mechanism of cyclization. ..
- Kang Y, Stevenson A, Yau P, Kollmar R. Sparc protein is required for normal growth of zebrafish otoliths. J Assoc Res Otolaryngol. 2008;9:436-51 pubmed publisher..Smaller size was the predominant phenotype and independent of the severity of otic-vesicle defects. These results suggested that Sparc is directly required for normal otolith growth. ..
- Li L, Palencia A, Lukk T, Li Z, Luthey Schulten Z, Cusack S, et al. Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens. Proc Natl Acad Sci U S A. 2013;110:3817-22 pubmed publisher..These include distal control of specificity and enzyme activity in the ancient canonical core, as well as providing a separate hydrolytic active site for clearing mischarged tRNA...
- Li S, Cronan J. The gene encoding the biotin carboxylase subunit of Escherichia coli acetyl-CoA carboxylase. J Biol Chem. 1992;267:855-63 pubmed
- Yun C, Van Doren S, Crofts A, Gennis R. The use of gene fusions to examine the membrane topology of the L-subunit of the photosynthetic reaction center and of the cytochrome b subunit of the bc1 complex from Rhodobacter sphaeroides. J Biol Chem. 1991;266:10967-73 pubmed..These data demonstrate the utility of this approach for determining membrane protein topology and extend potential applications to include at least some proteins not normally expressed in E. coli. ..
- Althoff S, Stevens S, Wise J. The Srp54 GTPase is essential for protein export in the fission yeast Schizosaccharomyces pombe. Mol Cell Biol. 1994;14:7839-54 pubmed..These results form the basis of a simple model for the role of GTP hydrolysis by Srp54 during the SRP cycle. ..
- Kirsch M, Zuberi A, Henner D, Peters P, Yazdi M, Ordal G. Chemotactic methyltransferase promotes adaptation to repellents in Bacillus subtilis. J Biol Chem. 1993;268:25350-6 pubmed..We conclude from this work that CheRB functions to promote adaptation to repellent stimuli in B. subtilis, whereas CheRE functions to promote adaptation to attractant stimuli in E. coli. ..
- Robinson H, Gao Y, McCrary B, Edmondson S, Shriver J, Wang A. The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature. 1998;392:202-5 pubmed publisher..The kink results from the intercalation of specific hydrophobic side chains of Sac7d into the DNA structure, but without causing any significant distortion of the protein structure relative to the uncomplexed protein in solution...
- Moon J, Domier L, McCoppin N, D Arcy C, Jin H. Nucleotide sequence analysis shows that Rhopalosiphum padi virus is a member of a novel group of insect-infecting RNA viruses. Virology. 1998;243:54-65 pubmed publisher..These data suggest that RhPV, Drosophila C virus, Plautia stali intestine virus, and probably cricket paralysis virus are members of a unique group of small RNA viruses that infect primarily insects...
- Cymes G, Ni Y, Grosman C. Probing ion-channel pores one proton at a time. Nature. 2005;438:975-80 pubmed..A comparison with closed-channel data leads us to propose that the rotation of M2, which is frequently invoked as a hallmark of the gating mechanism of Cys-loop receptors, is minimal, if any. ..
- Han Q, Kim S, Ding H, Li J. Evolution of two alanine glyoxylate aminotransferases in mosquito. Biochem J. 2006;397:473-81 pubmed publisher..Our results suggest that the physiological requirements of mosquitoes and the interaction between the mosquito and its host appear to be the driving force in mosquito AGT evolution...
- Li Y, Berthold D, Frericks H, Gennis R, Rienstra C. Partial (13)C and (15)N chemical-shift assignments of the disulfide-bond-forming enzyme DsbB by 3D magic-angle spinning NMR spectroscopy. Chembiochem. 2007;8:434-42 pubmed..Structural and dynamic information derived from SSNMR studies can give insight into DsbB in a state that so far has not been successfully crystallized. ..
- Han Y, Sun F, Rosales Mendoza S, Korban S. Three orthologs in rice, Arabidopsis, and Populus encoding starch branching enzymes (SBEs) are different from other SBE gene families in plants. Gene. 2007;401:123-30 pubmed..Based on phylogenetic analysis and genomic structure comparison, it is proposed that the three SBE genes represent a new family of SBEs. ..
- Hemp J, Gennis R. Diversity of the heme-copper superfamily in archaea: insights from genomics and structural modeling. Results Probl Cell Differ. 2008;45:1-31 pubmed publisher..We conclude with a brief analysis of the phylogenetic distribution and evolution of Archaeal heme-copper oxygen reductases. ..
- Glekas G, Foster R, Cates J, Estrella J, Wawrzyniak M, Rao C, et al. A PAS domain binds asparagine in the chemotaxis receptor McpB in Bacillus subtilis. J Biol Chem. 2010;285:1870-8 pubmed publisher..Taken together, these results reveal not only a novel chemoreceptor sensing domain architecture but also, possibly, a different mechanism for chemoreceptor activation...
- Bai L, Romanova E, Sweedler J. Distinguishing endogenous D-amino acid-containing neuropeptides in individual neurons using tandem mass spectrometry. Anal Chem. 2011;83:2794-800 pubmed publisher..We demonstrate that this approach is well suited for confirming DAACPs directly from cells and tissue, advancing our understanding of the l to d modification and the role it plays in cell-to-cell signaling. ..
- Fuhrer D, Ordal G. Bacillus subtilis CheN, a homolog of CheA, the central regulator of chemotaxis in Escherichia coli. J Bacteriol. 1991;173:7443-8 pubmed..subtilis does excitation lead to methyl transfer and methanol formation. Thus, the overall mechanism of chemotaxis is different in the two organisms. ..
- Lu H, Schulten K. The key event in force-induced unfolding of Titin's immunoglobulin domains. Biophys J. 2000;79:51-65 pubmed..Only when those bonds are broken can the generic unfolding take place, which involves hydrophobic interactions of the protein core and exerts weaker resistance against stretching than the key event. ..
- Hinthong O, Jin X, Shisler J. Characterization of wild-type and mutant vaccinia virus M2L proteins' abilities to localize to the endoplasmic reticulum and to inhibit NF-kappaB activation during infection. Virology. 2008;373:248-62 pubmed publisher..However, this C-terminal deleted mutant protein is compromised in its ability to inhibit NF-kappaB activation. Determination of the ER location of the M2L proteins provides important insights for its function in future investigations...
- Luan B, Carr R, Caffrey M, Aksimentiev A. The effect of calcium on the conformation of cobalamin transporter BtuB. Proteins. 2010;78:1153-62 pubmed publisher..Finally, we characterize conformation dynamics of the TonB box in different X-ray structures and find an interesting correlation between the stability of the TonB box structure and calcium binding. ..
- Zuberi A, Ying C, Bischoff D, Ordal G. Gene-protein relationships in the flagellar hook-basal body complex of Bacillus subtilis: sequences of the flgB, flgC, flgG, fliE and fliF genes. Gene. 1991;101:23-31 pubmed..However, we observed some differences in size and amino acid composition between some of the corresponding homologues that suggest the basal body proteins may be organized slightly differently within B. subtilis. ..
- Hurley W, Schuler L. Molecular cloning and nucleotide sequence of a bovine alpha-lactalbumin cDNA. Gene. 1987;61:119-22 pubmed..When compared with previously reported sequences, the bovine alpha LA mRNA sequence has 74% similarity with rat alpha LA mRNA, 79% similarity with human mRNA and 74% similarity with guinea pig mRNA. ..
- Chu LaGraff Q, Wright D, McNeil L, Doe C. The prospero gene encodes a divergent homeodomain protein that controls neuronal identity in Drosophila. Dev Suppl. 1991;Suppl 2:79-85 pubmed..These data are consistent with a model in which pros controls neuroblast cell lineages by regulating gene expression. ..
- Yun C, Beci R, Crofts A, Kaplan S, Gennis R. Cloning and DNA sequencing of the fbc operon encoding the cytochrome bc1 complex from Rhodobacter sphaeroides. Characterization of fbc deletion mutants and complementation by a site-specific mutational variant. Eur J Biochem. 1990;194:399-411 pubmed
- Floyd P, Li L, Rubakhin S, Sweedler J, Horn C, Kupfermann I, et al. Insulin prohormone processing, distribution, and relation to metabolism in Aplysia californica. J Neurosci. 1999;19:7732-41 pubmed..The expression of AI mRNA decreases when the animal is deprived of food, and injections of AI reduce hemolymph glucose levels, suggesting that the function of insulin-regulating metabolism has been conserved...
- Luo Z, Farrand S. The Agrobacterium tumefaciens rnd homolog is required for TraR-mediated quorum-dependent activation of Ti plasmid tra gene expression. J Bacteriol. 2001;183:3919-30 pubmed..Our data suggest that the defect in tra gene induction in the mutants results from lowered levels of TraR. In turn, production of sufficient amounts of TraR apparently is sensitive to a cellular function requiring RNase D. ..
- H kansson K, Miller C. Structure of peptidase T from Salmonella typhimurium. Eur J Biochem. 2002;269:443-50 pubmed..A putative binding site for the C-terminal end of the tripeptide substrate was found at a peptidase T specific fingerprint sequence motif...
- Hellwig P, Yano T, Ohnishi T, Gennis R. Identification of the residues involved in stabilization of the semiquinone radical in the high-affinity ubiquinone binding site in cytochrome bo(3) from Escherichia coli by site-directed mutagenesis and EPR spectroscopy. Biochemistry. 2002;41:10675-9 pubmed..Details of the possible binding motif and mechanistic implications are discussed. ..
- Yew W, Wise E, Rayment I, Gerlt J. Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2004;43:6427-37 pubmed..This study further highlights the opportunistic nature of divergent evolution in conscripting the active site of a progenitor to catalyze a mechanistically distinct reaction. ..
- Thomas J, Cronan J. The enigmatic acyl carrier protein phosphodiesterase of Escherichia coli: genetic and enzymological characterization. J Biol Chem. 2005;280:34675-83 pubmed..The purified enzyme has been shown to cleave acyl-ACP species with acyl chains of 6-16 carbon atoms and is active on some, but not all, non-native ACP species tested. Possible physiological roles for AcpH are discussed. ..
- Flanigan A, Gardner J. Structural prediction and mutational analysis of the Gifsy-I Xis protein. BMC Microbiol. 2008;8:199 pubmed publisher..2 kDa and a pI of 10.2. Electrophoretic Mobility Shift Assays (EMSA) suggested at least one region of the protein is responsible for protein-DNA interactions with a tripartite DNA binding site composed of three direct imperfect repeats...
- Hung J, Fogle E, Christman H, Johannes T, Zhao H, Metcalf W, et al. Investigation of the role of Arg301 identified in the X-ray structure of phosphite dehydrogenase. Biochemistry. 2012;51:4254-62 pubmed publisher..The importance of these residues was also investigated by site-directed mutagenesis. All of the mutants had k(cat) values similar to that of the wild-type enzyme, indicating these residues are not important for catalysis. ..
- Schuler M, Denisov I, Sligar S. Nanodiscs as a new tool to examine lipid-protein interactions. Methods Mol Biol. 2013;974:415-33 pubmed publisher..Special attention is paid to the opportunities afforded by nanodisc system for the detailed studies of the role of different lipid properties and protein-lipid interactions in the functional behavior of membrane proteins. ..
- Holman P, Lacy M, Roth M, Kranz D. Mechanisms that generate junctional diversity in alpha and delta chains that use the Tcrd-V3 gene product. Immunogenetics. 1992;35:33-40 pubmed..Finally, a comparison of the variable domains of these alpha and delta chains shows that a notable difference is the variability in length of the CDR 3 region which can be significantly longer in delta-chains than in alpha-chains. ..
- Grabau C, Chang Y, Cronan J. Lipid binding by Escherichia coli pyruvate oxidase is disrupted by small alterations of the carboxyl-terminal region. J Biol Chem. 1989;264:12510-9 pubmed..This mutant enzyme appeared to dissociate from detergent vesicles more readily than does the normal enzyme. A model for the membrane interaction of the carboxyl terminus based on the properties of these mutant proteins is presented. ..
- Xu A, McKenna K, Lewin H. Sequencing and genetic analysis of a bovine DQA cDNA clone. Immunogenetics. 1993;37:231-4 pubmed
- Kyrpides N, Woese C. Universally conserved translation initiation factors. Proc Natl Acad Sci U S A. 1998;95:224-8 pubmed..However, significant development and refinement subsequently occurred independently on both the bacterial lineage and on the archaeal/eukaryotic line...
- Xu E, Kim S, Replogle K, Rine J, Rivier D. Identification of SAS4 and SAS5, two genes that regulate silencing in Saccharomyces cerevisiae. Genetics. 1999;153:13-23 pubmed..Similarly, SAS5 is a member of a gene family that included two human genes that are the sites of recurring translocations involved in acute myeloid leukemia. ..
- O Donoghue P, Amaro R, Luthey Schulten Z. On the structure of hisH: protein structure prediction in the context of structural and functional genomics. J Struct Biol. 2001;134:257-68 pubmed..This work allows us to develop a preliminary model for the structure of the entire IGPS holoenzyme. ..
- Schoenherr C, Levorse J, Tilghman S. CTCF maintains differential methylation at the Igf2/H19 locus. Nat Genet. 2003;33:66-9 pubmed..Conversely, maternal H19 expression is reduced, suggesting a positive role for CTCF in the transcription of that gene. This study constitutes the first in vivo demonstration of the multiple functions of CTCF in an ICR. ..
- O Donoghue P, Luthey Schulten Z. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev. 2003;67:550-73 pubmed..We also discuss the effect of functional specificity on protein shape over the complex evolutionary course of the tRNA synthetases. ..
- Zhang J, Hellwig P, Osborne J, Gennis R. Arginine 391 in subunit I of the cytochrome bd quinol oxidase from Escherichia coli stabilizes the reduced form of the hemes and is essential for quinol oxidase activity. J Biol Chem. 2004;279:53980-7 pubmed..The fact that the midpoint potentials of heme d and heme b(595) are also significantly lowered in the R391A mutant is consistent with these hemes being physically close together on the periplasmic side of the membrane. ..
- Amaro R, Myers R, Davisson V, Luthey Schulten Z. Structural elements in IGP synthase exclude water to optimize ammonia transfer. Biophys J. 2005;89:475-87 pubmed