| role of a ribosomal rna phosphate oxygen during the ef-g-triggered gtp hydrolysis. | elongation factor-catalyzed gtp hydrolysis is a key reaction during the ribosomal elongation cycle. recent crystal structures of g proteins, such as elongation factor g (ef-g) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational gtpases (trgtpases) with the sarcin-ricin loop (srl) of ribosomal rna (rrna) is pivotal for hydrolysis. however, the precise mechanism remains elusive and is intensively debated. based on the close prox ... | 2015 | 25941362 |
| salinity regulation of the interaction of halovirus snj1 with its host and alteration of the halovirus replication strategy to adapt to the variable ecosystem. | halovirus is a major force that affects the evolution of extreme halophiles and the biogeochemistry of hypersaline environments. however, until now, the systematic studies on the halovirus ecology and the effects of salt concentration on virus-host systems are lacking. to provide more valuable information for understanding ecological strategies of a virus-host system in the hypersaline ecosystem, we studied the interaction between halovirus snj1 and its host natrinema sp.j7-2 under various nacl ... | 2015 | 25853566 |
| molecular analysis of codon 548 in the rpob gene involved in mycobacterium tuberculosis resistance to rifampin. | most mycobacterium tuberculosis rifampin-resistant strains have been associated with mutations in an 81-bp rifampin resistance-determining region (rrdr) in the gene rpob. however, if this region alone were targeted, rifampin-resistant strains with mutations outside the rrdr would not be detected. in this study, among 51 rifampin-resistant clinical isolates analyzed by sequencing 1,681-bp-long dna fragments containing the rrdr, 47 isolates contained mutations within the rrdr, three isolates conta ... | 2015 | 25534743 |
| a selb/ef-tu/aif2γ-like protein from methanosarcina mazei in the gtp-bound form binds cysteinyl-trna(cys.). | the putative translation elongation factor mbar_a0971 from the methanogenic archaeon methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of ef-tu ("ef-pyl"). in the present study, the crystal structures of its homologue from methanosarcina mazei (mm1309) were determined in the gmppnp-bound, gdp-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. the three mm1309 structures are quite similar (r.m.s.d. < 0.1 å). the three domains, correspond ... | 2015 | 25618148 |
| long-range pcr amplification of dna by dna polymerase iii holoenzyme from thermus thermophilus. | dna replication in bacteria is accomplished by a multicomponent replicase, the dna polymerase iii holoenzyme (pol iii he). the three essential components of the pol iii he are the α polymerase, the β sliding clamp processivity factor, and the dnax clamp-loader complex. we report here the assembly of the functional holoenzyme from thermus thermophilus (tth), an extreme thermophile. the minimal holoenzyme capable of dna synthesis consists of α, β and dnax (τ and γ), δ and δ' components of the clam ... | 2015 | 25688300 |
| draft genome sequence of thermus sp. isolate 2.9, obtained from a hot water spring located in salta, argentina. | thermus sp. isolate 2.9 was obtained from a hot water spring in salta, argentina. here, we report the draft genome sequence (2,485,434 bp) of this isolate, which consists of 11 scaffolds of >10 kbp and 2,719 protein-coding sequences. | 2015 | 25593256 |
| trueprime is a novel method for whole-genome amplification from single cells based on tthprimpol. | sequencing of a single-cell genome requires dna amplification, a process prone to introducing bias and errors into the amplified genome. here we introduce a novel multiple displacement amplification (mda) method based on the unique dna primase features of thermus thermophilus (tth) primpol. tthprimpol displays a potent primase activity preferring dntps as substrates unlike conventional primases. a combination of tthprimpol's unique ability to synthesize dna primers with the highly processive phi ... | 2016 | 27897270 |
| high-resolution phenotypic landscape of the rna polymerase ii trigger loop. | the active sites of multisubunit rna polymerases have a "trigger loop" (tl) that multitasks in substrate selection, catalysis, and translocation. to dissect the saccharomyces cerevisiae rna polymerase ii tl at individual-residue resolution, we quantitatively phenotyped nearly all tl single variants en masse. three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among tl residues. we find that mutations disrupting an intra-tl ... | 2016 | 27898685 |
| adaptation in bacillus cereus: from stress to disease. | bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. after ingestion, b. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic ph in the stomach and changing oxygen conditions in the human intestine. b. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and m ... | 2016 | 27757102 |
| origin of a folded repeat protein from an intrinsically disordered ancestor. | repetitive proteins are thought to have arisen through the amplification of subdomain-sized peptides. many of these originated in a non-repetitive context as cofactors of rna-based replication and catalysis, and required the rna to assume their active conformation. in search of the origins of one of the most widespread repeat protein families, the tetratricopeptide repeat (tpr), we identified several potential homologs of its repeated helical hairpin in non-repetitive proteins, including the put ... | 2016 | 27623012 |
| visualizing the phage t4 activated transcription complex of dna and e. coli rna polymerase. | the ability of rna polymerase (rnap) to select the right promoter sequence at the right time is fundamental to the control of gene expression in all organisms. however, there is only one crystallized structure of a complete activator/rnap/dna complex. in a process called σ appropriation, bacteriophage t4 activates a class of phage promoters using an activator (mota) and a co-activator (asia), which function through interactions with the σ(70) subunit of rnap. we have developed a holistic, struct ... | 2016 | 27458207 |
| cold shock proteins: a minireview with special emphasis on csp-family of enteropathogenic yersinia. | bacteria have evolved a number of mechanisms for coping with stress and adapting to changing environmental conditions. many bacteria produce small cold shock proteins (csp) as a response to rapid temperature downshift (cold shock). during cold shock, the cell membrane fluidity and enzyme activity decrease, and the efficiency of transcription and translation is reduced due to stabilization of nucleic acid secondary structures. moreover, protein folding is inefficient and ribosome function is hamp ... | 2016 | 27499753 |
| application of a euryarchaeota-specific helicase from thermococcus kodakarensis for noise reduction in pcr. | dna/rna helicases, which are enzymes for eliminating hydrogen bonds between bases of dna/dna, dna/rna, and rna/rna using the energy of atp hydrolysis, contribute to various biological activities. in the present study, the euryarchaeota-specific helicase esha (tk0566) from the hyperthermophilic archaeon thermococcus kodakarensis (tk-esha) was obtained as a recombinant form, and its enzymatic properties were examined. tk-esha exhibited maximal atpase activity in the presence of rna at 80°c. unwind ... | 2016 | 26969705 |
| mycobacterium tuberculosis transcription machinery: ready to respond to host attacks. | regulating responses to stress is critical for all bacteria, whether they are environmental, commensal, or pathogenic species. for pathogenic bacteria, successful colonization and survival in the host are dependent on adaptation to diverse conditions imposed by the host tissue architecture and the immune response. once the bacterium senses a hostile environment, it must enact a change in physiology that contributes to the organism's survival strategy. inappropriate responses have consequences; h ... | 2016 | 26883824 |
| structures of e. coli σs-transcription initiation complexes provide new insights into polymerase mechanism. | in bacteria, multiple σ factors compete to associate with the rna polymerase (rnap) core enzyme to form a holoenzyme that is required for promoter recognition. during transcription initiation rnap remains associated with the upstream promoter dna via sequence-specific interactions between the σ factor and the promoter dna while moving downstream for rna synthesis. as rna polymerase repetitively adds nucleotides to the 3'-end of the rna, a pyrophosphate ion is generated after each nucleotide inco ... | 2016 | 27035955 |
| illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. | illumina's sequencing platforms are currently the most utilised sequencing systems worldwide. the technology has rapidly evolved over recent years and provides high throughput at low costs with increasing read-lengths and true paired-end reads. however, data from any sequencing technology contains noise and our understanding of the peculiarities and sequencing errors encountered in illumina data has lagged behind this rapid development. | 2016 | 26968756 |
| the inhibitory effect of non-substrate and substrate dna on the ligation and self-adenylylation reactions catalyzed by t4 dna ligase. | dna ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. prior characterization of dna ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsdna substrate, with no interaction evident on dsdna lacking a nick. in the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation a ... | 2016 | 26954034 |
| physiological properties and genome structure of the hyperthermophilic filamentous phage φoh3 which infects thermus thermophilus hb8. | a filamentous bacteriophage, φoh3, was isolated from hot spring sediment in obama hot spring in japan with the hyperthermophilic bacterium thermus thermophilus hb8 as its host. phage φoh3, which was classified into the inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φoh3 was stable at temperatures ranging from 70 to 90°c and at phs ranging from 6 to 9. a one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, ... | 2016 | 26941711 |
| single-cell-genomics-facilitated read binning of candidate phylum em19 genomes from geothermal spring metagenomes. | the vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. this "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. in this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "calescamantes" (em19) to calibrate machine learning algorithms and define metagenomic bins directly ... | 2016 | 26637598 |
| mutations in the nucleotide binding and hydrolysis domains of helicobacter pylori muts2 lead to altered biochemical activities and inactivation of its in vivo function. | helicobacter pylori muts2 (hpmuts2), an inhibitor of recombination during transformation is a non-specific nuclease with two catalytic sites, both of which are essential for its anti-recombinase activity. although hpmuts2 belongs to a highly conserved family of abc transporter atpases, the role of its atp binding and hydrolysis activities remains elusive. | 2016 | 26843368 |
| lineage-specific variations in the trigger loop modulate rna proofreading by bacterial rna polymerases. | rna cleavage by bacterial rna polymerase (rnap) has been implicated in transcriptional proofreading and reactivation of arrested transcription elongation complexes but its molecular mechanism is less understood than the mechanism of nucleotide addition, despite both reactions taking place in the same active site. rnap from the radioresistant bacterium deinococcus radiodurans is characterized by highly efficient intrinsic rna cleavage in comparison with escherichia coli rnap. we find that the enh ... | 2016 | 26733581 |
| amylose recognition and ring-size determination of amylomaltase. | starch is a major carbon and energy source throughout all kingdoms of life. it consists of two carbohydrate polymers, branched amylopectin and linear amylose, which are sparingly soluble in water. hence, the enzymatic breakdown by glycoside hydrolases (ghs) is of great biological and societal importance. amylomaltases (ams) are ghs specialized in the hydrolysis of α-1,4-linked sugar chains such as amylose. they are able to catalyze an intramolecular transglycosylation of a bound sugar chain yiel ... | 2017 | 28097217 |
| the core of allosteric motion in thermus caldophilus l-lactate dehydrogenase. | for thermus caldophilus l-lactate dehydrogenase (tcldh), fructose 1,6-bisphosphate (fbp) reduced the pyruvate s(0.5) value 10(3)-fold and increased the v(max) value 4-fold at 30 °c and ph 7.0, indicating that tcldh has a much more t state-sided allosteric equilibrium than thermus thermophilus l-lactate dehydrogenase, which has only two amino acid replacements, a154g and h179y. the inactive (t) and active (r) state structures of tcldh were determined at 1.8 and 2.0 å resolution, respectively. the ... | 2014 | 25258319 |
| evaluation and directed evolution for thermostability improvement of a gh 13 thermostable α-glucosidase from thermus thermophilus tc11. | thermal stable α-glucosidases with transglycosylation activity could be applied to the industrial production of oligosaccharides as well as conjugation of sugars to biologically useful materials. therefore, α-glucosidases isolated from thermophiles have gained attention over the past decade. in this study, the characterization of a highly thermostable α-glucosidase and its thermostability improved mutant from newly isolated strain thermus thermophilus tc11 were investigated. | 2015 | 26490269 |
| recent advances in laboratory diagnosis of hepatitis c virus infection. | | 1994 | 22346511 |
| sequencing of hepatitis c virus cdna with polymerase chain reaction directed sequencing. | to explore a rapid and easy sequencing method for hepatitis c virus (hcv) genome and establish a new sequencing method in china. | 1997 | 27006575 |
| superoxide dismutase in arabidopsis: an eclectic enzyme family with disparate regulation and protein localization. | a number of environmental stresses can lead to enhanced production of superoxide within plant tissues, and plants are believed to rely on the enzyme superoxide dismutase (sod) to detoxify this reactive oxygen species. we have identified seven cdnas and genes for sod in arabidopsis. these consist of three cuznsods (csd1, csd2, and csd3), three fesods (fsd1, fsd2, and fsd3), and one mnsod (msd1). the chromosomal location of these seven sod genes has been established. to study this enzyme family, a ... | 1998 | 9765550 |
| abnormal t cell receptor v gene usage in myasthenia gravis: prevalence and characterization of expanded t cell populations. | the usage of t cell receptor (tcr) valpha/vbeta chains on cells from 38 patients with myasthenia gravis (mg) was determined by flow cytometry. there was a decreased number of cells expressing vbeta2 in cd8+ and vbeta3 in cd4+ cells in patients compared with healthy individuals. abnormal expansions of t cells using particular tcr valpha/vbeta gene products were found in 18/38 patients. a significantly higher usage of vbeta13 was observed but there was no restriction with regard to other tcr valph ... | 1998 | 9737677 |
| association of ferredoxin-nadp oxidoreductase with the chloroplastic pyridine nucleotide dehydrogenase complex in barley leaves | barley (hordeum vulgare l.) leaves were used to isolate and characterize the chloroplast nad(p)h dehydrogenase complex. the stroma fraction and the thylakoid fraction solubilized with sodium deoxycholate were analyzed by native polyacrylamide gel electrophoresis, and the enzymes detected with nadh and nitroblue tetrazolium were electroeluted. the enzymes electroeluted from band s from the stroma fraction and from bands t1 (et1) and t2 from the thylakoid fraction solubilized with sodium deoxychol ... | 1998 | 9576793 |
| salt-induced detour through compact regions of the protein folding landscape. | in several cases, inorganic salts have been used to induce partly structured states in protein folding. but what is the nature of these states: do they represent key stepping stones in the folding process, or are they circumstantial pitfalls in the energy landscape? here we report that, in the case of the two-state protein s6, the salt-induced collapsed state is off the usual folding routes in the sense that it is prematurely collapsed and slows down folding by several orders of magnitude. altho ... | 1999 | 10518521 |
| the kinetoplast structure-specific endonuclease i is related to the 5' exo/endonuclease domain of bacterial dna polymerase i and colocalizes with the kinetoplast topoisomerase ii and dna polymerase beta during replication. | the mitochondrial dna (kinetoplast dna) of the trypanosomatid crithidia fasciculata has an unusual structure composed of minicircles and maxicircles topologically interlocked into a single network and organized in a disc-shaped structure at the base of the flagellum. we previously purified a structure-specific endonuclease (sse1), based on its rnase h activity, that is enriched in isolated kinetoplasts. the endonuclease gene has now been cloned, sequenced, and found to be closely related to the ... | 1999 | 10411896 |
| distribution of hepatitis c virus genotypes in canada: results from the lcdc sentinel health unit surveillance system. | in a sentinel hepatitis surveillance study conducted by sentinel health units, 1469 patients were enrolled, and 959 (65.3%) were positive for antibody to hepatitis c virus (hcv). samples from 387 patients (40.4%) were tested for hcv rna, and 289 (74.7%) were positive for rna. the major risk factor for hcv infection was injection drug use, reported in 71% of cases. the genotyping of hcv isolates showed that subtype 1a (48%) was predominant in canada. the other subtypes detected were 1b (19%), 2a ... | 1999 | 22346372 |
| aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance. | | 2000 | 11083623 |
| a new era for the rna world. conference: rna 2000. | | 2000 | 11258477 |
| structural and mechanistic conservation in dna ligases. | dna ligases are enzymes required for the repair, replication and recombination of dna. dna ligases catalyse the formation of phosphodiester bonds at single-strand breaks in double-stranded dna. despite their occurrence in all organisms, dna ligases show a wide diversity of amino acid sequences, molecular sizes and properties. the enzymes fall into two groups based on their cofactor specificity, those requiring nad(+) for activity and those requiring atp. the eukaryotic, viral and archael bacteri ... | 2000 | 11058099 |
| tissue-specific and developmental pattern of expression of the rice sps1 gene. | sucrose-phosphate synthase (sps) is one of the key regulatory enzymes in carbon assimilation and partitioning in plants. sps plays a central role in the production of sucrose in photosynthetic cells and in the conversion of starch or fatty acids into sucrose in germinating seeds. to explore the mechanisms that regulate the tissue-specific and developmental distribution of sps, the expression pattern of rice (oryza sativa) sps1 (genbank accession no. u33175) was examined by in situ reverse transc ... | 2000 | 11027714 |
| designed protein tetramer zipped together with a hydrophobic alzheimer homology: a structural clue to amyloid assembly. | limited solubility and precipitation of amyloidogenic sequences such as the alzheimer peptide (beta-ap) are major obstacles to a molecular understanding of protein fibrillation and deposition processes. here we have circumvented the solubility problem by stepwise engineering a beta-ap homology into a soluble scaffold, the monomeric protein s6. the s6 construct with the highest beta-ap homology crystallizes as a tetramer that is linked by the beta-ap residues forming intermolecular antiparallel b ... | 2000 | 10944185 |
| a recurrent rna-binding domain is appended to eukaryotic aminoacyl-trna synthetases. | aminoacyl-trna synthetases of higher eukaryotes possess polypeptide extensions in contrast to their prokaryotic counterparts. these extra domains of poorly understood function are believed to be involved in protein-protein or protein-rna interactions. here we showed by gel retardation and filter binding experiments that the repeated units that build the linker region of the bifunctional glutamyl-prolyl-trna synthetase had a general rna-binding capacity. the solution structure of one of these rep ... | 2000 | 10654942 |
| distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal rna. | the relative substitution rate of each nucleotide site in bacterial small subunit rrna, large subunit rrna and 5s rrna was calculated from sequence alignments for each molecule. two-dimensional and three-dimensional variability maps of the rrnas were obtained by plotting the substitution rates on secondary structure models and on the tertiary structure of the rrnas available from x-ray diffraction results. this showed that the substitution rates are generally low near the centre of the ribosome, ... | 2001 | 11812832 |
| aaa proteins: in search of a common molecular basis. international meeting on cellular functions of aaa proteins. | | 2001 | 11713188 |
| gene cassette pcr: sequence-independent recovery of entire genes from environmental dna. | the vast majority of bacteria in the environment have yet to be cultured. consequently, a major proportion of both genetic diversity within known gene families and an unknown number of novel gene families reside in these uncultured organisms. isolation of these genes is limited by lack of sequence information. where such sequence data exist, pcr directed at conserved sequence motifs recovers only partial genes. here we outline a strategy for recovering complete open reading frames from environme ... | 2001 | 11679351 |
| electrostatics of nanosystems: application to microtubules and the ribosome. | evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. foremost among the models used to elucidate the electrostatic potential is the poisson-boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. here we present the application of numerical methods to enable the trivially parallel solution of the poisson-boltzmann eq ... | 2001 | 11517324 |
| functional relevance of the disulfide-linked complex of the n-terminal pdz domain of inad with norpa. | in drosophila, phototransduction is mediated by g(q)-activation of phospholipase c and is a well studied model system for understanding the kinetics of signal initiation, propagation and termination controlled by g proteins. the proper intracellular targeting and spatial arrangement of most proteins involved in fly phototransduction require the multi-domain scaffolding protein inad, composed almost entirely of five pdz domains, which independently bind various proteins including norpa, the relev ... | 2001 | 11500369 |
| survey and summary: the applications of universal dna base analogues. | a universal base analogue forms 'base pairs' with each of the natural dna/rna bases with little discrimination between them. a number of such analogues have been prepared and their applications as biochemical tools investigated. most of these analogues are non-hydrogen bonding, hydrophobic, aromatic 'bases' which stabilise duplex dna by stacking interactions. this review of the literature of universal bases (to 2000) details the analogues investigated, and their uses and limitations are discusse ... | 2001 | 11410649 |
| enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity. | the incorporation of potentially catalytic groups in dna is of interest for the in vitro selection of novel deoxyribozymes. a series of 10 c5-modified analogues of 2'-deoxyuridine triphosphate have been synthesised that possess side chains of differing flexibility and bearing a primary amino or imidazole functionality. for each series of nucleotide analogues differing degrees of flexibility of the c5 side chain was achieved through the use of alkynyl, alkenyl and alkyl moieties. the imidazole fu ... | 2001 | 11266559 |
| chloroplast ribosomal protein s7 of chlamydomonas binds to chloroplast mrna leader sequences and may be involved in translation initiation. | certain mutations isolated in the 5' untranslated region (5'utr) of the chloroplast rps7 gene in chlamydomonas reduce expression of reporter genes. second site suppressors in this 5'utr sequence restore reporter expression. 5'utr sequences with the original mutations fail to bind a 20-kd protein, one of five proteins that bind to leaders of several chloroplast genes. however, 5'utrs from suppressed mutants restore binding to this protein but do not bind a 47-kd protein present on the wild type a ... | 2001 | 11158540 |
| aminoacyl-trna synthetases database. | aminoacyl-trna synthetases (aarss) are at the center of the question of the origin of life. they constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. aarss arose early in evolution and are believed to be a group of ancient proteins. they are responsible for attaching amino acid residues to their cognate trna molecules, which is the first step in the protein synthesis. the role they play in a living cell is essential for the precise decip ... | 2001 | 11125115 |
| molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils. | microorganisms that use nitrate as an alternative terminal electron acceptor play an important role in the global nitrogen cycle. the diversity of the nitrate-reducing community in soil and the influence of the maize roots on the structure of this community were studied. the narg gene encoding the membrane bound nitrate reductase was selected as a functional marker for the nitrate-reducing community. the use of narg is of special interest because the phylogeny of the narg gene closely reflects t ... | 2002 | 12450836 |
| the ribosome filter hypothesis. | a variety of posttranscriptional mechanisms affects the processing, subcellular localization, and translation of messenger rnas (mrnas). translational control appears to occur primarily at the initiation rather than the elongation stage. it has been suggested that translation is mediated largely by means of a cap-binding/scanning mechanism. on the basis of recent findings, we propose here that differential binding of particular mrnas to eukaryotic 40s ribosomal subunits before translation may al ... | 2002 | 12221294 |
| the non-watson-crick base pairs and their associated isostericity matrices. | rna molecules exhibit complex structures in which a large fraction of the bases engage in non-watson-crick base pairing, forming motifs that mediate long-range rna-rna interactions and create binding sites for proteins and small molecule ligands. the rapidly growing number of three-dimensional rna structures at atomic resolution requires that databases contain the annotation of such base pairs. an unambiguous and descriptive nomenclature was proposed recently in which rna base pairs were classif ... | 2002 | 12177293 |
| linamarase expression in cassava cultivars with roots of low- and high-cyanide content. | this paper reports the expression and localization of linamarase in roots of two cassava (manihot esculenta crantz) cultivars of low and high cyanide. two different patterns of linamarase activity were observed. in the low-cyanide type, young leaves displayed very high enzyme activity during the early plant growing stage (3 months), whereas in root peel, the activity increased progressively to reach a peak in 11-month-old plants. conversely, in the high-cyanide cultivar (hcv), root peel linamara ... | 2002 | 12177481 |
| bruce: a program for the detection of transfer-messenger rna genes in nucleotide sequences. | a computer program, bruce, was developed for the identification of transfer-messenger rna (tmrna) genes. the program employs heuristic algorithms to search for a trna(ala)-like secondary structure surrounding a short sequence encoding the tag peptide. in the 57 completely sequenced bacterial genomes where tmrna genes have been reported previously, bruce identified all with no false positives. in addition, bruce found 99 of the 100 tmrnas identified previously in other bacteria, red chloroplasts ... | 2002 | 12140330 |
| the time course of changes in mrna levels in tree shrew sclera during induced myopia and recovery. | in tree shrews, visual form deprivation produces increased axial elongation of the deprived eye and a myopic shift in refractive state. a change in scleral extensibility (creep rate) is closely associated with the change in axial elongation rate. these effects may be due to scleral tissue remodeling produced by a change in scleral gene expression. in this study, the authors investigated the time course of changes in scleral mrna levels for selected proteins during the development of form depriva ... | 2002 | 12091398 |
| parameter optimized surfaces (pops): analysis of key interactions and conformational changes in the ribosome. | we present a new method for the calculation of solvent accessible surface areas at the atomic and residue levels, which we call parameter optimized surfaces (pops-a and pops-r ). atomic and residue areas (the latter simulated with a single sphere centered at the c(alpha)s atom for amino acids and at the p atom for nucleotides) have been optimized versus accurate all-atoms methods. we concentrated on an analytical formula for the approximation of solvent accessibilities. the formula is simple, ea ... | 2002 | 12087181 |
| trilogy: discovery of sequence-structure patterns across diverse proteins. | we describe a new computer program, trilogy, for the automated discovery of sequence-structure patterns in proteins. trilogy implements a pattern discovery algorithm that begins with an exhaustive analysis of flexible three-residue patterns; a subset of these patterns are selected as seeds for an extension process in which longer patterns are identified. a key feature of the method is explicit treatment of both the sequence and structure components of these motifs: each trilogy pattern is a pair ... | 2002 | 12084910 |
| integration of dna ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms. | association studies using common sequence variants or single nucleotide polymorphisms (snps) may provide a powerful approach to dissect the genetic inheritance of common complex traits. such studies necessitate the development of cost-effective, high throughput technologies for scoring snps. the method described in this paper for the co-detection of both alleles of a snp in a single homogeneous reaction combines the specificity of a high fidelity dna ligation step with the power of rolling circl ... | 2002 | 12060698 |
| tracing the evolution of rna structure in ribosomes. | the elucidation of ribosomal structure has shown that the function of ribosomes is fundamentally confined to dynamic interactions established between the rna components of the ribosomal ensemble. these findings now enable a detailed analysis of the evolution of ribosomal rna (rrna) structure. the origin and diversification of rrna was studied here using phylogenetic tools directly at the structural level. a rooted universal tree was reconstructed from the combined secondary structures of large ( ... | 2002 | 12034847 |
| high affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands. | we have isolated 2'-fluoro-substituted rna aptamers that bind to streptavidin (sa) with an affinity around 7 +/- 1.8 nm, comparable with that of recently described peptide aptamers. binding to sa was not prevented by prior saturation with biotin, enabling nucleic acid aptamers to form useful ternary complexes. mutagenesis, secondary structure analysis, ribonuclease footprinting and deletion analysis provided evidence for the essential structural features of sa-binding aptamers. in order to provi ... | 2002 | 12000850 |
| the accessory subunit of dna polymerase gamma is essential for mitochondrial dna maintenance and development in drosophila melanogaster. | dna polymerase gamma, pol gamma, is the key replicative enzyme in animal mitochondria. the drosophila enzyme is a heterodimer comprising catalytic and accessory subunits of 125 kda and 35 kda, respectively. both subunits have been cloned and characterized in a variety of model systems, and genetic mutants of the catalytic subunit were first identified in drosophila, as chemically induced mutations that disrupt larval behavior (tamas). mutations in the gene encoding the accessory subunit have not ... | 2002 | 11917141 |
| 5s ribosomal rna database. | ribosomal 5s rna (5s rrna) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. it is thought to enhance protein synthesis by stabilization of a ribosome structure. this paper presents the updated database of 5s rrna and their genes (5s rdna). its short characteristics are presented in the introduction. the database contains 2280 primary structures of 5s rrna and 5s rrna genes. these include 536 eu ... | 2002 | 11752286 |
| the european database on small subunit ribosomal rna. | the european database on ssu rrna can be consulted via the world wideweb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal rna sequences. sequences are provided in aligned format. the alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also av ... | 2002 | 11752288 |
| mmdb: entrez's 3d-structure database. | three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. the goal of entrez's 3d-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. to this end entrez's search engine provides three powerful features. (i) sequence and structure neighbors; one may select all sequences similar to one of ... | 2002 | 11752307 |
| toward an understanding of the structural basis of translation. | the recently solved x-ray crystal structures of the ribosome have provided opportunities for studying the molecular basis of translation with a variety of methods including cryo-electron microscopy - where maps give the first glimpses of ribosomal evolution - and fluorescence spectroscopy techniques. | 2003 | 14659007 |
| position of eukaryotic initiation factor eif1 on the 40s ribosomal subunit determined by directed hydroxyl radical probing. | eukaryotic initiation factor (eif) eif1 maintains the fidelity of initiation codon selection by enabling 43s complexes to reject codon-anticodon mismatches, to recognize the initiation codon context, and to discriminate against establishing a codon-anticodon interaction with augs located <8 nt from the 5'-end of mrna. to understand how eif1 plays its discriminatory role, we determined its position on the 40s ribosomal subunit using directed hydroxyl radical cleavage. the cleavage of 18s rrna in ... | 2003 | 14600024 |
| solvation change and ion release during aminoacylation by aminoacyl-trna synthetases. | discrimination between cognate and non-cognate trnas by aminoacyl-trna synthetases occurs at several steps of the aminoacylation pathway. we have measured changes of solvation and counter-ion distribution at various steps of the aminoacylation pathway of glutamyl- and glutaminyl-trna synthetases. the decrease in the association constant with increasing kcl concentration is relatively small for cognate trna binding when compared to known dna-protein interactions. the electro-neutral nature of the ... | 2003 | 14530451 |
| over-expression of interleukin 10 in mucosal t cells of patients with active ulcerative colitis. | ulcerative colitis (uc), a chronic inflammatory bowel disease, exhibits pronounced increase of t lymphocytes in the inflamed mucosa. to understand the role of intestinal t lymphocytes in the pathogenesis of uc their cytokine production in the mucosa was analysed. intestinal t lymphocytes of uc, crohn's disease and control patients were analysed for cytokine mrna levels by real-time quantitative reverse transcription-polymerase chain reaction (rt-pcr) directly after isolation without in vitro sti ... | 2003 | 12974765 |
| biochemical characterization of the kink-turn rna motif. | rna, which acts as a medium for transmitting genetic information, plays a variety of roles in a cell. as with proteins, elucidation of the three- dimensional (3d) structures of rnas is important for understanding their various roles. determination of the atomic structures of crystallized ribosome has enabled the identification of previously unknown rna structural motifs. the kink-turn (k-turn or ga) motif, which causes a sharp bend in an rna double helix, was identified as one of these structura ... | 2003 | 14500816 |
| rna structure comparison, motif search and discovery using a reduced representation of rna conformational space. | given the wealth of new rna structures and the growing list of rna functions in biology, it is of great interest to understand the repertoire of rna folding motifs. the ability to identify new and known motifs within novel rna structures, to compare tertiary structures with one another and to quantify the characteristics of a given rna motif are major goals in the field of rna research; however, there are few systematic ways to address these issues. using a novel approach for visualizing and mat ... | 2003 | 12907716 |
| trna synthetase paralogs: evolutionary links in the transition from trna-dependent amino acid biosynthesis to de novo biosynthesis. | | 2003 | 12913115 |
| pops: a fast algorithm for solvent accessible surface areas at atomic and residue level. | pops (parameter optimsed surfaces) is a new method to calculate solvent accessible surface areas, which is based on an empirically parameterisable analytical formula and fast to compute. atomic and residue areas (the latter represented by a single sphere centered on the c(alpha) atom of amino acids and at the p atom of nucleotides) have been optimised versus accurate all-atom methods. the parameterisation has been derived from a selected dataset of proteins and nucleic acids of different sizes a ... | 2003 | 12824328 |
| the long-range electrostatic interactions control trna-aminoacyl-trna synthetase complex formation. | in most cases aminoacyl-trna synthetases (aarss) are negatively charged, as are the trna substrates. it is apparent that there are driving forces that provide a long-range attraction between like charge aars and trna, and ensure formation of "close encounters." based on numerical solutions to the nonlinear poisson-boltzmann equation, we evaluated the electrostatic potential generated by different aarss. the 3d-isopotential surfaces calculated for different aarss at 0.01 kt/e contour level reveal ... | 2003 | 12761395 |
| unified two-metal mechanism of rna synthesis and degradation by rna polymerase. | in dna-dependent rna polymerases, reactions of rna synthesis and degradation are performed by the same active center (in contrast to dna polymerases in which they are separate). we propose a unified catalytic mechanism for multisubunit rna polymerases based on the analysis of its 3'-5' exonuclease reaction in the context of crystal structure. the active center involves a symmetrical pair of mg(2+) ions that switch roles in synthesis and degradation. one ion is retained permanently and the other ... | 2003 | 12727889 |
| atom depth as a descriptor of the protein interior. | atom depth, defined as the distance (dpx, a) of a nonhydrogen atom from its closest solvent-accessible protein neighbor, provides a simple but precise description of the protein interior. mean residue depths can be easily computed and are very sensitive to structural features. from the analysis of the average and maximum atom depths of a set of 136 protein structures, we derive a limit of approximately 200 residues for protein and protein domain size. the average and maximum atom depths in a pro ... | 2003 | 12668463 |
| deep trefoil knot implicated in rna binding found in an archaebacterial protein. | | 2003 | 12486711 |
| structural classification of zinc fingers: survey and summary. | zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation and apoptosis. zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic aci ... | 2003 | 12527760 |
| interstice mutations that block site-to-site translocation of a misactivated amino acid bound to a class i trna synthetase. | class i aminoacyl-trna synthetases catalyze editing reactions that prevent ambiguity from entering the genetic code. misactivated amino acids are translocated in cis from the active site for aminoacylation to the center for editing, located approximately 30 a away. mutational analysis has functionally separated the two sites by creating mutations that disrupt the catalytic center for editing but not for aminoacylation and vice versa. what is not known is whether translocation per se can be disru ... | 2003 | 12515858 |
| the identification of novel rna structural motifs using compadres: an automated approach to structural discovery. | recurring rna structural motifs are important sites of tertiary interaction and as such, are integral to rna macromolecular structure. although numerous rna motifs have been classified and characterized, the identification of new motifs is of great interest. in this study, we discovered four new conformationally recurring motifs: the pi-turn, the omega-turn, the alpha-loop and the c2'-endo mediated flipped adenosine motif. not only do they have complex and interesting structures, but they partic ... | 2004 | 15608296 |
| 4scopmap: automated assignment of protein structures to evolutionary superfamilies. | inference of remote homology between proteins is very challenging and remains a prerogative of an expert. thus a significant drawback to the use of evolutionary-based protein structure classifications is the difficulty in assigning new proteins to unique positions in the classification scheme with automatic methods. to address this issue, we have developed an algorithm to map protein domains to an existing structural classification scheme and have applied it to the scop database. | 2004 | 15598351 |
| correspondence between anomalous m- and deltacp-values in protein folding. | proteins folding according to a classical two-state system characteristically show v-shaped chevron plots. we have previously interpreted the symmetrically curved chevron plot of the protein u1a as denaturant-dependent movements in the position of the transition state ensemble (tse). s6, a structural analog of u1a, shows a classical v-shaped chevron plot indicative of straightforward two-state kinetics, but the mutant la30 has a curved unfolding limb, which is most consistent with tse mobility. ... | 2004 | 15557266 |
| the driving force for molecular evolution of translation. | it is widely argued that protein synthesis evolved out of an rna world, in which catalytic and other biological functions now carried out by proteins were performed by rnas. however, it is not clear what selective advantage would have provided the driving force for evolution of a primitive translation apparatus, because of the unlikelihood that rudimentary polypeptides would have contributed sufficiently useful biological functions. here, i suggest that the availability of even simple peptides c ... | 2004 | 15547132 |
| chloroplast elongation factor ts pro-protein is an evolutionarily conserved fusion with the s1 domain-containing plastid-specific ribosomal protein-7. | the components of chloroplast translation are similar to those of prokaryotic translation but contain some additional unique features. proteomic analysis of the chlamydomonas reinhardtii chloroplast ribosome identified an s1-like protein, plastid-specific ribosomal protein-7 (psrp-7), as a stoichiometric component of the 30s subunit. here, we report that psrp-7 is part of a polyprotein that contains psrp-7 on its amino end and two translation elongation factor ts (ef-ts) domains at the carboxy e ... | 2004 | 15548736 |
| shear rate moderates community diversity in freshwater biofilms. | the development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. however, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. we hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. in order to study this hypothesis, freshwater biofilms were ... | 2004 | 15574945 |
| helical packing patterns in membrane and soluble proteins. | this article presents the results of a detailed analysis of helix-helix interactions in membrane and soluble proteins. a data set of interacting pairs of helices in membrane proteins of known structure was constructed and a structure alignment algorithm was used to identify pairs of helices in soluble proteins that superimpose well with pairs of helices in the membrane-protein data set. most helix pairs in membrane proteins are found to have a significant number of structural homologs in soluble ... | 2004 | 15465852 |
| pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. | polymerase chain reaction (pcr)-based assays can target either dna (the genome) or rna (the transcriptome). targeting the genome generates robust data that are informative and, most importantly, generally applicable. this is because the information contained within the genome is context-independent; i.e., generally, every normal cell contains the same dna sequence--the same mutations and polymorphisms. the transcriptome, on the other hand, is context-dependent; i.e., the mrna complement and leve ... | 2004 | 15331581 |
| bayesfold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned rna sequences. | bayesfold is a web application that folds an alignment of closely related sequences and evaluates hypotheses about their shared structure. it uses bayes's theorem to combine information from several sources, including chemical mapping (if available), thermodynamic folding, and observed sequence variations. its method provides a rational basis for integrating results, even when these methods conflict. on a gapped alignment of 86 trnaphe sequences each 77 bases long, bayesfold takes 31 sec to perf ... | 2004 | 15317972 |
| structure of the photolyase-like domain of cryptochrome 1 from arabidopsis thaliana. | signals generated by cryptochrome (cry) blue-light photoreceptors are responsible for a variety of developmental and circadian responses in plants. the crys are also identified as circadian blue-light photoreceptors in drosophila and components of the mammalian circadian clock. these flavoproteins all have an n-terminal domain that is similar to photolyase, and most have an additional c-terminal domain of variable length. we present here the crystal structure of the photolyase-like domain of cry ... | 2004 | 15299148 |
| application of sparse nmr restraints to large-scale protein structure prediction. | the protein structure prediction algorithm touchstonex that uses sparse distance restraints derived from nmr nuclear overhauser enhancement (noe) data to predict protein structures at low-to-medium resolution was evaluated as follows: first, a representative benchmark set of the protein data bank library consisting of 1365 proteins up to 200 residues was employed. using n/8 simulated long-range restraints, where n is the number of residues, 1023 (75%) proteins were folded to a c(alpha) root-mean ... | 2004 | 15298926 |
| sequence-specific cleavage of small-subunit (ssu) rrna with oligonucleotides and rnase h: a rapid and simple approach to ssu rrna-based quantitative detection of microorganisms. | a rapid and simple approach to the small-subunit (ssu) rrna-based quantitative detection of a specific group of microorganisms in complex ecosystems has been developed. the method employs sequence-specific cleavage of rrna molecules with oligonucleotides and rnase h. defined mixtures of ssu rrnas were mixed with an oligonucleotide (referred to as a "scissor probe") that was specifically designed to hybridize with a particular site of targeted rrna and were subsequently digested with rnase h to p ... | 2004 | 15184170 |
| three-dimensional motifs from the scor, structural classification of rna database: extruded strands, base triples, tetraloops and u-turns. | release 2.0.1 of the structural classification of rna (scor) database, http://scor.lbl.gov, contains a classification of the internal and hairpin loops in a comprehensive collection of 497 nmr and x-ray rna structures. this report discusses findings of the classification that have not been reported previously. the scor database contains multiple examples of a newly described rna motif, the extruded helical single strand. internal loop base triples are classified in scor according to their three- ... | 2004 | 15121895 |
| structural basis of the interaction between the aaa atpase p97/vcp and its adaptor protein p47. | the aaa atpase p97/vcp is involved in many cellular events including ubiquitin-dependent processes and membrane fusion. in the latter, the p97 adaptor protein p47 is of central importance. in order to provide insight into the molecular basis of p97 adaptor binding, we have determined the crystal structure of p97 nd1 domains complexed with p47 c-terminal domain at 2.9 a resolution. the structure reveals that the p47 ubiquitin regulatory x domain (ubx) domain interacts with the p97 n domain via a ... | 2004 | 14988733 |
| the kink-turn motif in rna is dimorphic, and metal ion-dependent. | the kink-turn (k-turn) is a new motif in rna structure that was identified by examination of the crystal structures of the ribosome. we examined the structural and dynamic properties of this element in free solution. the k-turn rna exists in a dynamic equilibrium between a tightly kinked conformation and a more open structure similar to a simple bulge bend. the highly kinked form is stabilized by the noncooperative binding of metal ions, but a significant population of the less-kinked form is pr ... | 2004 | 14730024 |
| unscrambling an egg: protein disaggregation by aaa+ proteins. | aprotein quality control system, consisting of molecular chaperones and proteases, controls the folding status of proteins and prevents the aggregation of misfolded proteins by either refolding or degrading aggregation-prone species. during severe stress conditions this protection system can be overwhelmed by high substrate load, resulting in the formation of protein aggregates. in such emergency situations, hsp104/clpb becomes a key player for cell survival, as it has the extraordinary capacity ... | 2004 | 14728719 |
| estimation of phylogeny using a general markov model. | the non-homogeneous model of nucleotide substitution proposed by barry and hartigan (stat sci, 2: 191-210) is the most general model of dna evolution assuming an independent and identical process at each site. we present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. the log likelihood values returned by programs based on the f84 model (j mol evol, 29: 170-179), the gener ... | 2005 | 19325854 |
| estimation of phylogeny using a general markov model. | the non-homogeneous model of nucleotide substitution proposed by barry and hartigan (stat sci, 2: 191-210) is the most general model of dna evolution assuming an independent and identical process at each site. we present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. the log likelihood values returned by programs based on the f84 model (j mol evol, 29: 170-179), the gener ... | 2005 | 19325854 |
| size matters: a view of selenocysteine incorporation from the ribosome. | this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ... | 2005 | 16416259 |
| size matters: a view of selenocysteine incorporation from the ribosome. | this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ... | 2005 | 16416259 |
| the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results. | the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ... | 2005 | 16371706 |
| the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results. | the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ... | 2005 | 16371706 |
| the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih. | eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ... | 2005 | 16362046 |
| the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih. | eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ... | 2005 | 16362046 |