Publications

clpb n-terminal domain plays a regulatory role in protein disaggregation.	clpb/hsp100 is an atp-dependent disaggregase that solubilizes and reactivates protein aggregates in cooperation with the dnak/hsp70 chaperone system. the clpb-substrate interaction is mediated by conserved tyrosine residues located in flexible loops in nucleotide-binding domain-1 that extend into the clpb central pore. in addition to the tyrosines, the clpb n-terminal domain (ntd) was suggested to provide a second substrate-binding site; however, the manner in which the ntd recognizes and binds ...	2015	26621746
dancing through life: molecular dynamics simulations and network-centric modeling of allosteric mechanisms in hsp70 and hsp110 chaperone proteins.	hsp70 and hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. although many aspects of allosteric regulatory mechanisms in hsp70 and hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. in this work, ...	2015	26619280
characterization of aspartate kinase from corynebacterium pekinense and the critical site of arg169.	aspartate kinase (ak) is the key enzyme in the biosynthesis of aspartate-derived amino acids. recombinant ak was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. homogeneous ak was predicted as a decamer with a molecular weight of ~48 kda and a half-life of 4.5 h. the enzymatic activity was enhanced by ethanol and ni(2+). moreover, steady-state kinetic study confirmed that ak is an allosteric enzyme, and it ...	2015	26633359
active site coupling in plasmodium falciparum gmp synthetase is triggered by domain rotation.	gmp synthetase (gmps), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. crystal structures of plasmodium falciparum gmps in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the gatase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. we suggest that conformational ...	2015	26592566
identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna.	the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ...	2015	26590840
identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna.	the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ...	2015	26590840
metagenomics of an alkaline hot spring in galicia (spain): microbial diversity analysis and screening for novel lipolytic enzymes.	a fosmid library was constructed with the metagenomic dna from the water of the lobios hot spring (76°c, ph = 8.2) located in ourense (spain). metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 mbp. 23,207 orfs (open reading frames) were predicted from the assembly. biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. the six ...	2015	26635759
metagenomics: retrospect and prospects in high throughput age.	in recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. in the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. a brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenom ...	2015	26664751
natural guided genome engineering reveals transcriptional regulators controlling quorum-sensing signal degradation.	quorum-quenching (qq) are natural or engineered processes disrupting the quorum-sensing (qs) signalling which controls virulence and persistence (e.g. biofilm) in numerous bacteria. qq involves different enzymes including lactonases, amidases, oxidases and reductases which degrade the qs molecules such as n-acylhomoserine lactones (nahl). rhodococcus erythropolis known to efficiently degrade nahl is proposed as a biocontrol agent and a reservoir of qq-enzymes for biotechnology. in r. erythropoli ...	2015	26554837
spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha.	we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ...	2015	26553877
spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha.	we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ...	2015	26553877
extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals.	enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few ...	2015	26594201
thermus thermophilus as a source of thermostable lipolytic enzymes.	lipolytic enzymes, esterases (ec 3.1.1.1) and lipases (ec 3.1.1.3), catalyze the hydrolysis of ester bonds between alcohols and carboxylic acids, and its formation in organic media. at present, they represent about 20% of commercialized enzymes for industrial use. lipolytic enzymes from thermophilic microorganisms are preferred for industrial use to their mesophilic counterparts, mainly due to higher thermostability and resistance to several denaturing agents. however, the production at an indus ...	2015	27682117
structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism.	paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ...	2015	26538563
structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism.	paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ...	2015	26538563
the presence of highly disruptive 16s rrna mutations in clinical samples indicates a wider role for mutations of the mitochondrial ribosome in human disease.	mitochondrial dna mutations are well recognized as an important cause of disease, with over two hundred variants in the protein encoding and mt-trna genes associated with human disorders. in contrast, the two genes encoding the mitochondrial rrnas (mt-rrnas) have been studied in far less detail. this is because establishing the pathogenicity of mt-rrna mutations is a major diagnostic challenge. only two disease causing mutations have been identified at these loci, both mapping to the small subun ...	2015	26349026
coevolution of rtcb and archease created a multiple-turnover rna ligase.	rtcb is a noncanonical rna ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. the genes encoding rtcb and archease constitute a trna splicing operon in many organisms. archease is a cofactor of rtcb that accelerates rna ligation and alters the ntp specificity of the ligase from pyrococcus horikoshii. yet, not all organisms that encode rtcb also encode archease. here we sought to understand the differences between archease-dependent and archease-indepe ...	2015	26385509
structure and function of mitochondrial membrane protein complexes.	biological energy conversion in mitochondria is carried out by the membrane protein complexes of the respiratory chain and the mitochondrial atp synthase in the inner membrane cristae. recent advances in electron cryomicroscopy have made possible new insights into the structural and functional arrangement of these complexes in the membrane, and how they change with age. this review places these advances in the context of what is already known, and discusses the fundamental questions that remain ...	2015	26515107
current and future resources for functional metagenomics.	functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted dna of mixed microbial populations. a functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain dna cloned from environmental metagenomes. the information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. in this perspective, we b ...	2015	26579102
structure and two-metal mechanism of a eukaryal nick-sealing rna ligase.	atp-dependent rna ligases are agents of rna repair that join 3'-oh and 5'-po4 rna ends. naegleria gruberi rna ligase (ngrrnl) exemplifies a family of rna nick-sealing enzymes found in bacteria, viruses, and eukarya. crystal structures of ngrrnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-nζ)-amp•mn(2+) intermediate; ligase•atp•(mn(2+))2 michaelis complex; and ligase•mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound " ...	2015	26512110
enzyme-modified particles for selective biocatalytic hydrogenation by hydrogen-driven nadh recycling.	we describe a new approach to selective h2-driven hydrogenation that exploits a sequence of enzymes immobilised on carbon particles. we used a catalyst system that comprised alcohol dehydrogenase, hydrogenase and an nad(+) reductase on carbon black to demonstrate a greater than 98 % conversion of acetophenone to phenylethanol. oxidation of h2 by the hydrogenase provides electrons through the carbon for nad(+) reduction to recycle the nadh cofactor required by the alcohol dehydrogenase. this bioc ...	2015	26613009
defining the mrna recognition signature of a bacterial toxin protein.	bacteria contain multiple type ii toxins that selectively degrade mrnas bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (a) site, but how these endonucleases achieve substrate specificity remains poorly understood. here, we identify the critical features for how the host inhibition of growth b (higb) toxin recognizes each of the three a-sit ...	2015	26508639
thermodynamics of protein denaturation at temperatures over 100 °c: cuta1 mutant proteins substituted with hydrophobic and charged residues.	although the thermodynamics of protein denaturation at temperatures over 100 °c is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. we designed certain hydrophobic mutant proteins of cuta1 from escherichia coli, which have denaturation temperatures (td) ranging from 101 to 113 °c and show a reversible heat denaturation. using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mut ...	2015	26497062
saxs fingerprints of aldehyde dehydrogenase oligomers.	enzymes of the aldehyde dehydrogenase (aldh) superfamily catalyze the nicotinamide adenine dinucleotide-dependent oxidation of aldehydes to carboxylic acids. aldhs are important in detoxification of aldehydes, amino acid metabolism, embryogenesis and development, neurotransmission, oxidative stress, and cancer. mutations in genes encoding aldhs cause metabolic disorders, including alcohol flush reaction (aldh2), sjögren-larsson syndrome (aldh3a2), hyperprolinemia type ii (aldh4a1), γ-hydroxybuty ...	2015	26693506
crystal structure of the human trna m(1)a58 methyltransferase-trna(3)(lys) complex: refolding of substrate trna allows access to the methylation target.	human trna3(lys) is the primer for reverse transcription of hiv; the 3' end is complementary to the primer-binding site on hiv rna. the complementarity ends at the 18th base, a58, which in trna3(lys) is modified to remove watson-crick pairing. motivated to test the role of the modification in terminating the primer-binding sequence and thus limiting run-on transcription, we asked how the modification of rna could be accomplished. trna m(1)a58 methyltransferase (m(1)a58 mtase) methylates n1 of a5 ...	2015	26470919
discovery and functional characterization of diverse class 2 crispr-cas systems.	microbial crispr-cas systems are divided into class 1, with multisubunit effector complexes, and class 2, with single protein effectors. currently, only two class 2 effectors, cas9 and cpf1, are known. we describe here three distinct class 2 crispr-cas systems. the effectors of two of the identified systems, c2c1 and c2c3, contain ruvc-like endonuclease domains distantly related to cpf1. the third system, c2c2, contains an effector with two predicted hepn rnase domains. whereas production of mat ...	2015	26593719
how to show the real microbial biodiversity? a comparison of seven dna extraction methods for bacterial population analyses in matrices containing highly charged natural nanoparticles.	a dna extraction that comprises the dna of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged dna molecules after cell lysis within dna extraction. depending on the methodology of dna extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possibl ...	2015	27682112
a non-canonical multisubunit rna polymerase encoded by a giant bacteriophage.	the infection of pseudomonas aeruginosa by the giant bacteriophage phikz is resistant to host rna polymerase (rnap) inhibitor rifampicin. phikz encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit rnaps. polypeptides of one set are encoded by middle phage genes and are found in the phikz virions. polypeptides of the second set are encoded by early phage genes and are absent from virions. here, we report isolation of a five- ...	2015	26490960
mechanism of eif6 release from the nascent 60s ribosomal subunit.	sbds protein (deficient in the inherited leukemia-predisposition disorder shwachman-diamond syndrome) and the gtpase efl1 (an ef-g homolog) activate nascent 60s ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eif6 from nascent 60s ribosomal subunits. however, the mechanism is completely unknown. here, we present cryo-em structures of human sbds and sbds-efl1 bound to dictyostelium discoideum 60s ribosomal subunits with and without endogenous eif6. sbds ass ...	2015	26479198
computational analysis of candidate prion-like proteins in bacteria and their role.	prion proteins were initially associated with diseases such as creutzfeldt jakob and transmissible spongiform encephalopathies. however, deeper research revealed them as versatile tools, exploited by the cells to execute fascinating functions, acting as epigenetic elements or building membrane free compartments in eukaryotes. one of the most intriguing properties of prion proteins is their ability to propagate a conformational assembly, even across species. in this context, it has been observed ...	2015	26528269
structural insights into species-specific features of the ribosome from the pathogen staphylococcus aureus.	the emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. here we present the crystal structure of the large ribosomal subunit from staphylococcus aureus, a versatile gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, bc-3205. these crystal structures shed light on specific structural motifs of the s. aureus ribosome ...	2015	26464510
ribosome hibernation facilitates tolerance of stationary-phase bacteria to aminoglycosides.	upon entry into stationary phase, bacteria dimerize 70s ribosomes into translationally inactive 100s particles by a process called ribosome hibernation. previously, we reported that the hibernation-promoting factor (hpf) of listeria monocytogenes is required for 100s particle formation and facilitates adaptation to a number of stresses. here, we demonstrate that hpf is required for the high tolerance of stationary-phase cultures to aminoglycosides but not to beta-lactam or quinolone antibiotics. ...	2015	26324267
fr171456 is a specific inhibitor of mammalian nsdhl and yeast erg26p.	fr171456 is a natural product with cholesterol-lowering properties in animal models, but its molecular target is unknown, which hinders further drug development. here we show that fr171456 specifically targets the sterol-4-alpha-carboxylate-3-dehydrogenase (saccharomyces cerevisiae--erg26p, homo sapiens--nsdhl (nad(p) dependent steroid dehydrogenase-like)), an essential enzyme in the ergosterol/cholesterol biosynthesis pathway. fr171456 significantly alters the levels of cholesterol pathway inte ...	2015	26456460
structural analysis of nucleosomal barrier to transcription.	thousands of human and drosophila genes are regulated at the level of transcript elongation and nucleosomes are likely targets for this regulation. however, the molecular mechanisms of formation of the nucleosomal barrier to transcribing rna polymerase ii (pol ii) and nucleosome survival during/after transcription remain unknown. here we show that both dna-histone interactions and pol ii backtracking contribute to formation of the barrier and that nucleosome survival during transcription likely ...	2015	26460019
structural comparison between the open and closed forms of citrate synthase from thermus thermophilus hb8.	the crystal structures of citrate synthase from the thermophilic eubacteria thermus thermophilus hb8 (ttcs) were determined for an open form at 1.5 å resolution and for closed form at 2.3 å resolution, respectively. in the absence of ligands ttcs in the open form was crystalized into a tetragonal form with a single subunit in the asymmetric unit. ttcs was also co-crystallized with citrate and coenzyme-a to form an orthorhombic crystal with two homodimers in the asymmetric unit. citrate and coa a ...	2015	27493854
caenorhabditis elegans glp-4 encodes a valyl aminoacyl trna synthetase.	germline stem cell proliferation is necessary to populate the germline with sufficient numbers of cells for gametogenesis and for signaling the soma to control organismal properties such as aging. the caenorhabditis elegans gene glp-4 was identified by the temperature-sensitive allele bn2 where mutants raised at the restrictive temperature produce adults that are essentially germ cell deficient, containing only a small number of stem cells arrested in the mitotic cycle but otherwise have a morph ...	2015	26464357
structure of a human translation termination complex.	in contrast to bacteria that have two release factors, rf1 and rf2, eukaryotes only possess one unrelated release factor erf1, which recognizes all three stop codons of the mrna and hydrolyses the peptidyl-trna bond. while the molecular basis for bacterial termination has been elucidated, high-resolution structures of eukaryotic termination complexes have been lacking. here we present a 3.8 å structure of a human translation termination complex with erf1 decoding a uaa(a) stop codon. the complex ...	2015	26384426
structural insight into fungal cell wall recognition by a cvnh protein with a single lysm domain.	mgg_03307 is a lectin isolated from magnaporte oryzae, a fungus that causes devastating rice blast disease. its function is associated with protecting m. oryzae from the host immune response in plants. to provide the structural basis of how mgg_03307 protects the fungus, crystal structures of its cvnh-lysm module were determined in the absence and presence of glcnac-containing cell wall chitin constituents, which can act as pathogen-associated molecular patterns. our structures revealed that gly ...	2015	26455798
a particular silent codon exchange in a recombinant gene greatly influences host cell metabolic activity.	recombinant protein production using escherichia coli as expression host is highly efficient, however, it also induces strong host cell metabolic burden. energy and biomass precursors are withdrawn from the host's metabolism as they are required for plasmid replication, heterologous gene expression and protein production. rare codons in a heterologous gene may be a further drawback. this study aims to investigate the influence of particular silent codon exchanges within a heterologous gene on ho ...	2015	26438243
an extended dsrbd is required for post-transcriptional modification in human trnas.	in trna, dihydrouridine is a conserved modified base generated by the post-transcriptional reduction of uridine. formation of dihydrouridine 20, located in the d-loop, is catalyzed by dihydrouridine synthase 2 (dus2). human dus2 (hsdus2) expression is upregulated in lung cancers, offering a growth advantage throughout its ability to interact with components of the translation apparatus and inhibit apoptosis. here, we report the crystal structure of the individual domains of hsdus2 and their func ...	2015	26429968
effect of monovalent cations on the kinetics of hypoxic conformational change of mitochondrial complex i.	mitochondrial complex i is a large, membrane-bound enzyme central to energy metabolism, and its dysfunction is implicated in cardiovascular and neurodegenerative diseases. an interesting feature of mammalian complex i is the so-called a/d transition, when the idle enzyme spontaneously converts from the active (a) to the de-active, dormant (d) form. the a/d transition plays an important role in tissue response to ischemia and rate of the conversion can be a crucial factor determining outcome of i ...	2015	26009015
recent insights into the structure, regulation, and function of the v-atpases.	the vacuolar (h(+))-atpases (v-atpases) are atp-dependent proton pumps that acidify intracellular compartments and are also present at the plasma membrane. they function in such processes as membrane traffic, protein degradation, virus and toxin entry, bone resorption, ph homeostasis, and tumor cell invasion. v-atpases are large multisubunit complexes, composed of an atp-hydrolytic domain (v1) and a proton translocation domain (v0), and operate by a rotary mechanism. this review focuses on recen ...	2015	26410601
variation in the ribosome interacting loop of the sec61α from giardia lamblia.	the interaction between the ribosome and the endoplasmic reticulum-located sec61 protein translocon is mediated through an arginine residue of sec61α, which is conserved in all prokaryotic and eukaryotic orthologues characterized to date. using in silico approaches we report that instead of arginine, this ribosome-interaction function is most likely discharged by a lysine residue in the protist giardia lamblia. this functional substitution of the r with a k in glsec61α may have taken place to ac ...	2015	26424409
choosing a suitable method for the identification of replication origins in microbial genomes.	as the replication of genomic dna is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. making sense of dna replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. thus, clearly comprehending the positions and sequences of replicat ...	2015	26483774
affinity purification and structural features of the yeast vacuolar atpase vo membrane sector.	the membrane sector (vo) of the proton pumping vacuolar atpase (v-atpase, v1vo-atpase) from saccharomyces cerevisiae was purified to homogeneity, and its structure was characterized by em of single molecules and two-dimensional crystals. projection images of negatively stained vo two-dimensional crystals showed a ring-like structure with a large asymmetric mass at the periphery of the ring. a cryo-em reconstruction of vo from single-particle images showed subunits a and d in close contact on the ...	2015	26416888
acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals.	the diffuse scattering pattern produced by frozen crystals of the 70s ribosome from thermus thermophilus is as highly structured as it would be if it resulted entirely from domain-scale motions within these particles. however, the qualitative properties of the scattering pattern suggest that acoustic displacements of the crystal lattice make a major contribution to it.	2015	26457426
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