| suppression of capsule expression in δlon strains of escherichia coli by two novel rpob mutations in concert with hns: possible role for dna bending at rcsa promoter. | analyses of mutations in genes coding for subunits of rna polymerase always throw more light on the intricate events that regulate the expression of gene(s). lon protease of escherichia coli is implicated in the turnover of rcsa (positive regulator of genes involved in capsular polysaccharide synthesis) and sula (cell division inhibitor induced upon dna damage). failure to degrade rcsa and sula makes lon mutant cells to overproduce capsular polysaccharides and to become sensitive to dna damaging ... | 2015 | 26403574 |
| uncommon glycosidases for the enzymatic preparation of glycosides. | most of the reports in literature dedicated to the use of glycosyl hydrolases for the preparation of glycosides are about gluco- (α- and β-form) and galacto-sidase (β-form), reflecting the high-availability of both anomers of glucosides and of β-galactosides and their wide-ranging applications. hence, the idea of this review was to analyze the literature focusing on hardly-mentioned natural and engineered glycosyl hydrolases. their performances in the synthetic mode and natural hydrolytic potent ... | 2015 | 26404386 |
| ribosome structure reveals preservation of active sites in the presence of a p-site wobble mismatch. | translation initiation in the p site occasionally occurs at atypical (non-aug) start codons, including those forming a mismatch in the third (wobble) position. during elongation, however, a pyrimidine-pyrimidine wobble mismatch may trigger a translation quality-control mechanism, whereby the p-site mismatch is thought to perturb the downstream a-site codon or the decoding center, thereby reducing translation fidelity and inducing termination of aberrant translation. we report a crystal structure ... | 2015 | 26412335 |
| stay wet, stay stable? how internal water helps the stability of thermophilic proteins. | we present a systematic computational investigation of the internal hydration of a set of homologous proteins of different stability content and molecular complexities. the goal of the study is to verify whether structural water can be part of the molecular mechanisms ensuring enhanced stability in thermophilic enzymes. our free-energy calculations show that internal hydration in the thermophilic variants is generally more favorable, and that the cumulated effect of wetting multiple sites result ... | 2015 | 26335353 |
| ion-pumping microbial rhodopsins. | rhodopsins are light-sensing proteins used in optogenetics. the word "rhodopsin" originates from the greek words "rhodo" and "opsis," indicating rose and sight, respectively. although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmem ... | 2015 | 26442282 |
| simulating the function of sodium/proton antiporters. | the molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. this work explores the molecular origin of the function of the bacterial na+/h+ antiporter nhaa by evaluating the energetics of the na+ and h+ movement and then using the resulting landscape in monte carlo simulations that examine two transport models and explore which model can reprod ... | 2015 | 26392528 |
| nascent chain-monitored remodeling of the sec machinery for salinity adaptation of marine bacteria. | secdf interacts with the secyeg translocon in bacteria and enhances protein export in a proton-motive-force-dependent manner. vibrio alginolyticus, a marine-estuarine bacterium, contains two secdf paralogs, v.secdf1 and v.secdf2. here, we show that the export-enhancing function of v.secdf1 requires na+ instead of h+, whereas v.secdf2 is na+-independent, presumably requiring h+. in accord with the cation-preference difference, v.secdf2 was only expressed under limited na+ concentrations whereas v ... | 2015 | 26392525 |
| functional importance of mobile ribosomal proteins. | although the dynamic motions and peptidyl transferase activity seem to be embedded in the rrnas, the ribosome contains more than 50 ribosomal proteins (r-proteins), whose functions remain largely elusive. also, the precise forms of some of these r-proteins, as being part of the ribosome, are not structurally solved due to their high flexibility, which hinders the efforts in their functional elucidation. owing to recent advances in cryo-electron microscopy, single-molecule techniques, and theoret ... | 2015 | 26457300 |
| autophosphorylation of the bacterial tyrosine-kinase cpsd connects capsule synthesis with the cell cycle in streptococcus pneumoniae. | bacterial capsular polysaccharides (cps) are produced by a multi-protein membrane complex, in which a particular type of tyrosine-autokinases named by-kinases, regulate their polymerization and export. however, our understanding of the role of by-kinases in these processes remains incomplete. in the human pathogen streptococcus pneumoniae, the by-kinase cpsd localizes at the division site and participates in the proper assembly of the capsule. in this study, we show that the cytoplasmic c-termin ... | 2015 | 26378458 |
| directed evolution of the escherichia coli camp receptor protein at the camp pocket. | the escherichia coli camp receptor protein (crp) requires camp binding to undergo a conformational change for dna binding and transcriptional regulation. two crp residues, thr(127) and ser(128), are known to play important roles in camp binding through hydrogen bonding and in the camp-induced conformational change, but the connection between the two is not completely clear. here, we simultaneously randomized the codons for these two residues and selected crp mutants displaying high crp activity ... | 2015 | 26378231 |
| epoxyqueuosine reductase structure suggests a mechanism for cobalamin-dependent trna modification. | queuosine (q) is a hypermodified rna base that replaces guanine in the wobble positions of 5'-gun-3' trna molecules. q is exclusively made by bacteria, and the corresponding queuine base is a micronutrient salvaged by eukaryotic species. the final step in q biosynthesis is the reduction of the epoxide precursor, epoxyqueuosine, to yield the q cyclopentene ring. the epoxyqueuosine reductase responsible, queg, shares distant homology with the cobalamin-dependent reductive dehalogenase (rdha), howe ... | 2015 | 26378237 |
| biochemical characterization and validation of a catalytic site of a highly thermostable ts2631 endolysin from the thermus scotoductus phage vb_tsc2631. | phage vb_tsc2631 infects the extremophilic bacterium thermus scotoductus mat2631 and uses the ts2631 endolysin for the release of its progeny. the ts2631 endolysin is the first endolysin from thermophilic bacteriophage with an experimentally validated catalytic site. in silico analysis and computational modelling of the ts2631 endolysin structure revealed a conserved zn2+ binding site (his30, tyr58, his131 and cys139) similar to zn2+ binding site of eukaryotic peptidoglycan recognition proteins ... | 2015 | 26375388 |
| structural basis for a unique atp synthase core complex from nanoarcheaum equitans. | atp synthesis is a critical and universal life process carried out by atp synthases. whereas eukaryotic and prokaryotic atp synthases are well characterized, archaeal atp synthases are relatively poorly understood. the hyperthermophilic archaeal parasite, nanoarcheaum equitans, lacks several subunits of the atp synthase and is suspected to be energetically dependent on its host, ignicoccus hospitalis. this suggests that this atp synthase might be a rudimentary machine. here, we report the crysta ... | 2015 | 26370083 |
| structure of subcomplex iβ of mammalian respiratory complex i leads to new supernumerary subunit assignments. | mitochondrial complex i (proton-pumping nadh:ubiquinone oxidoreductase) is an essential respiratory enzyme. mammalian complex i contains 45 subunits: 14 conserved "core" subunits and 31 "supernumerary" subunits. the structure of bos taurus complex i, determined to 5-å resolution by electron cryomicroscopy, described the structure of the mammalian core enzyme and allowed the assignment of 14 supernumerary subunits. here, we describe the 6.8-å resolution x-ray crystallography structure of subcompl ... | 2015 | 26371297 |
| a high-throughput assay for the comprehensive profiling of dna ligase fidelity. | dna ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. in order to achieve a high sensitivity and low background, the ligase must efficiently join correctly base-paired substrates, while discriminating against the ligation of substrates co ... | 2015 | 26365241 |
| a high-throughput assay for the comprehensive profiling of dna ligase fidelity. | dna ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. in order to achieve a high sensitivity and low background, the ligase must efficiently join correctly base-paired substrates, while discriminating against the ligation of substrates co ... | 2015 | 26365241 |
| protein-protein interfaces in viral capsids are structurally unique. | viral capsids exhibit elaborate and symmetrical architectures of defined sizes and remarkable mechanical properties not seen with cellular macromolecular complexes. given the uniqueness of the higher-order organization of viral capsid proteins in the virosphere, we explored the question of whether the patterns of protein-protein interactions within viral capsids are distinct from those in generic protein complexes. our comparative analysis involving a non-redundant set of 551 inter-subunit inter ... | 2015 | 26375252 |
| loop recognition and copper-mediated disulfide reduction underpin metal site assembly of cua in human cytochrome oxidase. | maturation of cytochrome oxidases is a complex process requiring assembly of several subunits and adequate uptake of the metal cofactors. two orthologous sco proteins (sco1 and sco2) are essential for the correct assembly of the dicopper cua site in the human oxidase, but their function is not fully understood. here, we report an in vitro biochemical study that shows that sco1 is a metallochaperone that selectively transfers cu(i) ions based on loop recognition, whereas sco2 is a copper-dependen ... | 2015 | 26351686 |
| structures of archaeal dna segregation machinery reveal bacterial and eukaryotic linkages. | although recent studies have provided a wealth of information about archaeal biology, nothing is known about the molecular basis of dna segregation in these organisms. here, we unveil the machinery and assembly mechanism of the archaeal sulfolobus pnob8 partition system. this system uses three proteins: para; an atypical parb adaptor; and a centromere-binding component, aspa. aspa utilizes a spreading mechanism to create a dna superhelix onto which parb assembles. this supercomplex links to the ... | 2015 | 26339031 |
| mechanisms of microrna turnover. | micrornas (mirnas) are 20-24 nucleotide (nt) rnas that regulate gene expression by guiding argonaute (ago) proteins to specific target rnas to cause their degradation or translational repression. the abundance of mirnas is strictly controlled at the transcriptional or post-transcriptional levels. mirna turnover is presumably a necessary means to regulate mirna levels in response to physiological, developmental, and environmental changes. mirna 3' end methylation, 3' end nucleotide addition, ago ... | 2015 | 26342825 |
| facial primer provides immediate and long-term improvements in mild-to-moderate facial hyperpigmentation and fine lines associated with photoaging. | photoaged skin results from various environmental factors, most importantly chronic sun exposure. dyschromia and fine lines/wrinkles are common clinical manifestations of photodamaged skin. | 2015 | 26366102 |
| redox-induced activation of the proton pump in the respiratory complex i. | complex i functions as a redox-linked proton pump in the respiratory chains of mitochondria and bacteria, driven by the reduction of quinone (q) by nadh. remarkably, the distance between the q reduction site and the most distant proton channels extends nearly 200 å. to elucidate the molecular origin of this long-range coupling, we apply a combination of large-scale molecular simulations and a site-directed mutagenesis experiment of a key residue. in hybrid quantum mechanics/molecular mechanics s ... | 2015 | 26330610 |
| the landscape of intertwined associations in homooligomeric proteins. | we present an overview of the full repertoire of intertwined associations in homooligomeric proteins. this overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers ... | 2015 | 26340815 |
| defining the domain arrangement of the mammalian target of rapamycin complex component rictor protein. | mammalian target of rapamycin (mtor) complexes play a pivotal role in the cell. raptor and rictor proteins interact with mtor to form two distinct complexes, mtorc1 and mtorc2, respectively. while the domain structure of raptor is known, current bioinformatics tools failed to classify the domains in rictor. here we focus on identifying specific domains in rictor by searching for conserved regions. we scanned the pdb structural database and constructed three protein domain datasets. next we carri ... | 2015 | 26176550 |
| the use of polyoxometalates in protein crystallography - an attempt to widen a well-known bottleneck. | polyoxometalates (poms) are discrete polynuclear metal-oxo anions with a fascinating variety of structures and unique chemical and physical properties. their application in various fields is well covered in the literature, however little information about their usage in protein crystallization is available. this review summarizes the impact of the vast class of poms on the formation of protein crystals, a well-known (frustrating) bottleneck in macromolecular crystallography, with the associated ... | 2015 | 26339074 |
| toward a whole-cell model of ribosome biogenesis: kinetic modeling of ssu assembly. | central to all life is the assembly of the ribosome: a coordinated process involving the hierarchical association of ribosomal proteins to the rnas forming the small and large ribosomal subunits. the process is further complicated by effects arising from the intracellular heterogeneous environment and the location of ribosomal operons within the cell. we provide a simplified model of ribosome biogenesis in slow-growing escherichia coli. kinetic models of in vitro small-subunit reconstitution at ... | 2015 | 26333594 |
| evidence for an induced conformational change in the catalytic mechanism of homoisocitrate dehydrogenase for saccharomyces cerevisiae: characterization of the d271n mutant enzyme. | homoisocitrate dehydrogenase (hicdh) catalyzes the nad(+)-dependent oxidative decarboxylation of hic to α-ketoadipate, the fourth step in the α-aminoadipate pathway responsible for the de novo synthesis of l-lysine in fungi. a mechanism has been proposed for the enzyme that makes use of a lys-tyr pair as acid-base catalysts, with lys acting as a base to accept a proton from the α-hydroxyl of homoisocitrate, and tyr acting as an acid to protonate the c3 of the enol of α-ketoadipate in the enoliza ... | 2015 | 26325079 |
| plasmodium apicoplast gln-trnagln biosynthesis utilizes a unique gatab amidotransferase essential for erythrocytic stage parasites. | the malaria parasite plasmodium falciparum apicoplast indirect aminoacylation pathway utilizes a non-discriminating glutamyl-trna synthetase to synthesize glu-trna(gln) and a glutaminyl-trna amidotransferase to convert glu-trna(gln) to gln-trna(gln). here, we show that plasmodium falciparum and other apicomplexans possess a unique heterodimeric glutamyl-trna amidotransferase consisting of gata and gatb subunits (gatab). we localized the p. falciparum gata and gatb subunits to the apicoplast in b ... | 2015 | 26318454 |
| crystal structure of staphylococcus aureus cas9. | the rna-guided dna endonuclease cas9 cleaves double-stranded dna targets with a protospacer adjacent motif (pam) and complementarity to the guide rna. recently, we harnessed staphylococcus aureus cas9 (sacas9), which is significantly smaller than streptococcus pyogenes cas9 (spcas9), to facilitate efficient in vivo genome editing. here, we report the crystal structures of sacas9 in complex with a single guide rna (sgrna) and its double-stranded dna targets, containing the 5'-ttgaat-3' pam and th ... | 2015 | 26317473 |
| inhibition of human glut1 and glut5 by plant carbohydrate products; insights into transport specificity. | glucose transporters glut1 (transports glucose) and glut5 (transports fructose), in addition to their functions in normal metabolism, have been implicated in several diseases including cancer and diabetes. while glut1 has several inhibitors, none have been described for glut5. by transport activity assays we found two plant products, rubusoside (from rubus suavissimus) and astragalin-6-glucoside (a glycosylated derivative of astragalin, from phytolacca americana) that inhibited human glut5. thes ... | 2015 | 26306809 |
| a unique uracil-dna binding protein of the uracil dna glycosylase superfamily. | uracil dna glycosylases (udgs) are an important group of dna repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from dna. based on two short conserved sequences (motifs a and b), udgs have been classified into six families. here we report a novel udg, udgx, from mycobacterium smegmatis and other organisms. udgx specifically recognizes uracil in dna, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, ... | 2015 | 26304551 |
| pyranopterin coordination controls molybdenum electrochemistry in escherichia coli nitrate reductase. | we test the hypothesis that pyranopterin (ppt) coordination plays a critical role in defining molybdenum active site redox chemistry and reactivity in the mononuclear molybdoenzymes. the molybdenum atom of escherichia coli nitrate reductase a (narghi) is coordinated by two ppt-dithiolene chelates that are defined as proximal and distal based on their proximity to a [4fe-4s] cluster known as fs0. we examined variants of two sets of residues involved in ppt coordination: (i) those interacting dire ... | 2015 | 26297003 |
| structure of ribosomal silencing factor bound to mycobacterium tuberculosis ribosome. | the ribosomal silencing factor rsfs slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. the crystal structure of mycobacterium tuberculosis (mtb) rsfs, together with the cryo-electron microscopy (em) structure of the large subunit 50s of mtb ribosome, reveals how inhibition of protein synthesis by rsfs occurs. rsfs binds to the 50s at l14, which, when occupied, blocks the association of the small subunit 30s. although mtb rsfs is a dimer in solut ... | 2015 | 26299947 |
| parametrization of macrolide antibiotics using the force field toolkit. | macrolides are an important class of antibiotics that target the bacterial ribosome. computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. here, we determine charmm-compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (fftk) plugin in vmd. because of their large size, novel approaches for parametrizing them had to be developed. two methods for determining partial ... | 2015 | 26280362 |
| recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies. | this forum article focuses on recent advances in structural and spectroscopic studies of biosynthetic models of nitric oxide reductases (nors). nors are complex metalloenzymes found in the denitrification pathway of earth's nitrogen cycle where they catalyze the proton-dependent two-electron reduction of nitric oxide (no) to nitrous oxide (n2o). while much progress has been made in biochemical and biophysical studies of native nors and their variants, a clear mechanistic understanding of this im ... | 2015 | 26274098 |
| structural basis for the atp-dependent configuration of adenylation active site in bacillus subtilis o-succinylbenzoyl-coa synthetase. | o-succinylbenzoyl-coa synthetase, or mene, is an essential adenylate-forming enzyme targeted for development of novel antibiotics in the menaquinone biosynthesis. using its crystal structures in a ligand-free form or in complex with nucleotides, a conserved pattern is identified in the interaction between atp and adenylating enzymes, including acyl/aryl-coa synthetases, adenylation domains of nonribosomal peptide synthetases, and luciferases. it involves tight gripping interactions of the phosph ... | 2015 | 26276389 |
| the ribosomal s10 protein is a general target for decreased tigecycline susceptibility. | tigecycline is a translational inhibitor with efficacy against a wide range of pathogens. using experimental evolution, we adapted acinetobacter baumannii, enterococcus faecium, escherichia coli, and staphylococcus aureus to growth in elevated tigecycline concentrations. at the end of adaptation, 35 out of 47 replicate populations had clones with a mutation in rpsj, the gene that encodes the ribosomal s10 protein. to validate the role of mutations in rpsj in conferring tigecycline resistance, we ... | 2015 | 26124155 |
| degenerate connective polypeptide 1 (cp1) domain from human mitochondrial leucyl-trna synthetase. | the connective polypeptide 1 (cp1) editing domain of leucyl-trna synthetase (leurs) from various species either harbors a conserved active site to exclude trna mis-charging with noncognate amino acids or is evolutionarily truncated or lost because there is no requirement for high translational fidelity. however, human mitochondrial leurs (hmtleurs) contains a full-length but degenerate cp1 domain that has mutations in some residues important for post-transfer editing. the significance of such an ... | 2015 | 26272616 |
| allosteric activation of bacterial swi2/snf2 (switch/sucrose non-fermentable) protein rapa by rna polymerase: biochemical and structural studies. | members of the swi2/snf2 (switch/sucrose non-fermentable) family depend on their atpase activity to mobilize nucleic acid-protein complexes for gene expression. in bacteria, rapa is an rna polymerase (rnap)-associated swi2/snf2 protein that mediates rnap recycling during transcription. it is known that the atpase activity of rapa is stimulated by its interaction with rnap. it is not known, however, how the rapa-rnap interaction activates the enzyme. previously, we determined the crystal structur ... | 2015 | 26272746 |
| from genome to structure and back again: a family portrait of the transcarbamylases. | enzymes in the transcarbamylase family catalyze the transfer of a carbamyl group from carbamyl phosphate (cp) to an amino group of a second substrate. the two best-characterized members, aspartate transcarbamylase (atcase) and ornithine transcarbamylase (otcase), are present in most organisms from bacteria to humans. recently, structures of four new transcarbamylase members, n-acetyl-l-ornithine transcarbamylase (aotcase), n-succinyl-l-ornithine transcarbamylase (sotcase), ygew encoded transcarb ... | 2015 | 26274952 |
| collaborative protein filaments. | it is now well established that prokaryotic cells assemble diverse proteins into dynamic cytoskeletal filaments that perform essential cellular functions. although most of the filaments assemble on their own to form higher order structures, growing evidence suggests that there are a number of prokaryotic proteins that polymerise only in the presence of a matrix such as dna, lipid membrane or even another filament. matrix-assisted filament systems are frequently nucleotide dependent and cytomotiv ... | 2015 | 26271102 |
| initiation of mrna translation in bacteria: structural and dynamic aspects. | initiation of mrna translation is a major checkpoint for regulating level and fidelity of protein synthesis. being rate limiting in protein synthesis, translation initiation also represents the target of many post-transcriptional mechanisms regulating gene expression. the process begins with the formation of an unstable 30s pre-initiation complex (30s pre-ic) containing initiation factors (ifs) if1, if2 and if3, the translation initiation region of an mrna and initiator fmet-trna whose codon and ... | 2015 | 26259514 |
| molecular basis of ribosome recognition and mrna hydrolysis by the e. coli yafq toxin. | bacterial type ii toxin-antitoxin modules are protein-protein complexes whose functions are finely tuned by rapidly changing environmental conditions. e. coli toxin yafq is suppressed under steady state growth conditions by virtue of its interaction with its cognate antitoxin, dinj. during stress, dinj is proteolytically degraded and free yafq halts translation by degrading ribosome-bound mrna to slow growth until the stress has passed. although structures of the ribosome with toxins rele and yo ... | 2015 | 26261214 |
| linkage of catalysis and 5' end recognition in ribonuclease rnase j. | in diverse bacterial species, the turnover and processing of many rnas is mediated by the ribonuclease rnase j, a member of the widely occurring metallo-β-lactamase enzyme family. we present crystal structures of streptomyces coelicolor rnase j with bound rna in pre- and post-cleavage states, at 2.27 å and 2.80 å resolution, respectively. these structures reveal snapshots of the enzyme cleaving substrate directionally and sequentially from the 5' terminus. in the pre-cleavage state, a water mole ... | 2015 | 26253740 |
| knowledge-based discovery for designing crispr-cas systems against invading mobilomes in thermophiles. | clustered regularly interspaced short palindromic repeats (crisprs) are direct features of the prokaryotic genomes involved in resistance to their bacterial viruses and phages. herein, we have identified crispr loci together with crispr-associated sequences (cas) genes to reveal their immunity against genome invaders in the thermophilic archaea and bacteria. genomic survey of this study implied that genomic distribution of crispr-cas systems was varied from strain to strain, which was determined ... | 2015 | 26279704 |
| crucial hsp70 co-chaperone complex unlocks metazoan protein disaggregation. | protein aggregates are the hallmark of stressed and ageing cells, and characterize several pathophysiological states. healthy metazoan cells effectively eliminate intracellular protein aggregates, indicating that efficient disaggregation and/or degradation mechanisms exist. however, metazoans lack the key heat-shock protein disaggregase hsp100 of non-metazoan hsp70-dependent protein disaggregation systems, and the human hsp70 system alone, even with the crucial hsp110 nucleotide exchange factor, ... | 2015 | 26245380 |
| functional characterization and expression analysis of rice δ(1)-pyrroline-5-carboxylate dehydrogenase provide new insight into the regulation of proline and arginine catabolism. | while intracellular proline accumulation in response to various stress conditions has been investigated in great detail, the biochemistry and physiological relevance of proline degradation in plants is much less understood. moreover, the second and last step in proline catabolism, the oxidation of δ(1)-pyrroline-5-carboxylic acid (p5c) to glutamate, is shared with arginine catabolism. little information is available to date concerning the regulatory mechanisms coordinating these two pathways. ex ... | 2015 | 26300893 |
| membrane protein structures without crystals, by single particle electron cryomicroscopy. | it is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. however, two major hurdles still remain in the structural biology of membrane proteins. one is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. with single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane ... | 2015 | 26435463 |
| mutations of ribosomal protein s5 suppress a defect in late-30s ribosomal subunit biogenesis caused by lack of the rbfa biogenesis factor. | the in vivo assembly of ribosomal subunits requires assistance by maturation proteins that are not part of mature ribosomes. one such protein, rbfa, associates with the 30s ribosomal subunits. loss of rbfa causes cold sensitivity and defects of the 30s subunit biogenesis and its overexpression partially suppresses the dominant cold sensitivity caused by a c23u mutation in the central pseudoknot of 16s rrna, a structure essential for ribosome function. we have isolated suppressor mutations that r ... | 2015 | 26089326 |
| x-ray structure determination using low-resolution electron microscopy maps for molecular replacement. | structures of multisubunit macromolecular machines are primarily determined either by electron microscopy (em) or by x-ray crystallography. in many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with em and at a higher resolution (with finer detail) by x-ray crystallography. the integration of these two structural techniques is becoming increasingly important for the generation of atomic models of macromolecular complexes. a low-resolution em ima ... | 2015 | 26226459 |
| ratcheting of rna polymerase toward structural principles of rna polymerase operations. | rna polymerase (rnap) performs various tasks during transcription by changing its conformational states, which are gradually becoming clarified. a recent study focusing on the conformational transition of rnap between the ratcheted and tight forms illuminated the structural principles underlying its functional operations. | 2015 | 26226152 |
| physiological implications of arginine metabolism in plants. | nitrogen is a limiting resource for plant growth in most terrestrial habitats since large amounts of nitrogen are needed to synthesize nucleic acids and proteins. among the 21 proteinogenic amino acids, arginine has the highest nitrogen to carbon ratio, which makes it especially suitable as a storage form of organic nitrogen. synthesis in chloroplasts via ornithine is apparently the only operational pathway to provide arginine in plants, and the rate of arginine synthesis is tightly regulated by ... | 2015 | 26284079 |
| structures and functions of the multiple kow domains of transcription elongation factor spt5. | the eukaryotic spt4-spt5 heterodimer forms a higher-order complex with rna polymerase ii (and i) to regulate transcription elongation. extensive genetic and functional data have revealed diverse roles of spt4-spt5 in coupling elongation with chromatin modification and rna-processing pathways. a mechanistic understanding of the diverse functions of spt4-spt5 is hampered by challenges in resolving the distribution of functions among its structural domains, including the five kow domains in spt5, a ... | 2015 | 26217010 |
| profile of dinshaw j. patel. | | 2015 | 26216951 |
| computing the origin and evolution of the ribosome from its structure - uncovering processes of macromolecular accretion benefiting synthetic biology. | accretion occurs pervasively in nature at widely different timeframes. the process also manifests in the evolution of macromolecules. here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. phylogenetic trees of protein ... | 2015 | 27096056 |
| thiophenecarboxamide derivatives activated by etha kill mycobacterium tuberculosis by inhibiting the ctp synthetase pyrg. | to combat the emergence of drug-resistant strains of mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against m. tuberculosis in its replicating, non-replicating, and intracellular states: compounds 7947882 (5-methyl-n-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-n-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide). mutants resistant to both compou ... | 2015 | 26097035 |
| trna recognition by a bacterial trna xm32 modification enzyme from the spout methyltransferase superfamily. | trmj proteins from the spout methyltransferase superfamily are trna xm32 modification enzymes that occur in bacteria and archaea. unlike archaeal trmj, bacterial trmj require full-length trna molecules as substrates. it remains unknown how bacterial trmjs recognize substrate trnas and specifically catalyze a 2'-o modification at ribose 32. herein, we demonstrate that all six escherichia coli (ec) trnas with 2'-o-methylated nucleosides at position 32 are substrates of ectrmj, and we show that the ... | 2015 | 26202969 |
| recf and recr play critical roles in the homologous recombination and single-strand annealing pathways of mycobacteria. | mycobacteria encode three dna double-strand break repair pathways: (i) reca-dependent homologous recombination (hr), (ii) ku-dependent nonhomologous end joining (nhej), and (iii) recbcd-dependent single-strand annealing (ssa). mycobacterial hr has two presynaptic pathway options that rely on the helicase-nuclease adnab and the strand annealing protein reco, respectively. ablation of adnab or reco individually causes partial impairment of hr, but loss of adnab and reco in combination abolishes hr ... | 2015 | 26195593 |
| argonaute 2: a novel rising star in cancer research. | ago2 (argonaute 2, eif2c2) is the only member in ago family with catalytic activity and of extreme importance during small rnas guided gene silencing processes. the structural investigations have provided insights into details and functional mechanisms of the four major domains within ago2. as a multifunction player, ago2 has been revealed involved in tumorgenesis through mirnas-dependent or independent ways. and nowadays, ago2 has also been more importantly found ectopically over-expressed in c ... | 2015 | 26284139 |
| a derivative of the thiopeptide ge2270a highly selective against propionibacterium acnes. | a chemical derivative of the thiopeptide ge2270a, designated nai003, was found to possess a substantially reduced antibacterial spectrum in comparison to the parent compound, being active against just a few gram-positive bacteria. in particular, nai003 retained low mics against all tested isolates of propionibacterium acnes and, to a lesser extent, against enterococcus faecalis. furthermore, nai003 showed a time- and dose-dependent killing of both a clindamycin-resistant and a clindamycin-sensit ... | 2015 | 25987631 |
| star3d: a stack-based rna 3d structural alignment tool. | the various roles of versatile non-coding rnas typically require the attainment of complex high-order structures. therefore, comparing the 3d structures of rna molecules can yield in-depth understanding of their functional conservation and evolutionary history. recently, many powerful tools have been developed to align rna 3d structures. although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the rna seco ... | 2015 | 26184875 |
| characterization of a mannose-6-phosphate isomerase from bacillus amyloliquefaciens and its application in fructose-6-phosphate production. | the bam6pi gene encoding a mannose-6-phosphate isomerase (m6pi, ec 5.3.1.8) was cloned from bacillus amyloliquefaciens dsm7 and overexpressed in escherichia coli. the enzyme activity of bam6pi was optimal at ph and temperature of 7.5 and 70°c, respectively, with a kcat/km of 13,900 s-1 mm-1 for mannose-6-phosphate (m6p). the purified bam6pi demonstrated the highest catalytic efficiency of all characterized m6pis. although m6pis have been characterized from several other sources, bam6pi is distin ... | 2015 | 26171785 |
| structure and evolution of the archaeal lipid synthesis enzyme sn-glycerol-1-phosphate dehydrogenase. | one of the most critical events in the origins of cellular life was the development of lipid membranes. archaea use isoprenoid chains linked via ether bonds to sn-glycerol 1-phosphate (g1p), whereas bacteria and eukaryotes use fatty acids attached via ester bonds to enantiomeric sn-glycerol 3-phosphate. nad(p)h-dependent g1p dehydrogenase (g1pdh) forms g1p and has been proposed to have played a crucial role in the speciation of the archaea. we present here, to our knowledge, the first structures ... | 2015 | 26175150 |
| md simulations of trna and aminoacyl-trna synthetases: dynamics, folding, binding, and allostery. | while trna and aminoacyl-trna synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. recent molecular dynamics (md) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. throughout the review, we briefly discuss important historical events to provide a context for how far t ... | 2015 | 26184179 |
| biochemical and structural properties of a thermostable mercuric ion reductase from metallosphaera sedula. | mercuric ion reductase (mera), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (hg(2+)) and to catalyze their reduction to a more volatile, less toxic elemental form. here, we present a biochemical and structural characterization of mera from the thermophilic crenarchaeon metallosphaera sedula. mera from m. sedula is a thermostable enzyme, and remains active after extended incubation at 97°c. at 37°c, the nadph oxidation-linked hg(2+) reduc ... | 2015 | 26217660 |
| the extended at-hook is a novel rna binding motif. | the at-hook has been defined as a dna binding peptide motif that contains a glycine-arginine-proline (g-r-p) tripeptide core flanked by basic amino acids. recent reports documented variations in the sequence of at-hooks and revealed rna binding activity of some canonical at-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. here we describe the discovery and characterization of the extended at-hook peptide motif (eat-hook), in whi ... | 2015 | 26156556 |
| crystal structures of a hyperthermophilic archaeal homoserine dehydrogenase suggest a novel cofactor binding mode for oxidoreductases. | nad(p)-dependent dehydrogenases differ according to their coenzyme preference: some prefer nad, others nadp, and still others exhibit dual cofactor specificity. the structure of a newly identified archaeal homoserine dehydrogenase showed this enzyme to have a strong preference for nadp. however, nadp did not act as a cofactor with this enzyme, but as a strong inhibitor of nad-dependent homoserine oxidation. structural analysis and site-directed mutagenesis showed that the large number of interac ... | 2015 | 26154028 |
| structural and mechanistic insights into the pseudomonas fluorescens 2-nitrobenzoate 2-nitroreductase nbaa. | the bacterial 2-nitroreductase nbaa is the primary enzyme initiating the degradation of 2-nitrobenzoate (2-nba), and its activity is controlled by posttranslational modifications. to date, the structure of nbaa remains to be elucidated. in this study, the crystal structure of a cys194ala nbaa mutant was determined to a 1.7-å resolution. the substrate analog 2-nba methyl ester was used to decipher the substrate binding site by inhibition of the wild-type nbaa protein. tandem mass spectrometry sho ... | 2015 | 26025888 |
| phenotypic suppression of streptomycin resistance by mutations in multiple components of the translation apparatus. | the bacterial ribosome and its associated translation factors are frequent targets of antibiotics, and antibiotic resistance mutations have been found in a number of these components. such mutations can potentially interact with one another in unpredictable ways, including the phenotypic suppression of one mutation by another. these phenotypic interactions can provide evidence of long-range functional interactions throughout the ribosome and its functional complexes and potentially give insights ... | 2015 | 26148717 |
| structure and mechanism of the atpase that powers viral genome packaging. | many viruses package their genomes into procapsids using an atpase machine that is among the most powerful known biological motors. however, how this motor couples atp hydrolysis to dna translocation is still unknown. here, we introduce a model system with unique properties for studying motor structure and mechanism. we describe crystal structures of the packaging motor atpase domain that exhibit nucleotide-dependent conformational changes involving a large rotation of an entire subdomain. we al ... | 2015 | 26150523 |
| ecophysiology of an uncultivated lineage of aigarchaeota from an oxic, hot spring filamentous 'streamer' community. | the candidate archaeal phylum 'aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. the phylogeny and metabolic potential of aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of aigarchaeota in an oxic, hot spring filamento ... | 2015 | 26140529 |
| ecophysiology of an uncultivated lineage of aigarchaeota from an oxic, hot spring filamentous 'streamer' community. | the candidate archaeal phylum 'aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. the phylogeny and metabolic potential of aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of aigarchaeota in an oxic, hot spring filamento ... | 2015 | 26140529 |
| a dynamic search process underlies microrna targeting. | argonaute proteins play a central role in mediating post-transcriptional gene regulation by micrornas (mirnas). argonautes use the nucleotide sequences in mirnas as guides for identifying target messenger rnas for repression. here, we used single-molecule fret to directly visualize how human argonaute-2 (ago2) searches for and identifies target sites in rnas complementary to its mirna guide. our results suggest that ago2 initially scans for target sites with complementarity to nucleotides 2-4 of ... | 2015 | 26140593 |
| single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides. | argonaute proteins repress gene expression and defend against foreign nucleic acids using short rnas or dnas to specify the correct target rna or dna sequence. we have developed single-molecule methods to analyze target binding and cleavage mediated by the argonaute:guide complex, risc. we find that both eukaryotic and prokaryotic argonaute proteins reshape the fundamental properties of rna:rna, rna:dna, and dna:dna hybridization—a small rna or dna bound to argonaute as a guide no longer follows ... | 2015 | 26140592 |
| constraining the lateral helix of respiratory complex i by cross-linking does not impair enzyme activity or proton translocation. | complex i (nadh:ubiquinone oxidoreductase) is a multisubunit, membrane-bound enzyme of the respiratory chain. the energy from nadh oxidation in the peripheral region of the enzyme is used to drive proton translocation across the membrane. one of the integral membrane subunits, nuol in escherichia coli, has an unusual lateral helix of ∼75 residues that lies parallel to the membrane surface and has been proposed to play a mechanical role as a piston during proton translocation (efremov, r. g., bar ... | 2015 | 26134569 |
| analysis of r-protein and rna conformation of 30s subunit intermediates in bacteria. | the ribosome is a large macromolecular complex that must be assembled efficiently and accurately for the viability of all organisms. in bacteria, this process must be robust and tunable to support life in diverse conditions from the ice of arctic glaciers to thermal hot springs. assembly of the small ribosomal subunit (ssu) of escherichia coli has been extensively studied and is highly temperature-dependent. however, a lack of data on ssu assembly for other bacteria is problematic given the impo ... | 2015 | 25999315 |
| structural mapping of the clpb atpases of plasmodium falciparum: targeting protein folding and secretion for antimalarial drug design. | caseinolytic chaperones and proteases (clp) belong to the aaa+ protein superfamily and are part of the protein quality control machinery in cells. the eukaryotic parasite plasmodium falciparum, the causative agent of malaria, has evolved an elaborate network of clp proteins including two distinct clpb atpases. clpb1 and clpb2 are involved in different aspects of parasitic proteostasis. clpb1 is present in the apicoplast, a parasite-specific and plastid-like organelle hosting various metabolic pa ... | 2015 | 26130467 |
| implication from the predicted docked interaction of sigma h and exploration of its interaction with rna polymerase in mycobacterium tuberculosis. | m. tuberculosis is adapted to remain active in the extreme environmental condition due to the presence of atypical sigma factors commonly called extra cytoplasmic function (ecf) sigma factors. among the 13 sigma factors of m. tuberculosis, 10 are regarded as the ecf sigma factor that exerts their attributes in various stress response. therefore it is of interest to describe the structural prediction of one of the ecf sigma factors, sigma h (sigh), involved in oxidative and heat stress having int ... | 2015 | 26229290 |
| from bacterial to human dihydrouridine synthase: automated structure determination. | the reduction of uridine to dihydrouridine at specific positions in trna is catalysed by dihydrouridine synthase (dus) enzymes. increased expression of human dihydrouridine synthase 2 (hdus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. here, the x-ray crystal structure of a construct of hdus2 encompassing the catalytic and trna-recognition domains (residues 1 ... | 2015 | 26143927 |
| enhancement of e. coli acyl-coa synthetase fadd activity on medium chain fatty acids. | fadd catalyses the first step in e. coli beta-oxidation, the activation of free fatty acids into acyl-coa thioesters. this activation makes fatty acids competent for catabolism and reduction into derivatives like alcohols and alkanes. alcohols and alkanes derived from medium chain fatty acids (mcfas, 6-12 carbons) are potential biofuels; however, fadd has low activity on mcfas. herein, we generate mutations in fadd that enhance its acyl-coa synthetase activity on mcfas. homology modeling reveals ... | 2015 | 26157619 |
| identifying novel sequence variants of rna 3d motifs. | predicting rna 3d structure from sequence is a major challenge in biophysics. an important sub-goal is accurately identifying recurrent 3d motifs from rna internal and hairpin loop sequences extracted from secondary structure (2d) diagrams. we have developed and validated new probabilistic models for 3d motif sequences based on hybrid stochastic context-free grammars and markov random fields (scfg/mrf). the scfg/mrf models are constructed using atomic-resolution rna 3d structures. to parameteriz ... | 2015 | 26130723 |
| expression, purification, crystallization and crystallographic study of lutzomyia longipalpis ljl143. | leishmaniasis is a neglected vector-borne disease with a global prevalence of over 12 million cases and 59,000 annual deaths. transmission of the parasite requires salivary proteins, including ljl143 from the new world sandfly lutzomyia longipalpis. ljl143 is a known marker of sandfly exposure in zoonotic hosts. ljl143 was crystallized from soluble protein expressed using pichia pastoris. x-ray data were collected to 2.6 å resolution from orthorhombic crystals belonging to space group p2(1)2(1)2 ... | 2015 | 26144240 |
| identification of chemical compounds that inhibit the function of glutamyl-trna synthetase from pseudomonas aeruginosa. | pseudomonas aeruginosa glutamyl-trna synthetase (glurs) was overexpressed in escherichia coli. sequence analysis indicated that p. aeruginosa glurs is a discriminating glurs and, similar to other glurs proteins, requires the presence of trna(glu) to produce a glutamyl-amp intermediate. kinetic parameters for interaction with trna were determined and the k(cat) and km were 0.8 s(-1) and 0.68 µm, respectively, resulting in a k(cat)/km of 1.18 s(-1) µm(-1). a robust aminoacylation-based scintillati ... | 2015 | 26116192 |
| specificity and catalysis hardwired at the rna-protein interface in a translational proofreading enzyme. | proofreading modules of aminoacyl-trna synthetases are responsible for enforcing a high fidelity during translation of the genetic code. they use strategically positioned side chains for specifically targeting incorrect aminoacyl-trnas. here, we show that a unique proofreading module possessing a d-aminoacyl-trna deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. we show, using three distinct archaea, that a side-chain-stri ... | 2015 | 26113036 |
| cautions about the reliability of pairwise gene correlations based on expression data. | rapid growth in the availability of genome-wide transcript abundance levels through gene expression microarrays and rnaseq promises to provide deep biological insights into the complex, genome-wide transcriptional behavior of single-celled organisms. however, this promise has not yet been fully realized. | 2015 | 26167162 |
| transcriptional slippage in the positive-sense rna virus family potyviridae. | the family potyviridae encompasses ~30% of plant viruses and is responsible for significant economic losses worldwide. recently, a small overlapping coding sequence, termed pipo, was found to be conserved in the genomes of all potyvirids. pipo is expressed as part of a frameshift protein, p3n-pipo, which is essential for virus cell-to-cell movement. however, the frameshift expression mechanism has hitherto remained unknown. here, we demonstrate that transcriptional slippage, specific to the vira ... | 2015 | 26113364 |
| identification of determinants for trna substrate recognition by escherichia coli c/u34 2'-o-methyltransferase. | post-transcriptional modifications bring chemical diversity to trnas, especially at positions 34 and 37 of the anticodon stem-loop (asl). trml is the prokaryotic methyltransferase that catalyzes the transfer of the methyl group from s-adenosyl-l-methionine to the wobble base of trna(leu)caa and trna(leu)uaa isoacceptors. this cm34/um34 modification affects codon-anticodon interactions and is essential for translational fidelity. trml-catalyzed 2'-o-methylation requires its homodimerization; howe ... | 2015 | 26106808 |
| developmentally regulated heart stopper, a mitochondrially targeted l18 ribosomal protein gene, is required for cell division, differentiation, and seed development in arabidopsis. | evidence is presented for the role of a mitochondrial ribosomal (mitoribosomal) l18 protein in cell division, differentiation, and seed development after the characterization of a recessive mutant, heart stopper (hes). the hes mutant produced uncellularized endosperm and embryos arrested at the late globular stage. the mutant embryos differentiated partially on rescue medium with some forming callus. hes (at1g08845) encodes a mitochondrially targeted member of a highly diverged l18 ribosomal pro ... | 2015 | 26105995 |
| mechanism of protective immunity by vaccination with recombinant echinococcus granulosus glutathione s-transferase (chinese strain) in mice. | the aim of this study was to investigate the immunoprotective effects of recombinant echinococcus granulosus glutathione s-transferase (reggst) against the development of protoscolices (pscs), and to determine the mechanisms underlying this protection. icr mice were subcutaneously immunized three times with reggst at weeks 0, 2 and 4, followed by the intraperitoneal administration of e. granulosus pscs at week 10. six mice in each group were sacrificed at 0, 2, 4, 6, 10, 18 and 30 weeks followin ... | 2015 | 26622451 |
| co-chaperone specificity in gating of the polypeptide conducting channel in the membrane of the human endoplasmic reticulum. | in mammalian cells, signal peptide-dependent protein transport into the endoplasmic reticulum (er) is mediated by a dynamic polypeptide-conducting channel, the heterotrimeric sec61 complex. previous work has characterized the sec61 complex as a potential er ca(2+) leak channel in hela cells and identified er lumenal molecular chaperone immunoglobulin heavy-chain-binding protein (bip) as limiting ca(2+) leakage via the open sec61 channel by facilitating channel closing. this bip activity involves ... | 2015 | 26085089 |
| structural organization of enzymes of the phenylacetate catabolic hybrid pathway. | aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. they are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. in bacterial genomes, the phenylacetate (pa) utilization pathway is abundant and represents the central route for degradation of a variety of organic compound ... | 2015 | 26075354 |
| a mutation of rna polymerase β' subunit (rpoc) converts heterogeneously vancomycin-intermediate staphylococcus aureus (hvisa) into "slow visa". | various mutations in the rpob gene, which encodes the rna polymerase β subunit, are associated with increased vancomycin (van) resistance in vancomycin-intermediate staphylococcus aureus (visa) and heterogeneously visa (hvisa) strains. we reported that rpob mutations are also linked to the expression of the recently found "slow visa" (svisa) phenotype (m. saito, y. katayama, t. hishinuma, a. iwamoto, y. aiba, k kuwahara-arai, l. cui, m. matsuo, n. aritaka, and k. hiramatsu, antimicrob agents che ... | 2015 | 25941225 |
| halophiles and their enzymes: negativity put to good use. | halophilic microorganisms possess stable enzymes that function in very high salinity, an extreme condition that leads to denaturation, aggregation, and precipitation of most other proteins. genomic and structural analyses have established that the enzymes of halophilic archaea and many halophilic bacteria are negatively charged due to an excess of acidic over basic residues, and altered hydrophobicity, which enhance solubility and promote function in low water activity conditions. here, we provi ... | 2015 | 26066288 |
| e. coli rna polymerase determinants of open complex lifetime and structure. | in transcription initiation by escherichia coli rna polymerase (rnap), initial binding to promoter dna triggers large conformational changes, bending downstream duplex dna into the rnap cleft and opening 13bp to form a short-lived open intermediate (i2). subsequent conformational changes increase lifetimes of λpr and t7a1 open complexes (ocs) by >10(5)-fold and >10(2)-fold, respectively. oc lifetime is a target for regulation. to characterize late conformational changes, we determine effects on ... | 2015 | 26055538 |
| oxidized and reduced [2fe-2s] clusters from an iron(i) synthon. | synthetic [2fe-2s] clusters are often used to elucidate ligand effects on the reduction potentials and spectroscopy of natural electron-transfer sites, which can have anionic cys ligands or neutral his ligands. current synthetic routes to [2fe-2s] clusters are limited in their feasibility with a range of supporting ligands. here, we report a new synthetic route to synthetic [2fe-2s] clusters, through oxidation of an iron(i) source with elemental sulfur. this method yields a neutral diketiminate- ... | 2015 | 26044124 |
| r3d-2-msa: the rna 3d structure-to-multiple sequence alignment server. | the rna 3d structure-to-multiple sequence alignment server (r3d-2-msa) is a new web service that seamlessly links rna three-dimensional (3d) structures to high-quality rna multiple sequence alignments (msas) from diverse biological sources. in this first release, r3d-2-msa provides manual and programmatic access to curated, representative ribosomal rna sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3 ... | 2015 | 26048960 |
| a replisome's journey through the bacterial chromosome. | genome duplication requires the coordinated activity of a multi-component machine, the replisome. in contrast to the background of metabolic diversity across the bacterial domain, the composition and architecture of the bacterial replisome seem to have suffered few changes during evolution. this immutability underlines the replisome's efficiency in copying the genome. it also highlights the success of various strategies inherent to the replisome for responding to stress and avoiding problems dur ... | 2015 | 26097470 |
| exploring rna polymerase regulation by nmr spectroscopy. | rna synthesis is a central process in all organisms, with rna polymerase (rnap) as the key enzyme. multisubunit rnaps are evolutionary related and are tightly regulated by a multitude of transcription factors. although escherichia coli rnap has been studied extensively, only little information is available about its dynamics and transient interactions. this information, however, are crucial for the complete understanding of transcription regulation in atomic detail. to study rnap by nmr spectros ... | 2015 | 26043358 |
| biosynthesis of l-sorbose and l-psicose based on c-c bond formation catalyzed by aldolases in an engineered corynebacterium glutamicum strain. | the property of loose stereochemical control at aldol products from aldolases helped to synthesize multiple polyhydroxylated compounds with nonnatural stereoconfiguration. in this study, we discovered for the first time that some fructose 1,6-diphosphate aldolases (frua) and tagatose 1,6-diphosphate (taga) aldolases lost their strict stereoselectivity when using l-glyceraldehyde and synthesized not only l-sorbose but also a high proportion of l-psicose. among the aldolases tested, taga from baci ... | 2015 | 25888171 |
| structural insights into the translational infidelity mechanism. | the decoding of mrna on the ribosome is the least accurate process during genetic information transfer. here we propose a unified decoding mechanism based on 11 high-resolution x-ray structures of the 70s ribosome that explains the occurrence of missense errors during translation. we determined ribosome structures in rare states where incorrect trnas were incorporated into the peptidyl-trna-binding site. these structures show that in the codon-anticodon duplex, a g·u mismatch adopts the watson-c ... | 2015 | 26037619 |