| two conformational states in the crystal structure of the homo sapiens cytoplasmic ribosomal decoding a site. | the decoding a site of the small ribosomal subunit is an rna molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. we have solved the crystal structure of an rna fragment containing two homo sapiens cytoplasmic a sites. each of the two a sites presents a different conformational state. in one state, adenines a1492 and a1493 are fully bulged-out with c1409 forming a wobble-like pair to a1491. in the second state, adenines a1492 and a1493 form non-watson- ... | 2006 | 16452297 |
| structure of the tetrahymena thermophila telomerase rna helix ii template boundary element. | telomere addition by telomerase requires an internal templating sequence located in the rna subunit of telomerase. the correct boundary definition of this template sequence is essential for the proper addition of the nucleotide repeats. incorporation of incorrect telomeric repeats onto the ends of chromosomes has been shown to induce chromosomal instability in ciliate, yeast and human cells. a 5' template boundary defining element (tbe) has been identified in human, yeast and ciliate telomerase ... | 2006 | 16452301 |
| molecular dynamics simulations of sarcin-ricin rrna motif. | explicit solvent molecular dynamics (md) simulations were carried out for sarcin-ricin domain (srd) motifs from 23s (escherichia coli) and 28s (rat) rrnas. the srd motif consists of gaga tetraloop, g-bulged cross-strand a-stack, flexible region and duplex part. detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other srd features is presented. the srd is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean squa ... | 2006 | 16456030 |
| type a and b rnase p rnas are interchangeable in vivo despite substantial biophysical differences. | we show that structural type a and b bacterial ribonuclease p (rnase p) rnas can fully replace each other in vivo despite the many reported differences in their biogenesis, biochemical/biophysical properties and enzyme function in vitro. our findings suggest that many of the reported idiosyncrasies of type a and b enzymes either do not reflect the in vivo situation or are not crucial for rnase p function in vivo, at least under standard growth conditions. the discrimination of mature trna by rna ... | 2006 | 16470227 |
| isolation of a site-specifically modified rna from an unmodified transcript. | natural rnas contain many base modifications that have specific biological functions. the ability to functionally dissect individual modifications is facilitated by the identification and cloning of enzymes responsible for these modifications, but is hindered by the difficulty of isolating site-specifically modified rnas away from unmodified transcripts. using the m1g37 and m1a58 methyl modifications of trna as two examples, we demonstrate that non-pairing base modifications protect rnas against ... | 2006 | 16473844 |
| trna properties help shape codon pair preferences in open reading frames. | translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of trnas in the ribosomal a- and p-sites. here, we sought evidence of a- and p-site trna interaction by examining bias in codon pair choice within open reading frames from a range of genomes. three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. first, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combinati ... | 2006 | 16473853 |
| crystal structures of two putative phosphoheptose isomerases. | | 2006 | 16477602 |
| compositional discordance between prokaryotic plasmids and host chromosomes. | most plasmids depend on the host replication machinery and possess partitioning genes. these properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. however, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, ... | 2006 | 16480495 |
| effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein s12. | ribosomal protein s12 contains a highly conserved aspartic acid residue that is posttranslationally beta-methylthiolated. using mass spectrometry, we have determined the modification states of several s12 mutants of thermus thermophilus and conclude that beta-methylthiolation is not a determinant of the streptomycin phenotype. | 2006 | 16484214 |
| the molecular architecture of the metalloprotease ftsh. | the atp-dependent integral membrane protease ftsh is universally conserved in bacteria. orthologs exist in chloroplasts and mitochondria, where in humans the loss of a close ftsh-homolog causes a form of spastic paraplegia. ftsh plays a crucial role in quality control by degrading unneeded or damaged membrane proteins, but it also targets soluble signaling factors like sigma(32) and lambda-cii. we report here the crystal structure of a soluble ftsh construct that is functional in caseinolytic an ... | 2006 | 16484367 |
| dependency map of proteins in the small ribosomal subunit. | the assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. in this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30s small ribosomal subunit of thermus thermophilus. we determined the causal influence of the presence and absence of proteins in the 30s complex on the binding free energies of other proteins. the predicted dependencies are i ... | 2006 | 16485038 |
| recj exonuclease: substrates, products and interaction with ssb. | the recj exonuclease from escherichia coli degrades single-stranded dna (ssdna) in the 5'-3' direction and participates in homologous recombination and mismatch repair. the experiments described here address recj's substrate requirements and reaction products. recj complexes on a variety of 5' single-strand tailed substrates were analyzed by electrophoretic mobility shift in the absence of mg2+ ion required for substrate degradation. recj required single-stranded tails of 7 nt or greater for rob ... | 2006 | 16488881 |
| molecular localization of a ribosome-dependent atpase on escherichia coli ribosomes. | we have previously isolated and described an escherichia coli ribosome-bound atpase, rbba, that is required for protein synthesis in the presence of atp, gtp and the elongation factors, ef-tu and ef-g. the gene encoding rbba, yhih, has been cloned and the deduced protein sequence harbors two atp-motifs and one rna-binding motif and is homologous to the fungal ef-3. here, we describe the isolation and assay of a truncated form of the rbba protein that is stable to overproduction and purification. ... | 2006 | 16495476 |
| identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of sars-cov orf 3a variants. | programmed frameshifting is one of the translational recoding mechanisms that read the genetic code in alternative ways. this process is generally programmed by signals at defined locations in a specific mrna. in this study, we report the identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of severe acute respiratory syndrome coronavirus (sars-cov) orf 3a variants. sars-cov orf 3a encodes a minor structural prote ... | 2006 | 16500894 |
| crystallization of leucyl-trna synthetase complexed with trnaleu from the archaeon pyrococcus horikoshii. | all five trnaleu isoacceptors from the archaeon pyrococcus horikoshii have been transcribed in vitro and purified. the leucyl-trna synthetase (leurs) from p. horikoshii was overexpressed in escherichia coli and purified, and cocrystallizations with each of the trnaleu isoacceptors were attempted. cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the trnaleu isoacceptor with the anticodon caa was used. electrophoretic analyses revealed that the crystals contain b ... | 2005 | 16508082 |
| crystallization of leucyl-trna synthetase complexed with trnaleu from the archaeon pyrococcus horikoshii. | all five trnaleu isoacceptors from the archaeon pyrococcus horikoshii have been transcribed in vitro and purified. the leucyl-trna synthetase (leurs) from p. horikoshii was overexpressed in escherichia coli and purified, and cocrystallizations with each of the trnaleu isoacceptors were attempted. cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the trnaleu isoacceptor with the anticodon caa was used. electrophoretic analyses revealed that the crystals contain b ... | 2005 | 16508082 |
| purification, crystallization and preliminary crystallographic analysis of the vacuole-type atpase subunit e from pyrococcus horikoshii ot3. | the vacuole-type atpases in eukaryotic cells translocate protons across various biological membranes including the vacuolar membrane by consuming atp molecules. the e subunit of the multisubunit complex v-atpase from pyrococcus horikoshii ot3, which has a molecular weight of 22.88 kda, has been cloned, overexpressed in escherichia coli, purified and crystallized by the microbatch method using peg 4000 as a precipitant at 296 k. a data set to 1.85 a resolution with 98.8% completeness and an rmerg ... | 2005 | 16508090 |
| purification, crystallization and preliminary crystallographic analysis of the vacuole-type atpase subunit e from pyrococcus horikoshii ot3. | the vacuole-type atpases in eukaryotic cells translocate protons across various biological membranes including the vacuolar membrane by consuming atp molecules. the e subunit of the multisubunit complex v-atpase from pyrococcus horikoshii ot3, which has a molecular weight of 22.88 kda, has been cloned, overexpressed in escherichia coli, purified and crystallized by the microbatch method using peg 4000 as a precipitant at 296 k. a data set to 1.85 a resolution with 98.8% completeness and an rmerg ... | 2005 | 16508090 |
| a structural model for the large subunit of the mammalian mitochondrial ribosome. | protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. evolutionary changes in protein and rna sequences can affect the 3d organization of structural features in ribosomes in different species. the most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. the rna component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. ... | 2006 | 16510155 |
| specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48s translation initiation complex. | eukaryotic initiation factor (eif) 1 maintains the fidelity of initiation codon selection and enables mammalian 43s preinitiation complexes to discriminate against aug codons with a context that deviates from the optimum sequence gcc(a/g)ccaugg, in which the purines at (-)3 and (+)4 positions are most important. we hypothesize that eif1 acts by antagonizing conformational changes that occur in ribosomal complexes upon codon-anticodon base-pairing during 48s initiation complex formation, and that ... | 2006 | 16510876 |
| overproduction and preliminary crystallographic study of a human kynurenine aminotransferase ii homologue from pyrococcus horikoshii ot3. | the pyrococcus horikoshii ot3 genome contains a gene encoding a human kynurenine aminotransferase ii (kat ii) homologue, which consists of 428 amino-acid residues and shows an amino-acid sequence identity of 30% to human kat ii. this gene was overexpressed in escherichia coli and the recombinant protein (ph-kat ii) was purified. gel-filtration chromatography showed that ph-kat ii exists as a homodimer. ph-kat ii exhibited enzymatic activity that catalyzes the transamination of l-kynurenine to pr ... | 2005 | 16511030 |
| structure of the pseudouridine synthase rsua from haemophilus influenzae. | the structure of the pseudouridine synthase rsua from haemophilus influenza, which catalyzes the conversion of uridine to pseudouridine at a single position within 16s ribosomal rna, has been determined at 1.59 a resolution and compared with that of escherichia coli rsua. the h. influenza enzyme contains an n-terminal s4-like alpha3beta4 domain followed by a catalytic domain, as observed in the structure of e. coli rsua. whereas the individual domains of e. coli and h. influenza rsua are structu ... | 2005 | 16511038 |
| crystallization and preliminary x-ray crystallographic analysis of a conserved domain in plants and prokaryotes from pyrococcus horikoshii ot3. | a plant- and prokaryote-conserved domain (ppc) has previously been found in at-hook motif nuclear localized protein 1 (ahl1) localized in the nuclear matrix of arabidopsis thaliana (atahl1). atahl1 has a dna-binding function. mutation analyses of atahl1 has previously revealed that the hydrophobic region of the ppc domain is essential for its nuclear localization. in this study, the ppc of the hyperthermophilic archaebacterium pyrococcus horikoshii (phppc) was crystallized using the hanging-drop ... | 2005 | 16511056 |
| structure of purine nucleoside phosphorylase (deod) from bacillus anthracis. | protein structures from the causative agent of anthrax (bacillus anthracis) are being determined as part of a structural genomics programme. amongst initial candidates for crystallographic analysis are enzymes involved in nucleotide biosynthesis, since these are recognized as potential targets in antibacterial therapy. purine nucleoside phosphorylase is a key enzyme in the purine-salvage pathway. the crystal structure of purine nucleoside phosphorylase (deod) from b. anthracis has been solved by ... | 2005 | 16511068 |
| crystallization and preliminary x-ray crystallographic analysis of yeast nad+-specific isocitrate dehydrogenase. | nad+-specific isocitrate dehydrogenase (idh; ec 1.1.1.41) is a complex allosterically regulated enzyme in the tricarboxylic acid cycle. yeast idh is believed to be an octamer containing four catalytic idh2 and four regulatory idh1 subunits. crystals of yeast idh have been obtained and optimized using sodium citrate, a competitive inhibitor of the enzyme, as the precipitating agent. the crystals belong to space group r3, with unit-cell parameters a = 302.0, c = 112.1 a. diffraction data were coll ... | 2005 | 16511075 |
| preparation, crystallization and preliminary x-ray analysis of yjcg protein from bacillus subtilis. | bacillus subtilis yjcg is a functionally uncharacterized protein with 171 residues that has no structural homologue in the protein data bank. however, it shows sequence homology to bacterial and archaeal 2'-5' rna ligases. in order to identify its exact function via structural studies, the yjcg gene was amplified from b. subtilis genomic dna and cloned into the expression vector pet21-dest. the protein was expressed in a soluble form in escherichia coli and was purified to homogeneity. crystals ... | 2005 | 16511078 |
| crystallization and preliminary crystallographic analysis of a flavoprotein nadh oxidase from lactobacillus brevis. | nadh oxidase (nox) from lactobacillus brevis is a homotetrameric flavoenzyme composed of 450 amino acids per subunit. the molecular weight of each monomer is 48.8 kda. the enzyme catalyzes the oxidation of two equivalents of nadh and reduces one equivalent of oxygen to yield two equivalents of water, without releasing hydrogen peroxide after the reduction of the first equivalent of nadh. crystals of this protein were grown in the presence of 34% polyethylene glycol monomethyl ether 2000, 0.1 m s ... | 2005 | 16511087 |
| overexpression, purification and crystallographic analysis of a unique adenosine kinase from mycobacterium tuberculosis. | adenosine kinase from mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. the enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against m. tuberculosis. the mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine ... | 2005 | 16511094 |
| expression, purification, crystallization and preliminary x-ray analysis of a nucleoside kinase from the hyperthermophile methanocaldococcus jannaschii. | methanocaldococcus jannaschii nucleoside kinase (mjnk) is an atp-dependent non-allosteric phosphotransferase that shows high catalytic activity for guanosine, inosine and cytidine. mjnk is a member of the phosphofructokinase b family, but participates in the biosynthesis of nucleoside monophosphates rather than in glycolysis. mjnk was crystallized as the apoenzyme as well as in complex with an atp analogue and mg2+. the latter crystal form was also soaked with fructose-6-phosphate. synchrotron-r ... | 2005 | 16511104 |
| crystallization and avoiding the problem of hemihedral twinning in crystals of delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus. | delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus (ttp5cdh) has been crystallized in a citrate-bound form (ttp5cdh-cit). the crystals diffracted to well beyond 2 a resolution, but exhibited perfect or near-perfect hemihedral twinning. variation of crystallization conditions resulted in the growth of larger untwinned crystals or crystals with significantly reduced twin content, all with similar unit-cell parameters. the soaking of ttp5cdh-cit crystals in citrate-free solution ... | 2005 | 16511109 |
| a double mutation of escherichia coli2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate. | the essential enzyme 2c-methyl-d-erythritol-2,4-cyclodiphosphate (mecp) synthase, found in most eubacteria and the apicomplexan parasites, participates in isoprenoid-precursor biosynthesis and is a validated target for the development of broad-spectrum antimicrobial drugs. the structure and mechanism of the enzyme have been elucidated and the recent exciting finding that the enzyme actually binds diphosphate-containing isoprenoids at the interface formed by the three subunits that constitute the ... | 2005 | 16511114 |
| structure of a class ii trmh trna-modifying enzyme from aquifex aeolicus. | biological rnas contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. one of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of s-adenosylmethionine (sam) dependent methyltransferases. in bacteria, many of these modifications in trna and rrna are carried out by the alpha/beta-knot superfamily of enzymes, whose sam-binding pocket is created ... | 2005 | 16511140 |
| cloning, purification and crystallization of thermus thermophilus proline dehydrogenase. | nature recycles l-proline by converting it to l-glutamate. this four-electron oxidation process is catalyzed by the two enzymes: proline dehydrogenase (prodh) and delta1-pyrroline-5-carboxylate dehydrogenase. this note reports the cloning, purification and crystallization of thermus thermophilus prodh, which is the prototype of a newly discovered superfamily of bacterial monofunctional prodhs. the results presented here include production of a monodisperse protein solution through use of the det ... | 2005 | 16511143 |
| structures of a putative rna 5-methyluridine methyltransferase, thermus thermophilus ttha1280, and its complex with s-adenosyl-l-homocysteine. | the thermus thermophilus hypothetical protein ttha1280 belongs to a family of predicted s-adenosyl-l-methionine (adomet) dependent rna methyltransferases (mtases) present in many bacterial and archaeal species. inspection of amino-acid sequence motifs common to class i rossmann-fold-like mtases suggested a specific role as an rna 5-methyluridine mtase. selenomethionine (semet) labelled and native versions of the protein were expressed, purified and crystallized. two crystal forms of the semet-la ... | 2005 | 16511182 |
| crystallization and preliminary x-ray crystallographic study of the wild type and two mutants of the cp1 hydrolytic domain from aquifex aeolicus leucyl-trna synthetase. | the editing or hydrolytic cp1 domain of leucyl-trna synthetase (leurs) hydrolyses several misactivated amino acids. the cp1 domain of aquifex aeolicus leurs was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. crystals belong to space group p2(1)2(1)2(1), with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 a. crystals diffract to beyond 1.8 a resolution and contain two monomers in the asymmetric unit. two cp1 mutants in w ... | 2005 | 16511190 |
| crystallization and preliminary x-ray analysis of cryptochrome 3 from arabidopsis thaliana. | cryptochromes are flavoproteins which serve as blue-light receptors in plants, animals, fungi and prokaryotes and belong to the same protein family as the catalytically active dna photolyases. cryptochrome 3 from the plant arabidopsis thaliana (cry3; 525 amino acids, 60.7 kda) is a representative of the novel crydash subfamily of uv-a/blue-light receptors and has been expressed as a mature fad-containing protein in escherichia coli without the signal sequence that directs the protein into plant ... | 2005 | 16511200 |
| structure of a conserved hypothetical protein, ttha0849 from thermus thermophilus hb8, at 2.4 a resolution: a putative member of the star-related lipid-transfer (start) domain superfamily. | the crystal structure of a conserved hypothetical protein, ttha0849 from thermus thermophilus hb8, has been determined at 2.4 a resolution as a part of a structural and functional genomics project on t. thermophilus hb8. the main-chain folding shows a compact alpha+beta motif, forming a hydrophobic cavity in the molecule. a structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (start) domain, even though ttha0849 show ... | 2005 | 16511226 |
| purification, crystallization and preliminary x-ray crystallographic study of the l-fuculose-1-phosphate aldolase (fuca) from thermus thermophilus hb8. | fuculose phosphate aldolase catalyzes the reversible cleavage of l-fuculose-1-phosphate to dihydroxyacetone phosphate and l-lactaldehyde. the protein from thermus thermophilus hb8 is a biological tetramer with a subunit molecular weight of 21 591 da. purified fuca has been crystallized using sitting-drop vapour-diffusion and microbatch techniques at 293 k. the crystals belong to space group p4, with unit-cell parameters a = b = 100.94, c = 45.87 a. the presence of a dimer of the enzyme in the as ... | 2005 | 16511238 |
| cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors greb from escherichia coli and gfh1 from thermus thermophilus. | the escherichia coli gene encoding the transcription cleavage factor greb and the thermus thermophilus gene encoding the anti-grea transcription factor gfh1 were cloned and expressed and the purified proteins were crystallized by the sitting-drop vapor-diffusion technique. the greb and gfh1 crystals, which were improved by macroseeding, belong to space group p4(1)2(1)2 (or p4(3)2(1)2), with unit-cell parameters a = b = 148, c = 115.2 a and a = b = 59.3, c = 218.9 a, respectively. complete diffra ... | 2006 | 16511259 |
| expression, purification, crystallization and preliminary x-ray analysis of the human ruvb-like protein ruvbl1. | ruvbl1, an evolutionary highly conserved protein related to the aaa+ family of atpases, has been crystallized using the hanging-drop vapour-diffusion method at 293 k. the crystals are hexagonal and belong to space group p6, with unit-cell parameters a = b = 207.1, c = 60.7 a and three molecules in the asymmetric unit. | 2006 | 16511264 |
| expression, purification, crystallization and preliminary x-ray analysis of the human ruvb-like protein ruvbl1. | ruvbl1, an evolutionary highly conserved protein related to the aaa+ family of atpases, has been crystallized using the hanging-drop vapour-diffusion method at 293 k. the crystals are hexagonal and belong to space group p6, with unit-cell parameters a = b = 207.1, c = 60.7 a and three molecules in the asymmetric unit. | 2006 | 16511264 |
| purification, crystallization and preliminary characterization of a putative lmbe-like deacetylase from bacillus cereus. | the bacillus cereus bc1534 protein, a putative deacetylase from the lmbe family, has been purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. crystals of the 26 kda protein grown from mpd and acetate buffer belong to space group r32, with unit-cell parameters a = b = 76.7, c = 410.5 a (in the hexagonal setting). a complete native data set was collected to a resolution of 2.5 a from a single cryoprotected crystal using synchrotron radiation. as bc1534 shows si ... | 2006 | 16511317 |
| crystallization and preliminary x-ray crystallographic analysis of biodegradative threonine deaminase (tdcb) from salmonella typhimurium. | biodegradative threonine deaminase (tdcb) catalyzes the deamination of l-threonine to alpha-ketobutyrate, the first reaction in the anaerobic breakdown of l-threonine to propionate. unlike the biosynthetic threonine deaminase, tdcb is insensitive to l-isoleucine and is activated by amp. here, the cloning of tdcb (molecular weight 36 kda) from salmonella typhimurium with an n-terminal hexahistidine affinity tag and its overexpression in escherichia coli is reported. tdcb was purified to homogenei ... | 2006 | 16511321 |
| use of single-point genome signature tags as a universal tagging method for microbial genome surveys. | we developed single-point genome signature tags (sp-gsts), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. the technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. sp-gsts are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the a ... | 2006 | 16517658 |
| comparison of conventional pcr with real-time pcr and branched dna-based assays for hepatitis c virus rna quantification and clinical significance for genotypes 1 to 5. | the key parameter for diagnosis and management of hepatitis c virus (hcv) infection is hcv rna. standardization of hcv rna assays to iu is mainly based on genotype 1 panels. little is known about the variability of commercially available hcv rna assays for quantification of different genotypes. two real-time reverse transcription (rt)-pcr assays (cobas taqman hcv test for use with the high-pure system [hps/ctm] and cobas ampliprep/cobas taqman hcv test [cap/ctm]), one standard rt-pcr assay (coba ... | 2006 | 16517847 |
| structural and evolutionary classification of g/u wobble basepairs in the ribosome. | we present a comprehensive structural, evolutionary and molecular dynamics (md) study of the g/u wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent escherichia coli structure. these basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. g/u basepairs participating in tertiary interactions are more conserved than those lacking any interactions. specific interactions occurring in ... | 2006 | 16522645 |
| computer-aided nmr assay for detecting natively folded structural domains. | structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. for large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. however, protein dissection essentially remains an empirical and often a tedious process. here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. this approach combines the com ... | 2006 | 16522794 |
| kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from thermus thermophilus. | hacn (homoaconitase) is a member of a family of [4fe-4s] cluster-dependent enzymes that catalyse hydration/dehydration reactions. the best characterized example of this family is the ubiquitous acn (aconitase), which catalyses the dehydration of citrate to cis-aconitate, and the subsequent hydration of cis-aconitate to isocitrate. hacn is an enzyme from the alpha-aminoadipate pathway of lysine biosynthesis, and has been identified in higher fungi and several archaea and one thermophilic species ... | 2006 | 16524361 |
| adaptor protein controlled oligomerization activates the aaa+ protein clpc. | the aaa+ protein clpc is not only involved in the removal of misfolded and aggregated proteins but also controls, through regulated proteolysis, key steps of several developmental processes in the gram-positive bacterium bacillus subtilis. in contrast to other aaa+ proteins, clpc is unable to mediate these processes without an adaptor protein like meca. here, we demonstrate that the general activation of clpc is based upon the ability of meca to participate in the assembly of an active and subst ... | 2006 | 16525504 |
| discrimination of cognate and noncognate substrates at the active site of class i lysyl-trna synthetase. | the aminoacyl-trna synthetases are divided into two unrelated structural classes, with lysyl-trna synthetase (lysrs) being the only enzyme represented in both classes. on the basis of the structure of l-lysine complexed with pyrococcus horikoshii class i lysrs (lysrs1) and homology to glutamyl-trna synthetase (glurs), residues implicated in amino acid recognition and noncognate substrate discrimination were systematically replaced in borrelia burgdorferi lysrs1. the catalytic efficiency of stead ... | 2006 | 16533047 |
| pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota. | marine crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. we report here analysis of fosmid sequences derived from the uncultivated mar ... | 2006 | 16533068 |
| nabp1, a novel rorgamma-regulated gene encoding a single-stranded nucleic-acid-binding protein. | rorgamma2 (retinoid-related orphan receptor gamma2) plays a critical role in the regulation of thymopoiesis. microarray analysis was performed in order to uncover differences in gene expression between thymocytes of wild-type and rorgamma-/- mice. this analysis identified a novel gene encoding a 22 kda protein, referred to as nabp1 (nucleic-acid-binding protein 1). this subsequently led to the identification of an additional protein, closely related to nabp1, designated nabp2. both proteins cont ... | 2006 | 16533169 |
| explanation of the stability of thermophilic proteins based on unique micromorphology. | two mesophilic/thermophilic variants of the g-domain of the elongation factor tu were studied via molecular dynamics simulations. by analyzing the simulation data via the voronoi space tessellation, we have found that the two proteins have the same macromolecular packing, while the water-exposed surface area is larger for the thermophile. a larger coordination with water is probably due to a peculiar corrugation of the exposed surface of this species. from an enthalpic point of view, the thermop ... | 2006 | 16533850 |
| compatible solutes in the thermophilic bacteria rhodothermus marinus and "thermus thermophilus". | (sup13)c nuclear magnetic resonance spectroscopy and (sup1)h nuclear magnetic resonance spectroscopy were used to identify and quantify the organic solutes of several strains of halophilic or halotolerant thermophilic bacteria. two strains of rhodothermus marinus and four strains of "thermus thermophilus" grown in complex medium containing nacl were examined. 2-o-mannosylglycerate was a major compatible solute in all strains: the thermus strains accumulated the (beta)-anomer only, whereas both a ... | 1995 | 16535053 |
| residues in substrate proteins that interact with groel in the capture process are buried in the native state. | we have used a bioinformatic approach to predict the natural substrate proteins for the escherichia coli chaperonin groel based on two simple criteria. natural substrate proteins should contain binding motifs similar in sequence to the mobile loop peptide of groes that displaces the binding motif during the chaperonin cycle. secondly, each substrate protein should contain multiple copies of the binding motif so that the chaperonin can perform "work" on the substrate protein. to validate these cr ... | 2006 | 16537402 |
| score-based prediction of genomic islands in prokaryotic genomes using hidden markov models. | horizontal gene transfer (hgt) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. it is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes hgt from gene genesis, duplications or mutations. for a precise characterization, algorithms are needed that identify transfer events with high reliability. frequently, the transferred pieces of dna have a considerable length, comprise several gene ... | 2006 | 16542435 |
| liberation of zinc-containing l31 (rpme) from ribosomes by its paralogous gene product, ytia, in bacillus subtilis. | we have found that alternative localization of two types of l31 ribosomal protein, rpme and ytia, is controlled by the intracellular concentration of zinc in bacillus subtilis. the detailed mechanisms for the alternation of l31 proteins under zinc-deficient conditions were previously unknown. to obtain further information about this regulatory mechanism, we have studied the stability of rpme in vivo and the binding affinity of these proteins to ribosomes in vitro, and we have found that liberati ... | 2006 | 16547061 |
| a pathway branching in transcription initiation in escherichia coli. | in transcription initiation, all rna polymerase molecules bound to a promoter have been conventionally supposed to proceed into elongation of transcript. however, for escherichia coli rna polymerase, evidence has been accumulated for a view that only its fraction can proceed into elongation and the rest is retained at a promoter in non-productive form: a pathway branching in transcription initiation. proteins such as grea and greb affect these fractions at several promoters in vitro. to reveal t ... | 2006 | 16553885 |
| identification of nucleotides in e. coli 16s rrna essential for ribosome subunit association. | the ribosome consists of two unequal subunits, which associate via numerous intersubunit contacts. medium-resolution structural studies have led to grouping of the intersubunit contacts into 12 directly visualizable intersubunit bridges. most of the intersubunit interactions involve rna. we have used an rna modification interference approach to determine escherichia coli 16s rrna positions that are essential for the association of functionally active 70s ribosomes. modification of the n1 positio ... | 2006 | 16556933 |
| structural basis for altering the stability of homologous rnas from a mesophilic and a thermophilic bacterium. | tertiary rna structures from thermophilic bacteria generally are more stable than their mesophilic homologs. to understand the structural basis of the increase in stability, we investigated equilibrium folding of the specificity domain (s-domain) of rnase p rna from a mesophilic (escherichia coli) and a thermophilic (thermus thermophilus) bacterium. equilibrium folding of both s-domains is described by a minimal, three-state folding scheme, u-to-i-to-n. in the i-to-n transition of the thermophil ... | 2006 | 16581805 |
| purification, crystallization and preliminary x-ray diffraction of secdf, a translocon-associated membrane protein, from thermus thermophilus. | thermus thermophilus has a multi-path membrane protein, tsecdf, as a single-chain homologue of escherichia coli secd and secf, which form a translocon-associated complex required for efficient preprotein translocation and membrane-protein integration. here, the cloning, expression in e. coli, purification and crystallization of tsecdf are reported. overproduced tsecdf was solubilized with dodecylmaltoside, chromatographically purified and crystallized by vapour diffusion in the presence of polye ... | 2006 | 16582489 |
| two putative c-type multiheme cytochromes required for the expression of omcb, an outer membrane protein essential for optimal fe(iii) reduction in geobacter sulfurreducens. | deletion of two homologous geobacter sulfurreducens c-type cytochrome genes, omcg and omch, decreased the rate of fe(iii) reduction and decreased the level of an outer membrane cytochrome critical for fe(iii) reduction, omcb, without affecting its transcription. expression of either gene restored fe(iii) reduction and omcb expression, suggesting functional similarity. | 2006 | 16585776 |
| nmr structure of the aquifex aeolicus tmrna pseudoknot pk1: new insights into the recoding event of the ribosomal trans-translation. | the transfer-messenger rna (tmrna) pseudoknot pk1 is essential for bacterial trans-translation, a ribosomal rescue mechanism. we report the solution structure of pk1 from aquifex aeolicus, which despite an unprecedented small number of nucleotides and thus an unprecented compact size, displays a very high thermal stability. several unusual structural features account for these properties and indicate that pk1 belongs to the class of ribosomal frameshift pseudoknots. this suggests a similarity be ... | 2006 | 16595798 |
| crystal structure of the conserved protein ttha0727 from thermus thermophilus hb8 at 1.9 a resolution: a cmd family member distinct from carboxymuconolactone decarboxylase (cmd) and ahpd. | ttha0727 is a conserved hypothetical protein from thermus thermophilus hb8, with a molecular mass of 12.6 kda. ttha0727 belongs to the carboxymuconolactone decarboxylase (cmd) family (pfam 02627). a sequence comparison with its homologs suggested that ttha0727 is a distinct protein from alkylhydroperoxidase ahpd and gamma-carboxymuconolactone decarboxylase in the cmd family. here we report the 1.9 a crystal structure of ttha0727 (pdb id: 2cwq) determined by the multiwavelength anomalous dispersi ... | 2006 | 16597838 |
| characteristic signatures of the lyta gene provide a basis for rapid and reliable diagnosis of streptococcus pneumoniae infections. | the nucleotide sequences of the lyta gene from 29 pneumococcal isolates of various serotypes and 22 additional streptococci of the mitis group (including two streptococcus pseudopneumoniae strains) have been compared and found to correspond to 19 typical (927-bp-long) and 20 atypical (921-bp-long) alleles. all the streptococcus pneumoniae strains harbored typical lyta alleles, whereas nonpneumococcal isolates belonging to the mitis group always carried atypical alleles. a sequence alignment show ... | 2006 | 16597847 |
| molecular characterization of subject-specific oral microflora during initial colonization of enamel. | the initial microbial colonization of tooth surfaces is a repeatable and selective process, with certain bacterial species predominating in the nascent biofilm. characterization of the initial microflora is the first step in understanding interactions among community members that shape ensuing biofilm development. using molecular methods and a retrievable enamel chip model, we characterized the microbial diversity of early dental biofilms in three subjects. a total of 531 16s rrna gene sequences ... | 2006 | 16597990 |
| a phylogenomic profile of globins. | globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. the latter comprise the flavohemoglobins with a c-terminal fad-binding domain and the gene-regulating globin coupled sensors, with variable c-terminal domains. the single-domain globins encompass sequences related to chimeric globins and "truncated" hemoglobins with a 2-over-2 instead of the canonical 3-over-3 alpha-helical fold. | 2006 | 16600051 |
| crystal structure of bacillus subtilis trmb, the trna (m7g46) methyltransferase. | the structure of bacillus subtilis trmb (bstrmb), the trna (m7g46) methyltransferase, was determined at a resolution of 2.1 a. this is the first structure of a member of the trmb family to be determined by x-ray crystallography. it reveals a unique variant of the rossmann-fold methyltransferase (rfm) structure, with the n-terminal helix folded on the opposite site of the catalytic domain. the architecture of the active site and a computational docking model of bstrmb in complex with the methyl g ... | 2006 | 16600901 |
| melanocyte transformation associated with substrate adhesion impediment. | exclude experimental models of malignant transformation employ chemical and physical carcinogens or genetic manipulations to study tumor progression. in this work, different melanoma cell lines were established after submitting a nontumorigenic melanocyte lineage (melan-a) to sequential cycles of forced anchorage impediment. the great majority of these cells underwent anoikis when maintained in suspension. after one deadhesion cycle, phenotypic alterations were noticeable in the few surviving ce ... | 2006 | 16611417 |
| small protein b interacts with the large and the small subunits of a stalled ribosome during trans-translation. | during trans-translation, stalled bacterial ribosomes are rescued by small protein b (smpb) and by transfer-messenger rna (tmrna). stalled ribosomes switch translation from the defective messages to a short internal reading frame on tmrna that tags the nascent peptide chain for degradation and recycles the ribosomes. we present evidences that smpb binds the large and small ribosomal subunits in vivo and in vitro. the binding between smpb and the ribosomal subunits is very tight, with a dissociat ... | 2006 | 16611927 |
| the domain of the bacillus subtilis dead-box helicase yxin that is responsible for specific binding of 23s rrna has an rna recognition motif fold. | the yxin protein of bacillus subtilis is a member of the dbpa subfamily of prokaryotic dead-box rna helicases. like dbpa, it binds with high affinity and specificity to segments of 23s ribosomal rna as short as 32 nucleotides (nt) that include hairpin 92. several experiments have shown that the 76-residue carboxy-terminal domain of yxin is responsible for the high-affinity rna binding. the domain has been crystallized and its structure has been solved to 1.7 angstroms resolution. the structure r ... | 2006 | 16611943 |
| comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms. | six diverse prokaryotic and five eukaryotic genomes were compared to deduce whether the protein synthesis termination signal has common determinants within and across both kingdoms. four of the six prokaryotic and all of the eukaryotic genomes investigated demonstrated a similar pattern of nucleotide bias both 5' and 3' of the stop codon. a preferred core signal of 4 nt was evident, encompassing the stop codon and the following nucleotide. codons decoded by hyper-modified trnas were over-represe ... | 2006 | 16614446 |
| proteins surrounding hairpin iiie of the hepatitis c virus internal ribosome entry site on the human 40s ribosomal subunit. | binding of the internal ribosome entry site (ires) of the hepatitis c virus (hcv) rna to the eif-free 40s ribosomal subunit is the first step of initiation of translation of the viral rna. hairpins iiid and iiie comprising 253-302 nt of the ires are known to be essential for binding to the 40s subunit. here we have examined the molecular environment of the hcv ires in its binary complex with the human 40s ribosomal subunit. for this purpose, two rna derivatives were used that bore a photoactivat ... | 2006 | 16614452 |
| domain stability in the aaa+ atpase clpb from escherichia coli. | clpb is a heat-shock protein that reactivates aggregated proteins in cooperation with the dnak chaperone system. clpb belongs to the family of aaa+ atpases and forms ring-shaped oligomers: heptamers in the absence of nucleotides and hexamers in the presence of nucleotides. we investigated the thermodynamic stability of clpb in its monomeric and oligomeric forms. clpb contains six distinct structural domains: the n-terminal domain involved in substrate binding, two aaa+ atp-binding modules, each ... | 2006 | 16615934 |
| prions adhere to soil minerals and remain infectious. | an unidentified environmental reservoir of infectivity contributes to the natural transmission of prion diseases (transmissible spongiform encephalopathies [tses]) in sheep, deer, and elk. prion infectivity may enter soil environments via shedding from diseased animals and decomposition of infected carcasses. burial of tse-infected cattle, sheep, and deer as a means of disposal has resulted in unintentional introduction of prions into subsurface environments. we examined the potential for soil t ... | 2006 | 16617377 |
| the three-dimensional structure of complex i from yarrowia lipolytica: a highly dynamic enzyme. | the structure of complex i from yarrowia lipolytica was determined by three-dimensional electron microscopy. a random conical data set was collected from deep stain embedded particles. more than 14000 image pairs were analyzed. through extensive classification combined with three-dimensional reconstruction, it was possible for the first time to show a much more detailed substructure of the complex. the peripheral arm is subdivided in at least six domains. the membrane arm shows two major protrus ... | 2006 | 16621601 |
| trnahis guanylyltransferase adds g-1 to the 5' end of trnahis by recognition of the anticodon, one of several features unexpectedly shared with trna synthetases. | all eukaryotic trna(his) molecules are unique among trna species because they require addition of a guanine nucleotide at the -1 position by trna(his) guanylyltransferase, encoded in yeast by thg1. this g(-1) residue is both necessary and sufficient for aminoacylation of trna by histidyl-trna synthetase in vitro and is required for aminoacylation in vivo. although thg1 is presumed to be highly specific for trna(his) to prevent misacylation of trnas, the source of this specificity is unknown. we ... | 2006 | 16625026 |
| ph-dependent conformational switch activates the inhibitor of transcription elongation. | gfh1, a transcription factor from thermus thermophilus, inhibits all catalytic activities of rna polymerase (rnap). we characterized the gfh1 structure, function and possible mechanism of action and regulation. gfh1 inhibits rnap by competing with ntps for coordinating the active site mg2+ ion. this coordination requires at least two aspartates at the tip of the gfh1 n-terminal coiled-coil domain (ntd). the overall structure of gfh1 is similar to that of the escherichia coli transcript cleavage ... | 2006 | 16628221 |
| differential gene transfers and gene duplications in primary and secondary endosymbioses. | most genes introduced into phototrophic eukaryotes during the process of endosymbiosis are either lost or relocated into the host nuclear genome. in contrast, groel homologues are found in different genome compartments among phototrophic eukaryotes. comparative sequence analyses of recently available genome data, have allowed us to reconstruct the evolutionary history of these genes and propose a hypothesis that explains the unusual genome distribution of groel homologues. | 2006 | 16640777 |
| crystal structure of hypothetical protein tthb192 from thermus thermophilus hb8 reveals a new protein family with an rna recognition motif-like domain. | we have determined the crystal structure of hypothetical protein tthb192 from thermus thermophilus hb8 at 1.9 a resolution. this protein is a member of the escherichia coli ygch sequence family, which contains approximately 15 sequence homologs of bacterial origin. these homologs have a high isoelectric point. the crystal structure reveals that tthb192 consists of two independently folded domains, and that each domain exhibits a ferredoxin-like fold with a four-stranded antiparallel beta-sheet p ... | 2006 | 16672237 |
| effect of biofilm growth on expression of surface proteins of actinomyces naeslundii genospecies 2. | the predominant surface proteins of biofilm and planktonic actinomyces naeslundii, a primary colonizer of the tooth surface, were examined. seventy-nine proteins (the products of 52 genes) were identified in biofilm cells, and 30 of these, including adhesins, chaperones, and stress-response proteins, were significantly up-regulated relative to planktonic cells. | 2006 | 16672534 |
| structural and functional analysis of rv3214 from mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase. | the availability of complete genome sequences has highlighted the problems of functional annotation of the many gene products that have only limited sequence similarity with proteins of known function. the predicted protein encoded by open reading frame rv3214 from the mycobacterium tuberculosis h37rv genome was originally annotated as entd through sequence similarity with the escherichia coli entd, a 4'-phosphopantetheinyl transferase implicated in siderophore biosynthesis. an alternative annot ... | 2006 | 16672613 |
| structure of the unusual seryl-trna synthetase reveals a distinct zinc-dependent mode of substrate recognition. | methanogenic archaea possess unusual seryl-trna synthetase (serrs), evolutionarily distinct from the serrss found in other archaea, eucaryotes and bacteria. the two types of serrss show only minimal sequence similarity, primarily within class ii conserved motifs 1, 2 and 3. here, we report a 2.5 a resolution crystal structure of the atypical methanogenic methanosarcina barkeri serrs and its complexes with atp, serine and the nonhydrolysable seryl-adenylate analogue 5'-o-(n-serylsulfamoyl)adenosi ... | 2006 | 16675947 |
| hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation. | we used a high flux synchrotron x-ray beam to map the structure of 16s rrna and rnase p in viable bacteria in situ. a 300 ms exposure to the x-ray beam was sufficient for optimal cleavage of the phosphodiester backbone. the in vivo footprints of the 16s rrna in frozen cells were similar to those obtained in vitro and were consistent with the predicted accessibility of the rna backbone to hydroxyl radical. protection or enhanced cleavage of certain nucleotides in vivo can be explained by interact ... | 2006 | 16682443 |
| 30s ribosomal subunits can be assembled in vivo without primary binding ribosomal protein s15. | assembly of 30s ribosomal subunits from escherichia coli has been dissected in detail using an in vitro system. such studies have allowed characterization of the role for ribosomal protein s15 in the hierarchical assembly of 30s subunits; s15 is a primary binding protein that orchestrates the assembly of ribosomal proteins s6, s11, s18, and s21 with the central domain of 16s ribosomal rna to form the platform of the 30s subunit. in vitro s15 is the sole primary binding protein in this cascade, p ... | 2006 | 16682557 |
| the mechanism of superoxide production by nadh:ubiquinone oxidoreductase (complex i) from bovine heart mitochondria. | nadh:ubiquinone oxidoreductase (complex i) is a major source of reactive oxygen species in mitochondria and a significant contributor to cellular oxidative stress. here, we describe the kinetic and molecular mechanism of superoxide production by complex i isolated from bovine heart mitochondria and confirm that it produces predominantly superoxide, not hydrogen peroxide. redox titrations and electron paramagnetic resonance spectroscopy exclude the iron-sulfur clusters and flavin radical as the s ... | 2006 | 16682634 |
| structure of ribose 5-phosphate isomerase from plasmodium falciparum. | the structure of ribose 5-phosphate isomerase from plasmodium falciparum, pfe0730c, has been determined by molecular replacement at 2.09 angstroms resolution. the enzyme, which catalyzes the isomerization reaction that interconverts ribose 5-phosphate and ribulose 5-phosphate, is a member of the pentose phosphate pathway. the p. falciparum enzyme belongs to the ribose 5-phosphate isomerase a family, pfam family pf06562 (duf1124), and is structurally similar to other members of the family. | 2006 | 16682767 |
| preliminary x-ray crystallographic analysis of the secreted chorismate mutase from mycobacterium tuberculosis: a tricky crystallization problem solved. | chorismate mutase catalyzes the conversion of chorismate to prephenate in the biosynthesis of the aromatic amino acids tyrosine and phenylalanine in bacteria, fungi and plants. here, the crystallization of the unusual secreted chorismate mutase from mycobacterium tuberculosis (encoded by rv1885c), a 37.2 kda dimeric protein belonging to the aroq(gamma) subclass of mutases, is reported. crystal optimization was non-trivial and is discussed in detail. to obtain crystals of sufficient quality, it w ... | 2006 | 16682771 |
| alterations in expression and chromatin configuration of the alpha hemoglobin-stabilizing protein gene in erythroid kruppel-like factor-deficient mice. | erythroid krüppel-like factor (eklf) is an erythroid zinc finger protein identified by its interaction with a caccc sequence in the beta-globin promoter, where it establishes local chromatin structure permitting beta-globin gene transcription. we sought to identify other eklf target genes and determine the chromatin status of these genes in the presence and absence of eklf. we identified alpha hemoglobin-stabilizing protein (ahsp) by subtractive hybridization and demonstrated a 95 to 99.9% reduc ... | 2006 | 16705186 |
| improvements of rolling circle amplification (rca) efficiency and accuracy using thermus thermophilus ssb mutant protein. | rolling circle amplification (rca) of plasmid or genomic dna using random hexamers and bacteriophage phi29 dna polymerase has become increasingly popular in the amplification of template dna in dna sequencing. we have found that the mutant protein of single-stranded dna binding protein (ssb) from thermus thermophilus (tth) hb8 enhances the efficiency of amplification of dna templates. in addition, the tthssb mutant protein increased the specificity of phi29 dna polymerase. we have overexpressed ... | 2006 | 16707659 |
| use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes. | amino acids in proteins are not used equally. some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, for example). as several factors contribute to the different amino acid usage in proteins, it is difficult both to analyze these differences and to separate the contributions made by each facto ... | 2006 | 16709240 |
| predicting shine-dalgarno sequence locations exposes genome annotation errors. | in prokaryotes, shine-dalgarno (sd) sequences, nucleotides upstream from start codons on messenger rnas (mrnas) that are complementary to ribosomal rna (rrna), facilitate the initiation of protein synthesis. the location of sd sequences relative to start codons and the stability of the hybridization between the mrna and the rrna correlate with the rate of synthesis. thus, accurate characterization of sd sequences enhances our understanding of how an organism's transcriptome relates to its cellul ... | 2006 | 16710451 |
| the potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases. | aberrant forms of proteins ubiquitin b and beta-amyloid precusor protein, ubb+1 and app+1, are implicated in human neurodegenerative diseases. they have their carboxyl-terminal regions derived from an alternative reading frame. transcription slippage has been invoked to explain the production of these proteins from abnormal mrna. however, ribosomal frameshifting on wild-type mrna may account for the great majority of the aberrant protein. ribosomal frameshifting may also be involved in the progr ... | 2006 | 16714280 |
| the obligate human pathogen, neisseria gonorrhoeae, is polyploid. | we show using several methodologies that the gram-negative, diplococcal-bacterium neisseria gonorrhoeae has more than one complete genome copy per cell. gene dosage measurements demonstrated that only a single replication initiation event per chromosome occurs per round of cell division, and that there is a single origin of replication. the region containing the origin does not encode any genes previously associated with bacterial origins of replication. quantitative pcr results showed that ther ... | 2006 | 16719561 |
| finding the region of pseudo-periodic tandem repeats in biological sequences. | the genomes of many species are dominated by short sequences repeated consecutively. it is estimated that over 10% of the human genome consists of tandemly repeated sequences. finding repeated regions in long sequences is important in sequence analysis. we develop a software, locrepeat, that finds regions of pseudo-periodic repeats in a long sequence. we use the definition of li et al. 1 for the pseudo-periodic partition of a region and extend the algorithm that can select the repeated region fr ... | 2006 | 16722520 |
| functional, biophysical, and structural bases for antibacterial activity of tigecycline. | tigecycline is a novel glycylcycline antibiotic that possesses broad-spectrum activity against many clinically relevant species of bacterial pathogens. the mechanism of action of tigecycline was delineated using functional, biophysical, and molecular modeling experiments in this study. functional assays showed that tigecycline specifically inhibits bacterial protein synthesis with potency 3- and 20-fold greater than that of minocycline and tetracycline, respectively. biophysical analyses demonst ... | 2006 | 16723578 |
| two conformations of a crystalline human trna synthetase-trna complex: implications for protein synthesis. | aminoacylation of trna is the first step of protein synthesis. here, we report the co-crystal structure of human tryptophanyl-trna synthetase and trnatrp. this enzyme is reported to interact directly with elongation factor 1alpha, which carries charged trna to the ribosome. crystals were generated from a 50/50% mixture of charged and uncharged trnatrp. these crystals captured two conformations of the complex, which are nearly identical with respect to the protein and a bound tryptophan. they are ... | 2006 | 16724112 |
| how initiation factors tune the rate of initiation of protein synthesis in bacteria. | the kinetics of initiator transfer rna (trna) interaction with the messenger rna (mrna)-programmed 30s subunit and the rate of 50s subunit docking to the 30s preinitiation complex were measured for different combinations of initiation factors in a cell-free escherichia coli system for protein synthesis with components of high purity. the major results are summarized by a michaelis-menten scheme for initiation. all three initiation factors are required for maximal efficiency (kcat/km) of initiati ... | 2006 | 16724118 |
| crystal structure of the yeast his6 enzyme suggests a reaction mechanism. | the saccharomyces cerevisiae his6 gene codes for the enzyme phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. to get an insight into the structure and function of this enzyme, we determined its x-ray structure at a resolution of 1.30 a using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 a wavelength. his6 folds in an (alpha/beta)8 barrel similar to hisa, which performs the same function in bac ... | 2006 | 16731983 |
| native state energetics of the src sh2 domain: evidence for a partially structured state in the denatured ensemble. | we have defined the free-energy profile of the src sh2 domain using a variety of biophysical techniques. equilibrium and kinetic experiments monitored by tryptophan fluorescence show that src sh2 is quite stable and folds rapidly by a two-state mechanism, without populating any intermediates. native state hydrogen-deuterium exchange confirms this two-state behavior; we detect no cooperative partially unfolded forms in equilibrium with the native conformation under any conditions. interestingly, ... | 2006 | 16751610 |