Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| the bridge helix coordinates movements of modules in rna polymerase. | the rna polymerase 'bridge helix' is a metastable α-helix that spans the leading edge of the enzyme active-site cleft. a new study published in bmc biology reveals surprising tolerance to helix-disrupting changes in a region previously thought crucial for translocation, and suggests roles for two hinge-like segments of the bridge helix in coordinating modules that move during the nucleotide-addition cycle. | 2010 | 21114873 |
| structural basis of molecular recognition of the leishmania small hydrophilic endoplasmic reticulum-associated protein (sherp) at membrane surfaces. | the 57-residue small hydrophilic endoplasmic reticulum-associated protein (sherp) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, leishmania major, the causative agent of human cutaneous leishmaniasis. previous studies have demonstrated that sherp localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests ... | 2010 | 21106528 |
| structural basis of molecular recognition of the leishmania small hydrophilic endoplasmic reticulum-associated protein (sherp) at membrane surfaces. | the 57-residue small hydrophilic endoplasmic reticulum-associated protein (sherp) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, leishmania major, the causative agent of human cutaneous leishmaniasis. previous studies have demonstrated that sherp localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests ... | 2010 | 21106528 |
| interaction of calmodulin with sec61α limits ca2+ leakage from the endoplasmic reticulum. | in eukaryotes, protein transport into the endoplasmic reticulum (er) is facilitated by a protein-conducting channel, the sec61 complex. the presence of large, water-filled pores with uncontrolled ion permeability, as formed by sec61 complexes in the er membrane, would seriously interfere with the regulated release of calcium from the er lumen into the cytosol, an essential mechanism for intracellular signalling. we identified a calmodulin (cam)-binding motif in the cytosolic n-terminus of mammal ... | 2010 | 21102557 |
| interaction of calmodulin with sec61α limits ca2+ leakage from the endoplasmic reticulum. | in eukaryotes, protein transport into the endoplasmic reticulum (er) is facilitated by a protein-conducting channel, the sec61 complex. the presence of large, water-filled pores with uncontrolled ion permeability, as formed by sec61 complexes in the er membrane, would seriously interfere with the regulated release of calcium from the er lumen into the cytosol, an essential mechanism for intracellular signalling. we identified a calmodulin (cam)-binding motif in the cytosolic n-terminus of mammal ... | 2010 | 21102557 |
| rsga releases rbfa from 30s ribosome during a late stage of ribosome biosynthesis. | rsga is a 30s ribosomal subunit-binding gtpase with an unknown function, shortage of which impairs maturation of the 30s subunit. we identified multiple gain-of-function mutants of escherichia coli rbfa, the gene for a ribosome-binding factor, that suppress defects in growth and maturation of the 30s subunit of an rsga-null strain. these mutations promote spontaneous release of rbfa from the 30s subunit, indicating that cellular disorders upon depletion of rsga are due to prolonged retention of ... | 2010 | 21102555 |
| rsga releases rbfa from 30s ribosome during a late stage of ribosome biosynthesis. | rsga is a 30s ribosomal subunit-binding gtpase with an unknown function, shortage of which impairs maturation of the 30s subunit. we identified multiple gain-of-function mutants of escherichia coli rbfa, the gene for a ribosome-binding factor, that suppress defects in growth and maturation of the 30s subunit of an rsga-null strain. these mutations promote spontaneous release of rbfa from the 30s subunit, indicating that cellular disorders upon depletion of rsga are due to prolonged retention of ... | 2010 | 21102555 |
| synonymous but not the same: the causes and consequences of codon bias. | despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. as a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. ongoing work to quantify the dynamics of initiation an ... | 2010 | 21102527 |
| synonymous but not the same: the causes and consequences of codon bias. | despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. as a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. ongoing work to quantify the dynamics of initiation an ... | 2010 | 21102527 |
| diversity of the early step of the futalosine pathway. | we recently demonstrated that the futalosine pathway was operating in some bacteria for the biosynthesis of menaquinone and that futalosine was converted into dehypoxanthinyl futalosine (dhfl) by an mqnb of thermus thermophilus. in this study, we found that aminodeoxyfutalosine, which has adenine instead of hypoxanthine in futalosine, was directly converted into dhfl by an mqnb of helicobacter pylori. therefore, this step is potentially an attractive target for the development of specific anti-h ... | 2010 | 21098241 |
| co impedes superfast o2 binding in ba3 cytochrome oxidase from thermus thermophilus. | kinetic studies of heme-copper terminal oxidases using the co flow-flash method are potentially compromised by the fate of the photodissociated co. in this time-resolved optical absorption study, we compared the kinetics of dioxygen reduction by ba(3) cytochrome c oxidase from thermus thermophilus in the absence and presence of co using a photolabile o(2)-carrier. a novel double-laser excitation is introduced in which dioxygen is generated by photolyzing the o(2)-carrier with a 355 nm laser puls ... | 2010 | 21097703 |
| thermus thermophilus glycoside hydrolase family 57 branching enzyme: crystal structure, mechanism of action, and products formed. | branching enzyme (ec 2.4.1.18; glycogen branching enzyme; gbe) catalyzes the formation of α1,6-branching points in glycogen. until recently it was believed that all gbes belong to glycoside hydrolase family 13 (gh13). here we describe the cloning and expression of the thermus thermophilus family gh57-type gbe and report its biochemical properties and crystal structure at 1.35-å resolution. the enzyme has a central (β/α)(7)-fold catalytic domain a with an inserted domain b between β2 and α5 and a ... | 2010 | 21097495 |
| pseudouridine at position 55 in trna controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium thermus thermophilus. | pseudouridine at position 55 (ψ55) in eubacterial trna is produced by trub. to clarify the role of the ψ55 modification, we constructed a trub gene disruptant (δtrub) strain of thermus thermophilus which is an extreme-thermophilic eubacterium. unexpectedly, the δtrub strain exhibited severe growth retardation at 50 °c. we assumed that these phenomena might be caused by lack of rna chaperone activity of trub, which was previously hypothetically proposed by others. to confirm this idea, we replace ... | 2010 | 21097467 |
| identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms. | fumarase catalyzes the reversible hydration of fumarate to l-malate and is a key enzyme in the tricarboxylic acid (tca) cycle and in amino acid metabolism. fumarase is also used for the industrial production of l-malate from the substrate fumarate. thermostable and high-activity fumarases from organisms that inhabit extreme environments may have great potential in industry, biotechnology, and basic research. the marine environment is highly complex and considered one of the main reservoirs of mi ... | 2010 | 21092234 |
| assembling networks of microbial genomes using linear programming. | microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem. | 2010 | 21092133 |
| carbon flux rerouting during mycobacterium tuberculosis growth arrest. | a hallmark of the mycobacterium tuberculosis life cycle is the pathogen's ability to switch between replicative and non-replicative states in response to host immunity. transcriptional profiling by qpcr of ∼ 50 m. tuberculosis genes involved in central and lipid metabolism revealed a re-routing of carbon flow associated with bacterial growth arrest during mouse lung infection. carbon rerouting was marked by a switch from metabolic pathways generating energy and biosynthetic precursors in growing ... | 2010 | 21091505 |
| role of recj-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation. | recj-like proteins belonging to the dhh family have been proposed to function as oligoribonucleases and 3'-phosphoadenosine 5'-phosphate (pap) phosphatases in bacteria and archaea, which do not have orn (oligoribonuclease) and cysq (pap phosphatase) homologs. in this study, we analyzed the biochemical and physiological characterization of the recj-like protein ttha0118 from thermus thermophilus hb8. ttha0118 had high enzymatic activity as an oligodeoxyribonucleotide- and oligoribonucleotide-spec ... | 2010 | 21087930 |
| the role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase. | the oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. the synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. the present study used molecular dynamics and brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (trps). trps u ... | 2010 | 21085641 |
| product-assisted catalysis as the basis of the reaction specificity of threonine synthase. | threonine synthase (ts), which is a pyridoxal 5'-phosphate (plp)-dependent enzyme, catalyzes the elimination of the γ-phosphate group from o-phospho-l-homoserine (ophs) and the subsequent addition of water at cβ to form l-threonine. the catalytic course of ts is the most complex among the plp enzymes, and it is an intriguing problem how the elementary steps are controlled in ts to carry out selective reactions. when l-vinylglycine was added to thermus thermophilus hb8 ts in the presence of phosp ... | 2010 | 21084312 |
| effects of site-directed mutagenesis of mgla on motility and swarming of myxococcus xanthus. | the mgla gene from the bacterium myxococcus xanthus encodes a 22kda protein related to the ras superfamily of monomeric gtpases. mgla is required for the normal function of a-motility (adventurous), s-motility (social), fruiting body morphogenesis, and sporulation. mgla and its homologs differ from all eukaryotic and other prokaryotic gtpases because they have a threonine (thr78) in place of the highly conserved aspartate residue of the consensus pm3 (phosphate-magnesium binding) region. to iden ... | 2010 | 21083931 |
| idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of e. coli phenylalanyl-trna synthetase complexed with phenylalanine and amp. | the crystal structure of phenylalanyl-trna synthetase from e. coli (ecphers), a class ii aminoacyl-trna synthetase, complexed with phenylalanine and amp was determined at 3.05 å resolution. ecphers is a (αβ)₂ heterotetramer: the αβ heterodimer of ecphers consists of 11 structural domains. three of them: the n-terminus, a1 and a2 belong to the α-subunit and b1-b8 domains to the β subunit. the structure of ecphers revealed that architecture of four helix-bundle interface, characteristic of class i ... | 2011 | 21082706 |
| idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of e. coli phenylalanyl-trna synthetase complexed with phenylalanine and amp. | the crystal structure of phenylalanyl-trna synthetase from e. coli (ecphers), a class ii aminoacyl-trna synthetase, complexed with phenylalanine and amp was determined at 3.05 å resolution. ecphers is a (αβ)₂ heterotetramer: the αβ heterodimer of ecphers consists of 11 structural domains. three of them: the n-terminus, a1 and a2 belong to the α-subunit and b1-b8 domains to the β subunit. the structure of ecphers revealed that architecture of four helix-bundle interface, characteristic of class i ... | 2011 | 21082706 |
| the mycobacterium tuberculosis drugome and its polypharmacological implications. | we report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. the approach has been applied to the genome of mycobacterium tuberculosis (m.tb), the causative agent of one of today's most widely spread infectious diseases. the resulting drug-target interaction network for all structurally characterized approved drugs bound to putative m.tb receptors, we refer to as the ' ... | 2010 | 21079673 |
| application of a high-throughput fluorescent acetyltransferase assay to identify inhibitors of homocitrate synthase. | homocitrate synthase (hcs) catalyzes the first step of l-lysine biosynthesis in fungi by condensing acetyl-coenzyme a and 2-oxoglutarate to form 3r-homocitrate and coenzyme a. due to its conservation in pathogenic fungi, hcs has been proposed as a candidate for antifungal drug design. here we report the development and validation of a robust fluorescent assay for hcs that is amenable to high-throughput screening for inhibitors in vitro. using this assay, schizosaccharomyces pombe hcs was screene ... | 2010 | 21073853 |
| application of a high-throughput fluorescent acetyltransferase assay to identify inhibitors of homocitrate synthase. | homocitrate synthase (hcs) catalyzes the first step of l-lysine biosynthesis in fungi by condensing acetyl-coenzyme a and 2-oxoglutarate to form 3r-homocitrate and coenzyme a. due to its conservation in pathogenic fungi, hcs has been proposed as a candidate for antifungal drug design. here we report the development and validation of a robust fluorescent assay for hcs that is amenable to high-throughput screening for inhibitors in vitro. using this assay, schizosaccharomyces pombe hcs was screene ... | 2010 | 21073853 |
| psortdb--an expanded, auto-updated, user-friendly protein subcellular localization database for bacteria and archaea. | the subcellular localization (scl) of a microbial protein provides clues about its function, its suitability as a drug, vaccine or diagnostic target and aids experimental design. the first version of psortdb provided a valuable resource comprising a data set of proteins of known scl (epsortdb) as well as pre-computed scl predictions for proteomes derived from complete bacterial genomes (cpsortdb). psortdb 2.0 (http://db.psort.org) extends user-friendly functionalities, significantly expands epso ... | 2010 | 21071402 |
| psortdb--an expanded, auto-updated, user-friendly protein subcellular localization database for bacteria and archaea. | the subcellular localization (scl) of a microbial protein provides clues about its function, its suitability as a drug, vaccine or diagnostic target and aids experimental design. the first version of psortdb provided a valuable resource comprising a data set of proteins of known scl (epsortdb) as well as pre-computed scl predictions for proteomes derived from complete bacterial genomes (cpsortdb). psortdb 2.0 (http://db.psort.org) extends user-friendly functionalities, significantly expands epso ... | 2010 | 21071402 |
| the roles of rna in the synthesis of protein. | the crystal structures of ribosomes that have been obtained since 2000 have transformed our understanding of protein synthesis. in addition to proving that rna is responsible for catalyzing peptide bond formation, these structures have provided important insights into the mechanistic details of how the ribosome functions. this review emphasizes what has been learned about the mechanism of peptide bond formation, the antibiotics that inhibit ribosome function, and the fidelity of decoding. | 2011 | 21068149 |
| the c-terminal domain of the mutl homolog from neisseria gonorrhoeae forms an inverted homodimer. | the mismatch repair (mmr) pathway serves to maintain the integrity of the genome by removing mispaired bases from the newly synthesized strand. in e. coli, muts, mutl and muth coordinate to discriminate the daughter strand through a mechanism involving lack of methylation on the new strand. this facilitates the creation of a nick by muth in the daughter strand to initiate mismatch repair. many bacteria and eukaryotes, including humans, do not possess a homolog of muth. although the exact strateg ... | 2010 | 21060849 |
| packaging hiv virion components through dynamic equilibria of a human trna synthetase. | aminoacyl trna synthetases, components of the translation apparatus, have alternative functions outside of translation. the structural and mechanistic basis of these alternative functions is of great interest. as an example, reverse transcription of the hiv genome is primed by a human lysine-specific trna (trna(lys3)) that is packaged (into the virion) by the hiv gag protein with lysyl-trna synthetase (lysrs). not understood is the structural basis for simultaneous packaging of trna(lys3), lysrs ... | 2010 | 21058683 |
| characterization of cytochrome p450 monooxygenase cyp154h1 from the thermophilic soil bacterium thermobifida fusca. | cytochrome p450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. we have cloned the gene for a new cytochrome p450 monooxygenase, named cyp154h1, from the moderately thermophilic soil bacterium thermobifida fusca. the enzyme was overexpressed in escherichia coli at up to 14% of total soluble protein and purified to homogeneity in three steps. cyp154h1 activity was reconstituted using putidaredoxin reductase and putidare ... | 2010 | 21057946 |
| characterization of cytochrome p450 monooxygenase cyp154h1 from the thermophilic soil bacterium thermobifida fusca. | cytochrome p450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. we have cloned the gene for a new cytochrome p450 monooxygenase, named cyp154h1, from the moderately thermophilic soil bacterium thermobifida fusca. the enzyme was overexpressed in escherichia coli at up to 14% of total soluble protein and purified to homogeneity in three steps. cyp154h1 activity was reconstituted using putidaredoxin reductase and putidare ... | 2010 | 21057946 |
| yaej is a novel ribosome-associated protein in escherichia coli that can hydrolyze peptidyl-trna on stalled ribosomes. | in bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger rna (tmrna). in the absence of tmrna, however, there is evidence that stalled ribosomes are released from non-stop mrnas. here, we show a novel ribosome rescue system mediated by a small basic protein, yaej, from escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (rf). in vitro translation experiments us ... | 2010 | 21051357 |
| yaej is a novel ribosome-associated protein in escherichia coli that can hydrolyze peptidyl-trna on stalled ribosomes. | in bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger rna (tmrna). in the absence of tmrna, however, there is evidence that stalled ribosomes are released from non-stop mrnas. here, we show a novel ribosome rescue system mediated by a small basic protein, yaej, from escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (rf). in vitro translation experiments us ... | 2010 | 21051357 |
| temporal regulation of gene expression of the thermus thermophilus bacteriophage p23-45. | regulation of gene expression during infection of the thermophilic bacterium thermus thermophilus hb8 with the bacteriophage p23-45 was investigated. macroarray analysis revealed host transcription shut-off and identified three temporal classes of phage genes; early, middle and late. primer extension experiments revealed that the 5' ends of p23-45 early transcripts are preceded by a common sequence motif that likely defines early viral promoters. t. thermophilus hb8 rna polymerase (rnap) recogni ... | 2010 | 21050864 |
| quantum chemical studies of nucleic acids: can we construct a bridge to the rna structural biology and bioinformatics communities? | in this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and rna structural bioinformatics. our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. we identify research questions amenable to th ... | 2010 | 21049899 |
| identification, cloning, and characterization of l-phenylserine dehydrogenase from pseudomonas syringae nk-15. | the gene encoding d-phenylserine dehydrogenase from pseudomonas syringae nk-15 was identified, and a 9,246-bp nucleotide sequence containing the gene was sequenced. six orfs were confirmed in the sequenced region, four of which were predicted to form an operon. a homology search of each orf predicted that orf3 encoded l-phenylserine dehydrogenase. hence, orf3 was cloned and overexpressed in escherichia coli cells and recombinant orf3 was purified to homogeneity and characterized. the purified or ... | 2010 | 21048868 |
| fungal laccases: production, function, and applications in food processing. | laccases are increasingly being used in food industry for production of cost-effective and healthy foods. to sustain this trend widespread availability of laccase and efficient production systems have to be developed. the present paper delineate the recent developments that have taken place in understanding the role of laccase action, efforts in overexpression of laccase in heterologous systems, and various cultivation techniques that have been developed to efficiently produce laccase at the ind ... | 2010 | 21048859 |
| crystallization and preliminary x-ray diffraction analysis of human cytosolic seryl-trna synthetase. | human cytosolic seryl-trna synthetase (hsserrs) is responsible for the covalent attachment of serine to its cognate trna(ser). significant differences between the amino-acid sequences of eukaryotic, prokaryotic and archaebacterial serrss indicate that the domain composition of hsserrs differs from that of its eubacterial and archaebacterial analogues. as a consequence of an n-terminal insertion and a c-terminal extra-sequence, the binding mode of trna(ser) to hsserrs is expected to differ from t ... | 2010 | 21045311 |
| structure of dihydroorotase from bacillus anthracis at 2.6 å resolution. | dihydroorotase (ec 3.5.2.3) catalyzes the reversible cyclization of n-carbamoyl-l-aspartate to l-dihydroorotate in the third step of the pyrimidine-biosynthesis pathway in bacillus anthracis. a comparison is made between the structures of dihydroorotase from four different organisms, including b. anthracis dihydroorotase, and reveals substantial variations in the active site, dimer interface and overall tertiary structure. these differences demonstrate the utility of exploring multiple structure ... | 2010 | 21045288 |
| subunit dissociation and metal binding by escherichia coli apo-manganese superoxide dismutase. | metal binding by apo-manganese superoxide dismutase (apo-mnsod) is essential for functional maturation of the enzyme. previous studies have demonstrated that metal binding by apo-mnsod is conformationally gated, requiring protein reorganization for the metal to bind. we have now solved the x-ray crystal structure of apo-mnsod at 1.9å resolution. the organization of active site residues is independent of the presence of the metal cofactor, demonstrating that protein itself templates the unusual m ... | 2010 | 21044611 |
| subunit dissociation and metal binding by escherichia coli apo-manganese superoxide dismutase. | metal binding by apo-manganese superoxide dismutase (apo-mnsod) is essential for functional maturation of the enzyme. previous studies have demonstrated that metal binding by apo-mnsod is conformationally gated, requiring protein reorganization for the metal to bind. we have now solved the x-ray crystal structure of apo-mnsod at 1.9å resolution. the organization of active site residues is independent of the presence of the metal cofactor, demonstrating that protein itself templates the unusual m ... | 2010 | 21044611 |
| inactivation of the rlud pseudouridine synthase has minimal effects on growth and ribosome function in wild-type escherichia coli and salmonella enterica. | the escherichia coli rlud gene encodes a pseudouridine synthase responsible for the pseudouridine (ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23s rrna. it has been reported that deletion of rlud in k-12 strains of e. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50s ribosomal subunit assembly and 30s-50s subunit association. suppressor mutations in the prfb and prfc genes encoding release factor 2 (rf2) and rf3 that res ... | 2010 | 21037010 |
| inactivation of the rlud pseudouridine synthase has minimal effects on growth and ribosome function in wild-type escherichia coli and salmonella enterica. | the escherichia coli rlud gene encodes a pseudouridine synthase responsible for the pseudouridine (ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23s rrna. it has been reported that deletion of rlud in k-12 strains of e. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50s ribosomal subunit assembly and 30s-50s subunit association. suppressor mutations in the prfb and prfc genes encoding release factor 2 (rf2) and rf3 that res ... | 2010 | 21037010 |
| fluorescence-based assay to measure the real-time kinetics of nucleotide incorporation during transcription elongation. | understanding the mechanism and fidelity of transcription by the rna polymerase (rnap) requires measurement of the dissociation constant (k(d)) of correct and incorrect ntps and their incorporation rate constants (k(pol)). currently, such parameters are obtained from radiometric-based assays that are both tedious and discontinuous. here, we report a fluorescence-based assay for measuring the real-time kinetics of single-nucleotide incorporation during transcription elongation. the fluorescent ad ... | 2010 | 21035457 |
| fluorescence-based assay to measure the real-time kinetics of nucleotide incorporation during transcription elongation. | understanding the mechanism and fidelity of transcription by the rna polymerase (rnap) requires measurement of the dissociation constant (k(d)) of correct and incorrect ntps and their incorporation rate constants (k(pol)). currently, such parameters are obtained from radiometric-based assays that are both tedious and discontinuous. here, we report a fluorescence-based assay for measuring the real-time kinetics of single-nucleotide incorporation during transcription elongation. the fluorescent ad ... | 2010 | 21035457 |
| the nucleotide addition cycle of rna polymerase is controlled by two molecular hinges in the bridge helix domain. | cellular rna polymerases (rnaps) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. previous work showed that kinking of a hinge region near the c-terminus of the bridge helix (bh-h(c)) plays a critical role in controlling the catalytic rate. | 2010 | 21034443 |
| ph-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase. | p-hydroxyphenylacetate (hpa) 3-hydroxylase (hpah) catalyzes the hydroxylation of hpa at the ortho-position to yield 3,4-dihydroxyphenylacetate. the enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (c(2)). c(2) catalyzes the hydroxylation of hpa using oxygen and reduced fmn as co-substrates. to date, the effects of ph on the oxygenation of the two-component monooxygenases have never been reported. here, we report the reacti ... | 2010 | 21030590 |
| ph-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase. | p-hydroxyphenylacetate (hpa) 3-hydroxylase (hpah) catalyzes the hydroxylation of hpa at the ortho-position to yield 3,4-dihydroxyphenylacetate. the enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (c(2)). c(2) catalyzes the hydroxylation of hpa using oxygen and reduced fmn as co-substrates. to date, the effects of ph on the oxygenation of the two-component monooxygenases have never been reported. here, we report the reacti ... | 2010 | 21030590 |
| molecular mechanisms of the whole dna repair system: a comparison of bacterial and eukaryotic systems. | dna is subjected to many endogenous and exogenous damages. all organisms have developed a complex network of dna repair mechanisms. a variety of different dna repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. recent studies of the fundamental mechanisms for dna repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as f ... | 2010 | 20981145 |
| cryo-em structure and rrna model of a translating eukaryotic 80s ribosome at 5.5-a resolution. | protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. although x-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80s ribosomes are lacking. using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (triticum aestivum) 80s ribosome at 5.5-å resolution. this map, together with a 6.1-å map of a saccharomyces cere ... | 2010 | 20980660 |
| pivotal roles of three conserved carboxyl residues of the nuoc (30k) segment in the structural integrity of proton-translocating nadh-quinone oxidoreductase from escherichia coli. | the prokaryotic proton-translocating nadh-quinone oxidoreductase (ndh-1) is an l-shaped membrane-bound enzyme that contains 14 subunits (nuoa-nuon or nqo1-nqo14). all subunits have their counterparts in the eukaryotic enzyme (complex i). ndh-1 consists of two domains: the peripheral arm (nuob, -c, -d, -e, -f, -g, and -i) and the membrane arm (nuoa, -h, -j, -k, -l, -m, and -n). in escherichia coli ndh-1, the hydrophilic subunits nuoc/nqo5/30k and nuod/nqo4/49k are fused together in a single polyp ... | 2010 | 20979355 |
| integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. | many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. independent studies exist on the analysis and sequence-based prediction of some of these so-called one-dimensional features. however, there is little explanation of why certain residues are predicted in a wrong structural class or with large errors in the absolute values of these features. on the other hand, membrane proteins undergo conformati ... | 2010 | 20977780 |
| biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-iv. | mammalian maspat (mitochondrial aspartate aminotransferase) is recently reported to have kat (kynurenine aminotransferase) activity and plays a role in the biosynthesis of kyna (kynurenic acid) in rat, mouse and human brains. this study concerns the biochemical and structural characterization of mouse maspat. in this study, mouse maspat cdna was amplified from mouse brain first stand cdna and its recombinant protein was expressed in an escherichia coli expression system. sixteen oxo acids were t ... | 2011 | 20977429 |
| error-prone translesion dna synthesis by escherichia coli dna polymerase iv (dinb) on templates containing 1,2-dihydro-2-oxoadenine. | escherichia coli dna polymerase iv (pol iv) is involved in bypass replication of damaged bases in dna. reactive oxygen species (ros) are generated continuously during normal metabolism and as a result of exogenous stress such as ionizing radiation. ros induce various kinds of base damage in dna. it is important to examine whether pol iv is able to bypass oxidatively damaged bases. in this study, recombinant pol iv was incubated with oligonucleotides containing thymine glycol (dtg), 5-formyluraci ... | 2010 | 20976264 |
| genomic adaptation of prokaryotic organisms at high temperature. | one of the central issues of evolutionary genomics is to find out the adaptive strategies of microorganisms to stabilize nucleic acid molecules under high temperature. thermal adaptation hypothesis gives a link between g+c content and growth temperature if there is a considerable variation of guanine and cytosine content between species. however, there has been a long-standing debate regarding the correlations between genomic gc content and optimal growth temperature (topt). we urged that adapta ... | 2010 | 20975899 |
| omnipotent role of archaeal elongation factor 1 alpha (ef1α in translational elongation and termination, and quality control of protein synthesis. | the molecular mechanisms of translation termination and mrna surveillance in archaea remain unclear. in eukaryotes, erf3 and hbs1, which are homologous to the trna carrier gtpase ef1α, respectively bind erf1 and pelota to decipher stop codons or to facilitate mrna surveillance. however, genome-wide searches of archaea have failed to detect any orthologs to both gtpases. here, we report the crystal structure of arf1 from an archaeon, aeropyrum pernix, and present strong evidence that the authenti ... | 2010 | 20974926 |
| electron tunneling in respiratory complex i. | nadh:ubiquinone oxidoreductase (complex i) plays a central role in the respiratory electron transport chain by coupling the transfer of electrons from nadh to ubiquinone to the creation of the proton gradient across the membrane necessary for atp synthesis. here the atomistic details of electronic wiring of all fe/s clusters in complex i are revealed by using the tunneling current theory and computer simulations; both density functional theory and semiempirical electronic structure methods were ... | 2010 | 20974925 |
| phosphate binding sites identification in protein structures. | nearly half of known protein structures interact with phosphate-containing ligands, such as nucleotides and other cofactors. many methods have been developed for the identification of metal ions-binding sites and some for bigger ligands such as carbohydrates, but none is yet available for the prediction of phosphate-binding sites. here we describe pfinder, a method that predicts binding sites for phosphate groups, both in the form of ions or as parts of other non-peptide ligands, in proteins of ... | 2010 | 20974634 |
| phosphate binding sites identification in protein structures. | nearly half of known protein structures interact with phosphate-containing ligands, such as nucleotides and other cofactors. many methods have been developed for the identification of metal ions-binding sites and some for bigger ligands such as carbohydrates, but none is yet available for the prediction of phosphate-binding sites. here we describe pfinder, a method that predicts binding sites for phosphate groups, both in the form of ions or as parts of other non-peptide ligands, in proteins of ... | 2010 | 20974634 |
| new functional sulfide oxidase-oxygen reductase supercomplex in the membrane of the hyperthermophilic bacterium aquifex aeolicus. | aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. it was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (h(2)s) to molecular oxygen. h(2)s is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. we have purified and characterized a novel membrane-bound multienzyme supercomplex that bring ... | 2010 | 20971847 |
| modification of 16s ribosomal rna by the ksga methyltransferase restructures the 30s subunit to optimize ribosome function. | all organisms incorporate post-transcriptional modifications into ribosomal rna, influencing ribosome assembly and function in ways that are poorly understood. the most highly conserved modification is the dimethylation of two adenosines near the 3' end of the small subunit rrna. lack of these methylations due to deficiency in the ksga methyltransferase stimulates translational errors during both the initiation and elongation phases of protein synthesis and confers resistance to the antibiotic k ... | 2010 | 20962038 |
| structure of the mycobacterium tuberculosis d-alanine:d-alanine ligase, a target of the antituberculosis drug d-cycloserine. | d-alanine:d-alanine ligase (ec 6.3.2.4; ddl) catalyzes the atp-driven ligation of two d-alanine (d-ala) molecules to form the d-alanyl:d-alanine dipeptide. this molecule is a key building block in peptidoglycan biosynthesis, making ddl an attractive target for drug development. d-cycloserine (dcs), an analog of d-ala and a prototype ddl inhibitor, has shown promise for the treatment of tuberculosis. here, we report the crystal structure of mycobacterium tuberculosis ddl at a resolution of 2.1 å. ... | 2010 | 20956591 |
| structure of the mycobacterium tuberculosis d-alanine:d-alanine ligase, a target of the antituberculosis drug d-cycloserine. | d-alanine:d-alanine ligase (ec 6.3.2.4; ddl) catalyzes the atp-driven ligation of two d-alanine (d-ala) molecules to form the d-alanyl:d-alanine dipeptide. this molecule is a key building block in peptidoglycan biosynthesis, making ddl an attractive target for drug development. d-cycloserine (dcs), an analog of d-ala and a prototype ddl inhibitor, has shown promise for the treatment of tuberculosis. here, we report the crystal structure of mycobacterium tuberculosis ddl at a resolution of 2.1 å. ... | 2010 | 20956591 |
| tmrna-smpb: a journey to the centre of the bacterial ribosome. | ribosomes mediate protein synthesis by decoding the information carried by messenger rnas (mrnas) and catalysing peptide bond formation between amino acids. when bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger rna bound to small protein b (tmrna-smpb ribonucleoprotein complex). trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. here, we present the cryo-ele ... | 2010 | 20953161 |
| biochemical characterization of individual components of the allochromatium vinosum dsrmkjop transmembrane complex aids understanding of complex function in vivo. | the dsrmkjop transmembrane complex has a most important function in dissimilatory sulfur metabolism and consists of cytoplasmic, periplasmic, and membrane integral proteins carrying fes centers and b- and c-type cytochromes as cofactors. in this study, the complex was isolated from the purple sulfur bacterium allochromatium vinosum and individual components were characterized as recombinant proteins. the two integral membrane proteins dsrm and dsrp were successfully produced in escherichia coli ... | 2010 | 20952577 |
| prediction and analysis of the modular structure of cytochrome p450 monooxygenases. | cytochrome p450 monooxygenases (cyps) form a vast and diverse family of highly variable sequences. they catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. despite their differences in sequence and substrate specificity, the structures of cyps are highly similar. although being in research focus for years, factors mediating selectivity and activity remain vague. | 2010 | 20950472 |
| the structure of kpn03535 (gi|152972051), a novel putative lipoprotein from klebsiella pneumoniae, reveals an ob-fold. | kpn03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by klebsiella pneumoniae mgh 78578. the crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the ob-fold and structurally similar to the bacterial cpx-pathway protein nlpe, single-stranded dna-binding (ssb) proteins and toxins. k. pneumoniae mgh 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pat ... | 2010 | 20944219 |
| the structure of kpn03535 (gi|152972051), a novel putative lipoprotein from klebsiella pneumoniae, reveals an ob-fold. | kpn03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by klebsiella pneumoniae mgh 78578. the crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the ob-fold and structurally similar to the bacterial cpx-pathway protein nlpe, single-stranded dna-binding (ssb) proteins and toxins. k. pneumoniae mgh 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pat ... | 2010 | 20944219 |
| visualizing the transfer-messenger rna as the ribosome resumes translation. | bacterial ribosomes stalled by truncated mrnas are rescued by transfer-messenger rna (tmrna), a dual-function molecule that contains a trna-like domain (tld) and an internal open reading frame (orf). occupying the empty a site with its tld, the tmrna enters the ribosome with the help of elongation factor tu and a protein factor called small protein b (smpb), and switches the translation to its own orf. in this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-f ... | 2010 | 20940705 |
| archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in trna modification revealed by comparative genomic analysis. | the recent discovery of protein modification by samps, ubiquitin-like (ubl) proteins from the archaeon haloferax volcanii, prompted a comprehensive comparative-genomic analysis of archaeal ubl protein genes and the genes for enzymes thought to be functionally associated with ubl proteins. this analysis showed that most archaea encode members of two major groups of ubl proteins with the β-grasp fold, the this and moad families, and indicated that the this family genes are rarely linked to genes f ... | 2010 | 20936112 |
| an arabidopsis pentatricopeptide repeat protein, suppressor of variegation7, is required for ftsh-mediated chloroplast biogenesis. | the arabidopsis (arabidopsis thaliana) yellow variegated2 (var2) mutant has green- and white-sectored leaves due to loss of var2, a subunit of the chloroplast ftsh protease/chaperone complex. suppressor screens are a valuable tool to gain insight into var2 function and the mechanism of var2 variegation. here, we report the molecular characterization of 004-003, a line in which var2 variegation is suppressed. we found that the suppression phenotype in this line is caused by lack of a chloroplast ... | 2010 | 20935174 |
| crl binds to domain 2 of σ(s) and confers a competitive advantage on a natural rpos mutant of salmonella enterica serovar typhi. | the rpos sigma factor (σ(s)) is the master regulator of the bacterial response to a variety of stresses. mutants in rpos arise in bacterial populations in the absence of stress, probably as a consequence of a subtle balance between self-preservation and nutritional competence. we characterized here one natural rpos mutant of salmonella enterica serovar typhi (ty19). we show that the rpos allele of ty19 (rpos(ty19)) led to the synthesis of a σ(s)(ty19) protein carrying a single glycine-to-valine ... | 2010 | 20935100 |
| antisense tools for functional studies of human argonaute proteins. | the argonaute proteins play essential roles in development and cellular metabolism in many organisms, including plants, flies, worms, and mammals. whereas in organisms such as caenorhabditis elegans and arabidopsis thaliana, creation of argonaute mutant strains allowed the study of their biological functions, in mammals the application of this approach is limited by its difficulty and in the specific case of ago2 gene, by the lethality of such mutation. hence, in human cells, functional studies ... | 2010 | 20935067 |
| cleavage of model substrates by archaeal rnase p: role of protein cofactors in cleavage-site selection. | rnase p is a catalytic ribonucleoprotein primarily involved in trna biogenesis. archaeal rnase p comprises a catalytic rnase p rna (rpr) and at least four protein cofactors (rpps), which function as two binary complexes (pop5•rpp30 and rpp21• rpp29). exploiting the ability to assemble a functional pyrococcus furiosus (pfu) rnase p in vitro, we examined the role of rpps in influencing substrate recognition by the rpr. we first demonstrate that pfu rpr, like its bacterial and eukaryal counterparts ... | 2010 | 20935047 |
| cleavage of model substrates by archaeal rnase p: role of protein cofactors in cleavage-site selection. | rnase p is a catalytic ribonucleoprotein primarily involved in trna biogenesis. archaeal rnase p comprises a catalytic rnase p rna (rpr) and at least four protein cofactors (rpps), which function as two binary complexes (pop5•rpp30 and rpp21• rpp29). exploiting the ability to assemble a functional pyrococcus furiosus (pfu) rnase p in vitro, we examined the role of rpps in influencing substrate recognition by the rpr. we first demonstrate that pfu rpr, like its bacterial and eukaryal counterparts ... | 2010 | 20935047 |
| r3d align: global pairwise alignment of rna 3d structures using local superpositions. | comparing 3d structures of homologous rna molecules yields information about sequence and structural variability. to compare large rna 3d structures, accurate automatic comparison tools are needed. in this article, we introduce a new algorithm and web server to align large homologous rna structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of rna molecules. local alignments are merged to form a global alignment by employing a maximum clique algorithm on ... | 2010 | 20929913 |
| hemin binds to human cytoplasmic arginyl-trna synthetase and inhibits its catalytic activity. | the free form of human cytoplasmic arginyl-trna synthetase (hcargrs) is hypothesized to participate in ubiquitin-dependent protein degradation by offering arginyl-trna(arg) to arginyl-trna transferase (ate1). we investigated the effect of hemin on hcargrs based on the fact that hemin regulates several critical proteins in the "n-end rule" protein degradation pathway. extensive biochemical evidence has established that hemin could bind to both forms of hcargrs in vitro. based on the spectral chan ... | 2010 | 20923763 |
| fundamentals of three-dimensional reconstruction from projections. | three-dimensional (3d) reconstruction of an object mass density from the set of its 2d line projections lies at a core of both single-particle reconstruction technique and electron tomography. both techniques utilize electron microscope to collect a set of projections of either multiple objects representing in principle the same macromolecular complex in an isolated form, or a subcellular structure isolated in situ. therefore, the goal of macromolecular electron microscopy is to invert the proje ... | 2010 | 20888956 |
| iron-sulfur world in aerobic and hyperthermoacidophilic archaea sulfolobus. | the general importance of the fe-s cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the fe-s cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. in the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many fe-s enzymes are produced to participate in the ... | 2010 | 20885930 |
| binding and cleavage of crispr rna by cas6. | the crispr-cas system provides many prokaryotes with acquired resistance to viruses and other mobile genetic elements. the core components of this defense system are small, host-encoded prokaryotic silencing (psi)rnas and cas (crispr-associated) proteins. invader-derived sequences within the psirnas guide cas effector proteins to recognize and silence invader nucleic acids. critical for crispr-cas defense is processing of the psirnas from the primary transcripts of the host crispr (clustered reg ... | 2010 | 20884784 |
| crystal structure analysis of bacillus subtilis ferredoxin-nadp(+) oxidoreductase and the structural basis for its substrate selectivity. | bacillus subtilis yumc encodes a novel type of ferredoxin-nadp+ oxidoreductase (fnr) with a primary sequence and oligomeric conformation distinct from those of previously known fnrs. in this study, the crystal structure of b. subtilis fnr (bsfnr) complexed with nadp+ has been determined. bsfnr features two distinct binding domains for fad and nadph in accordance with its structural similarity to escherichia coli nadph-thioredoxin reductase (tdr) and tdr-like protein from thermus thermophilus hb8 ... | 2010 | 20878669 |
| promoting rna helical stacking via a-minor junctions. | rna molecules take advantage of prevalent structural motifs to fold and assemble into well-defined 3d architectures. the a-minor junction is a class of rna motifs that specifically controls coaxial stacking of helices in natural rnas. a sensitive self-assembling supra-molecular system was used as an assay to compare several natural and previously unidentified a-minor junctions by native polyacrylamide gel electrophoresis and atomic force microscopy. this class of modular motifs follows a topolog ... | 2010 | 20876687 |
| promoting rna helical stacking via a-minor junctions. | rna molecules take advantage of prevalent structural motifs to fold and assemble into well-defined 3d architectures. the a-minor junction is a class of rna motifs that specifically controls coaxial stacking of helices in natural rnas. a sensitive self-assembling supra-molecular system was used as an assay to compare several natural and previously unidentified a-minor junctions by native polyacrylamide gel electrophoresis and atomic force microscopy. this class of modular motifs follows a topolog ... | 2010 | 20876687 |
| evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in bacillus subtilis biofilm formation. | arginine decarboxylases (adcs; ec 4.1.1.19) from four different protein fold families are important for polyamine biosynthesis in bacteria, archaea, and plants. biosynthetic alanine racemase fold (ar-fold) adc is widespread in bacteria and plants. we report the discovery and characterization of an ancestral form of the ar-fold adc in the bacterial chloroflexi and bacteroidetes phyla. the ancestral ar-fold adc lacks a large insertion found in escherichia coli and plant ar-fold adc and is more sim ... | 2010 | 20876533 |
| revisiting the structures of several antibiotics bound to the bacterial ribosome. | the increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental pr ... | 2010 | 20876130 |
| designer drugs for discerning bugs. | 2010 | 20876111 | |
| hmp binding protein thiy and hmp-p synthase thi5 are structural homologues. | the atp-binding cassette transporter system thixyz transports n-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (famp), a thiamin salvage pathway intermediate, into cells. famp is then converted to 4-amino-5-(hydroxymethyl)-2-methylpyrimidine (hmp) and recycled into the thiamin biosynthetic pathway. thiy is the periplasmic substrate binding protein of the thixyz system and delivers the substrate famp to the transmembrane domain. we report the crystal structure of bacillus halodurans thiy with ... | 2010 | 20873853 |
| histidine 197 in release factor 1 is essential for a site binding and peptide release. | class i peptide release factors 1 and 2 (rf1 and rf2, respectively) recognize the stop codons in the ribosomal decoding center and catalyze peptidyl-trna hydrolysis. high-fidelity stop codon recognition by these release factors is essential for accurate peptide synthesis and ribosome recycling. x-ray crystal structures of rf1 and rf2 bound to the ribosome have identified residues in the mrna-protein interface that appear to be critical for stop codon recognition. especially interesting is a cons ... | 2010 | 20873815 |
| fidelity in archaeal information processing. | a key element during the flow of genetic information in living systems is fidelity. the accuracy of dna replication influences the genome size as well as the rate of genome evolution. the large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. on the other hand, an increase in fidelity generally coincides with a decrease in velocity. hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fi ... | 2010 | 20871851 |
| the roles of several residues of escherichia coli dna photolyase in the highly efficient photo-repair of cyclobutane pyrimidine dimers. | escherichia coli dna photolyase is an enzyme that repairs the major kind of uv-induced lesions, cyclobutane pyrimidine dimer (cpd) in dna utilizing 350-450 nm light as energy source. the enzyme has very high photo-repair efficiency (the quantum yield of the reaction is ~0.85), which is significantly greater than many model compounds that mimic photolyase. this suggests that some residues of the protein play important roles in the photo-repair of cpd. in this paper, we have focused on several res ... | 2010 | 20871655 |
| preparation and high-resolution microscopy of gold cluster labeled nucleic acid conjugates and nanodevices. | nanogold and undecagold are covalently linked gold cluster labels which enable the identification and localization of biological components with molecular precision and resolution. they can be prepared with different reactivities, which means they can be conjugated to a wide variety of molecules, including nucleic acids, at specific, unique sites. the location of these sites can be synthetically programmed in order to preserve the binding affinity of the conjugate and impart novel characteristic ... | 2010 | 20869258 |
| preparation and high-resolution microscopy of gold cluster labeled nucleic acid conjugates and nanodevices. | nanogold and undecagold are covalently linked gold cluster labels which enable the identification and localization of biological components with molecular precision and resolution. they can be prepared with different reactivities, which means they can be conjugated to a wide variety of molecules, including nucleic acids, at specific, unique sites. the location of these sites can be synthetically programmed in order to preserve the binding affinity of the conjugate and impart novel characteristic ... | 2010 | 20869258 |
| structure and mechanism of orf36, an amino sugar oxidizing enzyme in everninomicin biosynthesis . | everninomicin is a highly modified octasaccharide that belongs to the orthosomycin family of antibiotics and possesses potent gram-positive antibiotic activity, including broad-spectrum efficacy against multidrug resistant enterococci and staphylococcus aureus. among its distinctive structural features is a nitro sugar, l-evernitrose, analogues of which decorate a variety of natural products. recently, we identified a nitrososynthase enzyme encoded by orf36 from micromonospora carbonacea var. af ... | 2010 | 20866105 |
| comparative genomics of gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. | gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (bv). here we report the genome sequencing and comparative analyses of three strains of g. vaginalis. strains 317 (atcc 14019) and 594 (atcc 14018) were isolated from the vaginal tracts of women with symptomatic bv, while strain 409-05 was isolated from a healthy, asymptomatic individual with a nugent score of 9. | 2010 | 20865041 |
| structural basis for recognition of s-adenosylhomocysteine by riboswitches. | s-adenosyl-(l)-homocysteine (sah) riboswitches are regulatory elements found in bacterial mrnas that up-regulate genes involved in the s-adenosyl-(l)-methionine (sam) regeneration cycle. to understand the structural basis of sah-dependent regulation by rna, we have solved the structure of its metabolite-binding domain in complex with sah. this structure reveals an unusual pseudoknot topology that creates a shallow groove on the surface of the rna that binds sah primarily through interactions wit ... | 2010 | 20864509 |
| role of hsp70 atpase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with nefs. | catalysis of adp-atp exchange by nucleotide exchange factors (nefs) is central to the activity of hsp70 molecular chaperones. yet, the mechanism of interaction of this family of chaperones with nefs is not well understood in the context of the sequence evolution and structural dynamics of hsp70 atpase domains. we studied the interactions of hsp70 atpase domains with four different nefs on the basis of the evolutionary trace and co-evolution of the atpase domain sequence, combined with elastic ne ... | 2010 | 20862304 |
| complete structural model of escherichia coli rna polymerase from a hybrid approach. | the escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. nevertheless, a molecular understanding of the details of e. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on e. coli rna polymerase (rnap). we use a combination of approaches, including high-resolution x-ray crystallography, ab i ... | 2010 | 20856905 |
| lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes. | the structure of the protein-translocating channel secyeβ from pyrococcus furiosus at 3.1-å resolution suggests a mechanism for chaperoning transmembrane regions of a protein substrate during its lateral delivery into the lipid bilayer. cytoplasmic segments of secy orient the c-terminal α-helical region of another molecule, suggesting a general binding mode and a promiscuous guiding surface capable of accommodating diverse nascent chains at the exit of the ribosomal tunnel. to accommodate this p ... | 2010 | 20855604 |
| structural basis for 16s ribosomal rna cleavage by the cytotoxic domain of colicin e3. | the toxin colicin e3 targets the 30s subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. we present the crystal structure of the 70s ribosome in complex with the cytotoxic domain of colicin e3 (e3-rrnase). the structure reveals how the rrnase domain of colicin binds to the a site of the decoding center in the 70s ribosome and cleaves the 16s ribosomal rna (rrna) between a1493 and g1494. the cleavage mechanism involves the concerted action of conserved residue ... | 2010 | 20852642 |