Publications

synergism between a foldase and an unfoldase: reciprocal dependence between the thioredoxin-like activity of dnaj and the polypeptide-unfolding activity of dnak.	the role of bacterial hsp40, dnaj, is to co-chaperone the binding of misfolded or alternatively folded proteins to bacterial hsp70, dnak, which is an atp-fuelled unfolding chaperone. in addition to its dnak targeting activity, dnaj has a weak thiol-reductase activity. in between the substrate-binding domain and the j-domain anchor to dnak, dnaj has a unique domain with four conserved cxxc motives that bind two zn(2+) and partly contribute to polypeptide binding. here, we deleted in dnaj this zn- ...	2014	25988148
phylobiochemical characterization of class-ib aspartate/prephenate aminotransferases reveals evolution of the plant arogenate phenylalanine pathway.	the aromatic amino acid phe is required for protein synthesis and serves as the precursor of abundant phenylpropanoid plant natural products. while phe is synthesized from prephenate exclusively via a phenylpyruvate intermediate in model microbes, the alternative pathway via arogenate is predominant in plant phe biosynthesis. however, the molecular and biochemical evolution of the plant arogenate pathway is currently unknown. here, we conducted phylogenetically informed biochemical characterizat ...	2014	25070637
transcription regulation mechanisms of bacteriophages: recent advances and future prospects.	phage diversity significantly contributes to ecology and evolution of new bacterial species through horizontal gene transfer. therefore, it is essential to understand the mechanisms underlying phage-host interactions. after initial infection, the phage utilizes the transcriptional machinery of the host to direct the expression of its own genes. this review presents a view on the transcriptional regulation mechanisms of bacteriophages, and its contribution to phage diversity and classification. t ...	2014	25482231
evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution.	classically viewed as a cytosolic pathway, glycolysis is increasingly recognized as a metabolic pathway exhibiting surprisingly wide-ranging variations in compartmentalization within eukaryotic cells. trypanosomatid parasites provide an extreme view of glycolytic enzyme compartmentalization as several glycolytic enzymes are found exclusively in peroxisomes. here, we characterize trypanosoma brucei flagellar proteins resembling glyceraldehyde-3-phosphate dehydrogenase (gapdh) and phosphoglycerate ...	2014	25050549
an update on complex i assembly: the assembly of players.	defects in complex i assembly is one of the emerging underlying causes of severe mitochondrial disorders. the assembly of complex i has been difficult to understand due to its large size, dual genetic control and the number of proteins involved. mutations in complex i subunits as well as assembly factors have been reported to hinder its assembly and give rise to a range of mitochondria disorders. in this review, we summarize the recent progress made in understanding the complex i assembly pathwa ...	2014	25030182
the hypusine-containing translation factor eif5a.	in addition to the small and large ribosomal subunits, aminoacyl-trnas, and an mrna, cellular protein synthesis is dependent on translation factors. the eukaryotic translation initiation factor 5a (eif5a) and its bacterial ortholog elongation factor p (ef-p) were initially characterized based on their ability to stimulate methionyl-puromycin (met-pmn) synthesis, a model assay for protein synthesis; however, the function of these factors in cellular protein synthesis has been difficult to resolve ...	2014	25029904
structures of yeast 80s ribosome-trna complexes in the rotated and nonrotated conformations.	the structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. here, we present two subnanometer resolution structures of s. cerevisiae 80s ribosome complexes formed with either one or two trnas and bound in response to an mrna fragment containing the kozak consensus sequence. the ribosomes adopt two globally different conformations that are related to each other by the rotation of the small subunit. comparison with bacterial ribosome complexes rev ...	2014	25043550
biochemical and cellular analysis of human variants of the dyt1 dystonia protein, torsina/tor1a.	early-onset dystonia is associated with the deletion of one of a pair of glutamic acid residues (c.904_906delgag/c.907_909delgag; p.glu302del/glu303del; δe 302/303) near the carboxyl-terminus of torsina, a member of the aaa(+) protein family that localizes to the endoplasmic reticulum lumen and nuclear envelope. this deletion commonly underlies early-onset dyt1 dystonia. while the role of the disease-causing mutation, torsinaδe, has been established through genetic association studies, it is muc ...	2014	24930953
road rules for traffic on dna-systematic analysis of transcriptional roadblocking in vivo.	genomic dna is bound by many proteins that could potentially impede elongation of rna polymerase (rnap), but the factors determining the magnitude of transcriptional roadblocking in vivo are poorly understood. through systematic experiments and modeling, we analyse how roadblocking by the lac repressor (laci) in escherichia coli cells is controlled by promoter firing rate, the concentration and affinity of the roadblocker protein, the transcription-coupled repair protein mfd, and promoter-roadbl ...	2014	25034688
the cca-end of p-trna contacts both the human rpl36al and the a-site bound translation termination factor erf1 at the peptidyl transferase center of the human 80s ribosome.	we have demonstrated previously that the e-site specific protein rpl36al present in human ribosomes can be crosslinked with the cca-end of a p-trna in situ. here we report the following: (i) we modeled rpl36al into the structure of the archaeal ortholog rpl44e extracted from the known x-ray structure of the 50s subunit of haloarcula marismortui. superimposing the obtained rpl36al structure with that of p/e trna observed in eukaryotic 80s ribosomes suggested that rpl36al might in addition to its ...	2014	25191528
reverse gyrase--recent advances and current mechanistic understanding of positive dna supercoiling.	reverse gyrases are topoisomerases that introduce positive supercoils into dna in an atp-dependent reaction. they consist of a helicase domain and a topoisomerase domain that closely cooperate in catalysis. the mechanism of the functional cooperation of these domains has remained elusive. recent studies have shown that the helicase domain is a nucleotide-regulated conformational switch that alternates between an open conformation with a low affinity for double-stranded dna, and a closed state wi ...	2014	25013168
molecular characterization of the na+/h+-antiporter nhaa from salmonella typhimurium.	na+/h+ antiporters are integral membrane proteins that are present in almost every cell and in every kingdom of life. they are essential for the regulation of intracellular ph-value, na+-concentration and cell volume. these secondary active transporters exchange sodium ions against protons via an alternating access mechanism, which is not understood in full detail. na+/h+ antiporters show distinct species-specific transport characteristics and regulatory properties that correlate with respective ...	2014	25010413
phages preying on bacillus anthracis, bacillus cereus, and bacillus thuringiensis: past, present and future.	many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. however, less attention has been paid to phages preying on bacteria from the bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. therefore, this review brings together the main information for the b. cereus group phages, from their discovery to their modern biotechnological applications. a special focus is given to phages infect ...	2014	25010767
structure and function of pseudoknots involved in gene expression control.	natural rna molecules can have a high degree of structural complexity but even the most complexly folded rnas are assembled from simple structural building blocks. among the simplest rna elements are double-stranded helices that participate in the formation of different folding topologies and constitute the major fraction of rna structures. one common folding motif of rna is a pseudoknot, defined as a bipartite helical structure formed by base-pairing of the apical loop in the stem-loop structur ...	2014	25044223
structure of pneumococcal peptidoglycan hydrolase lytb reveals insights into the bacterial cell wall remodeling and pathogenesis.	streptococcus pneumoniae causes a series of devastating infections in humans. previous studies have shown that the endo-β-n-acetylglucosaminidase lytb is critical for pneumococcal cell division and nasal colonization, but the biochemical mechanism of lytb action remains unknown. here we report the 1.65 å crystal structure of the catalytic domain (residues lys-375-asp-658) of lytb (termed lytbcat), excluding the choline binding domain. lytbcat consists of three structurally independent modules: s ...	2014	25002590
ancient translation factor is essential for trna-dependent cysteine biosynthesis in methanogenic archaea.	methanogenic archaea lack cysteinyl-trna synthetase; they synthesize cys-trna and cysteine in a trna-dependent manner. two enzymes are required: phosphoseryl-trna synthetase (seprs) forms phosphoseryl-trna(cys) (sep-trna(cys)), which is converted to cys-trna(cys) by sep-trna:cys-trna synthase (sepcyss). this represents the ancestral pathway of cys biosynthesis and coding in archaea. here we report a translation factor, sepcyse, essential for methanococcal cys biosynthesis; its deletion in methan ...	2014	25002468
free-energy landscape of reverse trna translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.	to understand the mechanism of reverse trna translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-trnas-mrna-efg complex were performed. the complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-em density maps. between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. multistep structural changes, such ...	2014	24999999
proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric apex tagging.	obtaining complete protein inventories for subcellular regions is a challenge that often limits our understanding of cellular function, especially for regions that are impossible to purify and are therefore inaccessible to traditional proteomic analysis. we recently developed a method to map proteomes in living cells with an engineered peroxidase (apex) that bypasses the need for organellar purification when applied to membrane-bound compartments; however, it was insufficiently specific when app ...	2014	25002142
regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement.	the extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80s ribosome in the posttranslocational state and in complex with the eukaryotic eef1a⋅val-trna⋅gmppnp ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. surprisingly, and in contrast to bacterial riboso ...	2014	24995983
3'-biotin-tagged microrna-27 does not associate with argonaute proteins in cells.	synthetic 3'-biotin-tagged micrornas (mirnas) have often been used to select interacting messenger rna (mrna) and noncoding rna (ncrna) targets. here, we examined the extent of association of 3'-end biotinylated mir-27 with argonaute (ago) proteins in transfected human cells using a coimmunoprecipitation assay followed by northern blot analysis. we report that biotinylated mir-27 does not efficiently associate with ago compared to unmodified mir-27. these results suggest that 3'-end biotin-modif ...	2014	24821854
examining the gm18 and m(1)g modification positions in trna sequences.	the trna structure contains conserved modifications that are responsible for its stability and are involved in the initiation and accuracy of the translation process. trna modification enzymes are prevalent in bacteria, archaea, and eukaryotes. trna gm18 methyltransferase (trmh) and trna m(1)g37 methyltransferase (trmd) are prevalent and essential enzymes in bacterial populations. trmh involves itself in methylation process at the 2'-oh group of ribose at the 18th position of guanosine (g) in tr ...	2014	25031570
oral manifestations of hepatitis c virus infection.	extrahepatic manifestations (ehms) of hepatitis c virus (hcv) infection can affect a variety of organ systems with significant morbidity and mortality. some of the most frequently reported ehm of hcv infection, involve the oral region predominantly or exclusively. oral lichen planus (olp) is a chronic inflammatory condition that is potentially malignant and represents cell-mediated reaction to a variety of extrinsic antigens, altered self-antigens, or super antigens. robust epidemiological evide ...	2014	24976694
structural basis of transcription initiation by bacterial rna polymerase holoenzyme.	the bacterial rna polymerase (rnap) holoenzyme containing σ factor initiates transcription at specific promoter sites by de novo rna priming, the first step of rna synthesis where rnap accepts two initiating ribonucleoside triphosphates (intps) and performs the first phosphodiester bond formation. we present the structure of de novo transcription initiation complex that reveals unique contacts of the intps bound at the transcription start site with the template dna and also with rnap and demonst ...	2014	24973216
conjugation with polyamines enhances the antibacterial and anticancer activity of chloramphenicol.	chloramphenicol (cam) is a broad-spectrum antibiotic, limited to occasional only use in developed countries because of its potential toxicity. to explore the influence of polyamines on the uptake and activity of cam into cells, a series of polyamine-cam conjugates were synthesized. both polyamine architecture and the position of cam-scaffold substitution were crucial in augmenting the antibacterial and anticancer potency of the synthesized conjugates. compounds 4 and 5, prepared by replacement o ...	2014	24939899
crystal structure of clostridium acetobutylicum aspartate kinase (caak): an important allosteric enzyme for amino acids production.	aspartate kinase (ak) is an enzyme which is tightly regulated through feedback control and responsible for the synthesis of 4-phospho-l-aspartate from l-aspartate. this intermediate step is at an important branch point where one path leads to the synthesis of lysine and the other to threonine, methionine and isoleucine. concerted feedback inhibition of ak is mediated by threonine and lysine and varies between the species. the crystal structure of biotechnologically important clostridium acetobut ...	2014	25170437
macrolide antibiotics allosterically predispose the ribosome for translation arrest.	translation arrest directed by nascent peptides and small cofactors controls expression of important bacterial and eukaryotic genes, including antibiotic resistance genes, activated by binding of macrolide drugs to the ribosome. previous studies suggested that specific interactions between the nascent peptide and the antibiotic in the ribosomal exit tunnel play a central role in triggering ribosome stalling. however, here we show that macrolides arrest translation of the truncated ermdl regulato ...	2014	24961372
identification of promiscuous ene-reductase activity by mining structural databases using active site constellations.	the exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). as a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated c-c double bonds) and compare ...	2014	24954722
life at the border: adaptation of proteins to anisotropic membrane environment.	this review discusses main features of transmembrane (tm) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. we overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale confor ...	2014	24947665
homology modeling and comparative profiling of superoxide dismutase among extremophiles: exiguobacterium as a model organism.	superoxide dismutase (sod), a well known antioxidant enzyme, is known to exert its presence across bacteria to humans. apart from their well-known antioxidant defense mechanisms, their association with various extremophiles in response to various stress conditions is poorly understood. here, we have discussed the conservation and the prevalence of sods among 21 representative extremophiles. a systematic investigation of aligned amino acid sequences of sod from all the selected extremophiles reve ...	2014	25320445
xanthomonas campestris rpfb is a fatty acyl-coa ligase required to counteract the thioesterase activity of the rpff diffusible signal factor (dsf) synthase.	in xanthomonas campestris pv. campestris (xcc), the proteins encoded by the rpf (regulator of pathogenicity factor) gene cluster produce and sense a fatty acid signal molecule called diffusible signalling factor (dsf, 2(z)-11-methyldodecenoic acid). rpfb was reported to be involved in dsf processing and was predicted to encode an acyl-coa ligase. we report that rpfb activates a wide range of fatty acids to their coa esters in vitro. moreover, rpfb can functionally replace the paradigm bacterial ...	2014	24866092
lysine propionylation is a prevalent post-translational modification in thermus thermophilus.	recent studies of protein post-translational modifications revealed that various types of lysine acylation occur in eukaryotic and bacterial proteins. lysine propionylation, a newly discovered type of acylation, occurs in several proteins, including some histones. in this study, we identified 361 propionylation sites in 183 mid-exponential phase and late stationary phase proteins from thermus thermophilus hb8, an extremely thermophilic eubacterium. functional classification of the propionylprote ...	2014	24938286
the flavoprotein mcap0476 (rlmfo) catalyzes m5u1939 modification in mycoplasma capricolum 23s rrna.	efficient protein synthesis in all organisms requires the post-transcriptional methylation of specific ribosomal ribonucleic acid (rrna) and transfer rna (trna) nucleotides. the methylation reactions are almost invariably catalyzed by enzymes that use s-adenosylmethionine (adomet) as the methyl group donor. one noteworthy exception is seen in some bacteria, where the conserved trna methylation at m5u54 is added by the enzyme trmfo using flavin adenine dinucleotide together with n5,n10-methylenet ...	2014	24939895
the role of a novel auxiliary pocket in bacterial phenylalanyl-trna synthetase druggability.	the antimicrobial activity of phenyl-thiazolylurea-sulfonamides against staphylococcus aureus phers are dependent upon phenylalanine levels in the extracellular fluids. inhibitor efficacy in animal models of infection is substantially diminished by dietary phenylalanine intake, thereby reducing the perceived clinical utility of this inhibitor class. the search for novel antibacterial compounds against gram-negative pathogens led to a re-evaluation of this phenomenon, which is shown here to be un ...	2014	24936059
genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake.	salinivibrios are moderately halophilic bacteria found in salted meats, brines and hypersaline environments. we obtained three novel conspecific salinivibrio strains closely related to s. costicola, from socompa lake, a high altitude hypersaline andean lake (approx. 3,570 meters above the sea level).	2014	24927949
unravelling the structural and mechanistic basis of crispr-cas systems.	bacteria and archaea have evolved sophisticated adaptive immune systems, known as crispr-cas (clustered regularly interspaced short palindromic repeats-crispr-associated proteins) systems, which target and inactivate invading viruses and plasmids. immunity is acquired by integrating short fragments of foreign dna into crispr loci, and following transcription and processing of these loci, the crispr rnas (crrnas) guide the cas proteins to complementary invading nucleic acid, which results in targ ...	2014	24909109
the structural basis of transfer rna mimicry and conformational plasticity by a viral rna.	rna is arguably the most functionally diverse biological macromolecule. in some cases a single discrete rna sequence performs multiple roles, and this can be conferred by a complex three-dimensional structure. such multifunctionality can also be driven or enhanced by the ability of a given rna to assume different conformational (and therefore functional) states. despite its biological importance, a detailed structural understanding of the paradigm of rna structure-driven multifunctionality is la ...	2014	24909993
determination of kinetics and the crystal structure of a novel type 2 isopentenyl diphosphate: dimethylallyl diphosphate isomerase from streptococcus pneumoniae.	isopentenyl diphosphate isomerase (idi) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. type 1 idi (idi-1) is a metalloprotein that is found in eukaryotes, whereas the type 2 isoform (idi-2) is a flavoenzyme found in bacteria that is completely absent from human. idi-2 from the pathogenic bacterium streptococcus pneumoniae was recombinantly expressed in escherichia coli. steady-state kinetic studies ...	2014	24910111
archaeal tuc1/ncs6 homolog required for wobble uridine trna thiolation is associated with ubiquitin-proteasome, translation, and rna processing system homologs.	while cytoplasmic trna 2-thiolation protein 1 (tuc1/ncs6) and ubiquitin-related modifier-1 (urm1) are important in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2u) at wobble uridines of trnas in eukaryotes, the biocatalytic roles and properties of ncs6/tuc1 and its homologs are poorly understood. here we present the first report of an ncs6 homolog of archaea (ncsa of haloferax volcanii) that is essential for maintaining cellular pools of thiolated trna(lys)uuu and for growth a ...	2014	24906001
evidence for a catalytically and kinetically competent enzyme-substrate cross-linked intermediate in catalysis by lipoyl synthase.	lipoyl synthase (ls) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at c6 and c8 of an (n(6)-octanoyl)-lysyl residue on a lipoyl carrier protein (lcp). ls is a member of the radical sam superfamily, enzymes that use a [4fe-4s] cluster to effect the reductive cleavage of s-adenosyl-l-methionine (sam) to l-methionine and a 5'-deoxyadenosyl 5'-radical (5'-da(•)). in the ls reaction, two equivalents of 5'-da(•) are generated sequentially to abstract hydro ...	2014	24901788
crystal structure of trna m(1)a58 methyltransferase trmi from aquifex aeolicus in complex with s-adenosyl-l-methionine.	the n (1)-methyladenosine residue at position 58 of trna is found in the three domains of life, and contributes to the stability of the three-dimensional l-shaped trna structure. in thermophilic bacteria, this modification is important for thermal adaptation, and is catalyzed by the trna m(1)a58 methyltransferase trmi, using s-adenosyl-l-methionine (adomet) as the methyl donor. we present the 2.2 å crystal structure of trmi from the extremely thermophilic bacterium aquifex aeolicus, in complex w ...	2014	24894648
condensation and localization of the partitioning protein parb on the bacterial chromosome.	the parabs system mediates chromosome segregation and plasmid partitioning in many bacteria. as part of the partitioning mechanism, parb proteins form a nucleoprotein complex at pars sites. the biophysical basis underlying parb-dna complex formation and localization remains elusive. specifically, it is unclear whether parb spreads in 1d along dna or assembles into a 3d protein-dna complex. we show that a combination of 1d spreading bonds and a single 3d bridging bond between parb proteins consti ...	2014	24927534
oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code.	aminoacyl-trna synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. the physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost vs benefit of accurate protein synthesis is difficult to predict. we show that in escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein ...	2014	24891238
nd3, nd1 and 39kda subunits are more exposed in the de-active form of bovine mitochondrial complex i.	an intriguing feature of mitochondrial complex i from several species is the so-called a/d transition, whereby the idle enzyme spontaneously converts from the active (a) form to the de-active (d) form. the a/d transition plays an important role in tissue response to the lack of oxygen and hypoxic deactivation of the enzyme is one of the key regulatory events that occur in mitochondria during ischaemia. we demonstrate for the first time that the a/d conformational change of complex i does not aff ...	2014	24560811
life-history constraints on the mechanisms that control the rate of ros production.	the quest to understand why and how we age has led to numerous lines of investigation that have gradually converged to consider mitochondrial metabolism as a major player. during mitochondrial respiration a small and variable amount of the consumed oxygen is converted to reactive species of oxygen (ros). for many years, these ros have been perceived as harmful by-products of respiration. however, evidence from recent years indicates that ros fulfill important roles as cellular messengers. result ...	2014	24955029
parb spreading requires dna bridging.	the parabs system is a widely employed mechanism for plasmid partitioning and chromosome segregation in bacteria. parb binds to pars sites on plasmids and chromosomes and associates with broad regions of adjacent dna, a phenomenon known as spreading. although essential for parb function, the mechanism of spreading remains poorly understood. using single-molecule approaches, we discovered that bacillus subtilis parb (spo0j) is able to trap dna loops. point mutants in spo0j that disrupt dna bridgi ...	2014	24829297
randomly selected suppressor mutations in genes for nadh : quinone oxidoreductase-1, which rescue motility of a salmonella ubiquinone-biosynthesis mutant strain.	the primary mobile electron-carrier in the aerobic respiratory chain of salmonella is ubiquinone. demethylmenaquinone and menaquinone are alternative electron-carriers involved in anaerobic respiration. ubiquinone biosynthesis was disrupted in strains bearing deletions of the ubia or ubie genes. in soft tryptone agar both mutant strains swam poorly. however, the ubia deletion mutant strain produced suppressor mutant strains with somewhat rescued motility and growth. six independent suppressor mu ...	2014	24692644
chemical synthesis of the 5-taurinomethyl(-2-thio)uridine modified anticodon arm of the human mitochondrial trna(leu(uur)) and trna(lys).	5-taurinomethyluridine (τm(5)u) and 5-taurinomethyl-2-thiouridine (τm(5)s(2)u) are located at the wobble position of human mitochondrial (hmt) trna(leu(uur)) and trna(lys), respectively. both hypermodified units restrict decoding of the third codon letter to a and g. pathogenic mutations in the genes encoding hmt-trna(leu(uur)) and hmt-trna(lys) are responsible for the loss of the discussed modifications and, as a consequence, for the occurrence of severe mitochondrial dysfunctions (melas, merrf ...	2014	24757169
non-nearest-neighbor dependence of stability for group iii rna single nucleotide bulge loops.	thirty-five rna duplexes containing single nucleotide bulge loops were optically melted and the thermodynamic parameters for each duplex determined. the bulge loops were of the group iii variety, where the bulged nucleotide is either a ag/u or cu/g, leading to ambiguity to the exact position and identity of the bulge. all possible group iii bulge loops with watson-crick nearest-neighbors were examined. the data were used to develop a model to predict the free energy of an rna duplex containing a ...	2014	24742935
amino acid-dependent stability of the acyl linkage in aminoacyl-trna.	aminoacyl-trnas are the biologically active substrates for peptide bond formation in protein synthesis. the stability of the acyl linkage in each aminoacyl-trna, formed through an ester bond that connects the amino acid carboxyl group with the trna terminal 3'-oh group, is thus important. while the ester linkage is the same for all aminoacyl-trnas, the stability of each is not well characterized, thus limiting insight into the fundamental process of peptide bond formation. here, we show, by anal ...	2014	24751649
structural and bioinformatic characterization of an acinetobacter baumannii type ii carrier protein.	microorganisms produce a variety of natural products via secondary metabolic biosynthetic pathways. two of these types of synthetic systems, the nonribosomal peptide synthetases (nrpss) and polyketide synthases (pkss), use large modular enzymes containing multiple catalytic domains in a single protein. these multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. i ...	2014	24914982
prokaryotic ubiquitin-like protein modification.	prokaryotes form ubiquitin (ub)-like isopeptide bonds on the lysine residues of proteins by at least two distinct pathways that are reversible and regulated. in mycobacteria, the c-terminal gln of pup (prokaryotic ubiquitin-like protein) is deamidated and isopeptide linked to proteins by a mechanism distinct from ubiquitylation in enzymology yet analogous to ubiquitylation in targeting proteins for destruction by proteasomes. ub-fold proteins of archaea (samps, small archaeal modifier proteins) ...	2014	24995873
loss of quaternary structure is associated with rapid sequence divergence in the osbs family.	the rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. as a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (osbs) family, which catalyzes a step in menaquino ...	2014	24872444
crystallization and preliminary x-ray crystallographic analysis of a bacterial asn-transamidosome.	most canonical aminoacyl-trnas are synthesized directly by their cognate aminoacyl-trna synthetases (aarss), but glutaminyl-trna(gln) and asparaginyl-trna(asn) are synthesized indirectly by two-step processes. these processes are catalyzed by the transamidosome, a large ribonucleoprotein particle composed of gata, gatb, gatc, aars and trna. in this study, the asn-transamidosome from pseudomonas aeruginosa was reconstructed and crystallized by mixing purified gatcab complex, asprs and trna(asn). ...	2014	24915095
intact functional fourteen-subunit respiratory membrane-bound [nife]-hydrogenase complex of the hyperthermophilic archaeon pyrococcus furiosus.	the archaeon pyrococcus furiosus grows optimally at 100 °c by converting carbohydrates to acetate, co2, and h2, obtaining energy from a respiratory membrane-bound hydrogenase (mbh). this conserves energy by coupling h2 production to oxidation of reduced ferredoxin with generation of a sodium ion gradient. mbh is encoded by a 14-gene operon with both hydrogenase and na(+)/h(+) antiporter modules. herein a his-tagged mbh was expressed in p. furiosus and the detergent-solubilized complex purified u ...	2014	24860091
deletion of the cyclic di-amp phosphodiesterase gene (cnpb) in mycobacterium tuberculosis leads to reduced virulence in a mouse model of infection.	tuberculosis (tb) remains a major cause of morbidity and mortality worldwide. the pathogenesis by the causative agent, mycobacterium tuberculosis, is still not fully understood. we have previously reported that m. tuberculosis rv3586 (disa) encodes a diadenylate cyclase, which converts atp to cyclic di-amp (c-di-amp). in this study, we demonstrated that a protein encoded by rv2837c (cnpb) possesses c-di-amp phosphodiesterase activity and cleaves c-di-amp exclusively to amp. our results showed th ...	2014	24806618
evidence for a dna-relay mechanism in parabs-mediated chromosome segregation.	the widely conserved parabs system plays a major role in bacterial chromosome segregation. how the components of this system work together to generate translocation force and directional motion remains uncertain. here, we combine biochemical approaches, quantitative imaging and mathematical modeling to examine the mechanism by which para drives the translocation of the parb/pars partition complex in caulobacter crescentus. our experiments, together with simulations grounded on experimentally-det ...	2014	24859756
methylated nucleosides in trna and trna methyltransferases.	to date, more than 90 modified nucleosides have been found in trna and the biosynthetic pathways of the majority of trna modifications include a methylation step(s). recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in trna is important for correct and efficient protein synthesis. in this review, i focus on the methylated nucleosides and trna methyltransferases. the primary functions of trna methylations are linked to t ...	2014	24904644
coliphage hk022 nun protein inhibits rna polymerase translocation.	the nun protein of coliphage hk022 arrests rna polymerase (rnap) in vivo and in vitro at pause sites distal to phage λ n-utilization (nut) site rna sequences. we tested the activity of nun on ternary elongation complexes (tecs) assembled with templates lacking the λ nut sequence. we report that nun stabilizes both translocation states of rnap by restricting lateral movement of tec along the dna register. when nun stabilized tec in a pretranslocated register, immediately after nmp incorporation, ...	2014	24853501
structural and evolutionary aspects of antenna chromophore usage by class ii photolyases.	light-harvesting and resonance energy transfer to the catalytic fad cofactor are key roles for the antenna chromophores of light-driven dna photolyases, which remove uv-induced dna lesions. so far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. despite a common protein topology, structural analysis of the distantly related class ii photolyase from the archaeon methan ...	2014	24849603
reduced ribosomes of the apicoplast and mitochondrion of plasmodium spp. and predicted interactions with antibiotics.	apicomplexan protists such as plasmodium and toxoplasma contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. we carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite or ...	2014	24850912
the role of ribonucleases in regulating global mrna levels in the model organism thermus thermophilus hb8.	rna metabolism, including rna synthesis and rna degradation, is one of the most conserved biological systems and has been intensively studied; however, the degradation network of ribonucleases (rnases) and rna substrates is not fully understood.	2014	24884843
gla-rich protein is a potential new vitamin k target in cancer: evidences for a direct grp-mineral interaction.	gla-rich protein (grp) was described in sturgeon as a new vitamin-k-dependent protein (vkdp) with a high density of gla residues and associated with ectopic calcifications in humans. although vkdps function has been related with γ-carboxylation, the gla status of grp in humans is still unknown. here, we investigated the expression of recently identified grp spliced transcripts, the γ-carboxylation status, and its association with ectopic calcifications, in skin basal cell and breast carcinomas. ...	2014	24949434
specificity and catalytic mechanism in family 5 uracil dna glycosylase.	udgb belongs to family 5 of the uracil dna glycosylase (udg) superfamily. here, we report that family 5 udgb from thermus thermophilus hb8 is not only a uracil dna glycosyase acting on g/u, t/u, c/u, and a/u base pairs, but also a hypoxanthine dna glycosylase acting on g/i, t/i, and a/i base pairs and a xanthine dna glycosylase acting on all double-stranded and single-stranded xanthine-containing dna. analysis of potentials of mean force indicates that the tendency of hypoxanthine base flipping ...	2014	24838246
cu(i)-mediated allosteric switching in a copper-sensing operon repressor (csor).	the copper-sensing operon repressor (csor) is representative of a major cu(i)-sensing family of bacterial metalloregulatory proteins that has evolved to prevent cytoplasmic copper toxicity. it is unknown how cu(i) binding to tetrameric csors mediates transcriptional derepression of copper resistance genes. a phylogenetic analysis of 227 duf156 protein members, including biochemically or structurally characterized csor/rcnr repressors, reveals that geobacillus thermodenitrificans (gt) csor charac ...	2014	24831014
a complete landscape of post-transcriptional modifications in mammalian mitochondrial trnas.	in mammalian mitochondria, 22 species of trnas encoded in mitochondrial dna play crucial roles in the translation of 13 essential subunits of the respiratory chain complexes involved in oxidative phosphorylation. following transcription, mitochondrial trnas are modified by nuclear-encoded trna-modifying enzymes. these modifications are required for the proper functioning of mitochondrial trnas (mt trnas), and the absence of these modifications can cause pathological consequences. to date, howeve ...	2014	24831542
the amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the amazon river plume, june 2010.	the amazon river is by far the world's largest in terms of volume and area, generating a fluvial export that accounts for about a fifth of riverine input into the world's oceans. marine microbial communities of the western tropical north atlantic ocean are strongly affected by the terrestrial materials carried by the amazon plume, including dissolved (doc) and particulate organic carbon (poc) and inorganic nutrients, with impacts on primary productivity and carbon sequestration.	2014	24883185
allosteric regulation of the human and mouse deoxyribonucleotide triphosphohydrolase sterile α-motif/histidine-aspartate domain-containing protein 1 (samhd1).	the deoxyribonucleotide triphosphohydrolase samhd1 restricts lentiviral infection by depleting the dntps required for viral dna synthesis. in cultured human fibroblasts samhd1 is expressed maximally during quiescence preventing accumulation of dntps outside s phase. sirna silencing of samhd1 increases dntp pools, stops cycling human cells in g1, and blocks dna replication. surprisingly, knock-out of the mouse gene does not affect the well being of the animals. dntps are both substrates and allos ...	2014	24828500
prokaryotic argonautes defend genomes against invasive dna.	argonaute proteins are central players in small rna-mediated silencing mechanisms such as rna interference (rnai), microrna repression and pirna-mediated transposon silencing. in eukaryotes, argonautes bind small rnas that guide them to rna targets in order to regulate gene expression and repress invasive genomic elements. although argonaute proteins are conserved in all life forms from bacteria to eukaryotes, until now studies have focused on the biological functions of eukaryotic argonautes. h ...	2014	24836995
bacterial magnetosome biomineralization--a novel platform to study molecular mechanisms of human cdf-related type-ii diabetes.	cation diffusion facilitators (cdf) are part of a highly conserved protein family that maintains cellular divalent cation homeostasis in all organisms. cdfs were found to be involved in numerous human health conditions, such as type-ii diabetes and neurodegenerative diseases. in this work, we established the magnetite biomineralizing alphaproteobacterium magnetospirillum gryphiswaldense as an effective model system to study cdf-related type-ii diabetes. here, we introduced two znt-8 type-ii diab ...	2014	24819161
co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis.	sulphur is an essential element for life and is ubiquitous in living systems. yet how the sulphur atom is incorporated into many sulphur-containing secondary metabolites is poorly understood. for bond formation between carbon and sulphur in primary metabolites, the major ionic sulphur sources are the persulphide and thiocarboxylate groups on sulphur-carrier (donor) proteins. each group is post-translationally generated through the action of a specific activating enzyme. in all reported bacterial ...	2014	24814342
probing the global and local dynamics of aminoacyl-trna synthetases using all-atom and coarse-grained simulations.	coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. to evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-trna synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-trna synthetase ...	2014	24810463
sets of covariant residues modulate the activity and thermal stability of gh1 β-glucosidases.	the statistical coupling analysis of 768 β-glucosidases from the gh1 family revealed 23 positions in which the amino acid frequencies are coupled. the roles of these covariant positions in terms of the properties of β-glucosidases were investigated by alanine-screening mutagenesis using the fall armyworm spodoptera frugiperda β-glycosidase (sfβgly) as a model. the effects of the mutations on the sfβgly kinetic parameters (kcat/km) for the hydrolysis of three different p-nitrophenyl β-glycosides ...	2014	24804841
cryo-em structure of the small subunit of the mammalian mitochondrial ribosome.	the mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or atp generation for the eukaryotic cell. the mammalian 55s mitoribosome contains significantly smaller rrnas and a large mass of mitochondrial ribosomal proteins (mrps), including large mito-specific amino acid extensions and insertions in mrps that are homologous to bacterial ribosomal proteins and an ...	2014	24799711
cas1-cas2 complex formation mediates spacer acquisition during crispr-cas adaptive immunity.	the initial stage of crispr-cas immunity involves the integration of foreign dna spacer segments into the host genomic crispr locus. the nucleases cas1 and cas2 are the only proteins conserved among all crispr-cas systems, yet the molecular functions of these proteins during immunity are unknown. here we show that cas1 and cas2 from escherichia coli form a stable complex that is essential for spacer acquisition and determine the 2.3-å-resolution crystal structure of the cas1-cas2 complex. mutati ...	2014	24793649
current development in genetic engineering strategies of bacillus species.	the complete sequencing and annotation of the genomes of industrially-important bacillus species has enhanced our understanding of their properties, and allowed advances in genetic manipulations in other bacillus species. post-genomic studies require simple and highly efficient tools to enable genetic manipulation. here, we summarize the recent progress in genetic engineering strategies for bacillus species. we review the available genetic tools that have been developed in bacillus species, as w ...	2014	24885003
a pause sequence enriched at translation start sites drives transcription dynamics in vivo.	transcription by rna polymerase (rnap) is interrupted by pauses that play diverse regulatory roles. although individual pauses have been studied in vitro, the determinants of pauses in vivo and their distribution throughout the bacterial genome remain unknown. using nascent transcript sequencing, we identified a 16-nucleotide consensus pause sequence in escherichia coli that accounts for known regulatory pause sites as well as ~20,000 new in vivo pause sites. in vitro single-molecule and ensembl ...	2014	24789973
robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.	do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? if so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. we find that residue pairs identified using a pseudo-likelihood-based method to covary across protein-protein interfaces in the 50s ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, pr ...	2014	24842992
analysis of seca dimerization in solution.	the sec pathway mediates translocation of protein across the inner membrane of bacteria. seca is a motor protein that drives translocation of preprotein through the secyeg channel. seca reversibly dimerizes under physiological conditions, but different dimer interfaces have been observed in seca crystal structures. here, we have used biophysical approaches to address the nature of the seca dimer that exists in solution. we have taken advantage of the extreme salt sensitivity of seca dimerization ...	2014	24786965
metal-free camp-dependent protein kinase can catalyze phosphoryl transfer.	x-ray structures of several ternary product complexes of the catalytic subunit of camp-dependent protein kinase (pkac) have been determined with no bound metal ions and with na(+) or k(+) coordinated at two metal-binding sites. the metal-free pkac and the enzyme with alkali metals were able to facilitate the phosphoryl transfer reaction. in all studied complexes, the atp and the substrate peptide (sp20) were modified into the products adp and the phosphorylated peptide. the products of the phosp ...	2014	24786636
identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles.	longer- and/or branched-chain polyamines are unique polycations found in thermophiles. n(4)-aminopropylspermine is considered a major polyamine in thermococcus kodakarensis. to determine whether a quaternary branched penta-amine, n(4)-bis(aminopropyl)spermidine, an isomer of n(4)-aminopropylspermine, was also present, acid-extracted cytoplasmic polyamines were analyzed by high-pressure liquid chromatography, gas chromatography (hplc), and gas chromatography-mass spectrometry. n(4)-bis(aminopropy ...	2014	24610711
identifying mrna sequence elements for target recognition by human argonaute proteins.	it is commonly known that mammalian micrornas (mirnas) guide the rna-induced silencing complex (risc) to target mrnas through the seed-pairing rule. however, recent experiments that coimmunoprecipitate the argonaute proteins (agos), the central catalytic component of risc, have consistently revealed extensive ago-associated mrnas that lack seed complementarity with mirnas. we herein test the hypothesis that ago has its own binding preference within target mrnas, independent of guide mirnas. by s ...	2014	24663241
protein thermodynamics can be predicted directly from biological growth rates.	life on earth is capable of growing from temperatures well below freezing to above the boiling point of water, with some organisms preferring cooler and others hotter conditions. the growth rate of each organism ultimately depends on its intracellular chemical reactions. here we show that a thermodynamic model based on a single, rate-limiting, enzyme-catalysed reaction accurately describes population growth rates in 230 diverse strains of unicellular and multicellular organisms. collectively the ...	2014	24787650
involvement of proline oxidase (puta) in programmed cell death of xanthomonas.	xanthomonas campestris strains have been reported to undergo programmed cell death (pcd) in a protein rich medium. protein hydrolysates used in media such as nutrient broth comprise of casein digest with abundance of proline and glutamate. in the current study, x. campestris pv. campestris (xcc) cells displayed pcd when grown in pcd inducing medium (pim) containing casein tryptic digest. this pcd was also observed in pcd non-inducing carbohydrate rich medium (pnim) fortified with either proline ...	2014	24788936
transcription inhibition by the depsipeptide antibiotic salinamide a.	we report that bacterial rna polymerase (rnap) is the functional cellular target of the depsipeptide antibiotic salinamide a (sal), and we report that sal inhibits rnap through a novel binding site and mechanism. we show that sal inhibits rna synthesis in cells and that mutations that confer sal-resistance map to rnap genes. we show that sal interacts with the rnap active-center 'bridge-helix cap' comprising the 'bridge-helix n-terminal hinge', 'f-loop', and 'link region'. we show that sal inhib ...	2014	24843001
classification of intrinsically disordered regions and proteins.		2014	24773235
electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex i.	complex i serves as the primary electron entry point into the mitochondrial and bacterial respiratory chains. it catalyzes the reduction of quinones by electron transfer from nadh, and couples this exergonic reaction to the translocation of protons against an electrochemical proton gradient. the membrane domain of the enzyme extends ∼180 å from the site of quinone reduction to the most distant proton pathway. to elucidate possible mechanisms of the long-range proton-coupled electron transfer pro ...	2014	24778264
genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus, an extremely thermophilic bacterium, has been widely recognized as a model organism for studying how microbes can survive and adapt under high temperature environment. however, the thermotolerant mechanisms and cellular metabolism still remains mostly unravelled. thus, it is highly required to consider systems biological approaches where t. thermophilus metabolic network model can be employed together with high throughput experimental data for elucidating its physiological ...	2014	24774833
comparative structural modeling of six old yellow enzymes (oyes) from the necrotrophic fungus ascochyta rabiei: insight into novel oye classes with differences in cofactor binding, organization of active site residues and stereopreferences.	old yellow enzyme (oye1) was the first flavin-dependent enzyme identified and characterized in detail by the entire range of physical techniques. irrespective of this scrutiny, true physiological role of the enzyme remains a mystery. in a recent study, we systematically identified oye proteins from various fungi and classified them into three classes viz. class i, ii and iii. however, there is no information about the structural organization of class iii oyes, eukaryotic class ii oyes and class ...	2014	24776850
structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation.	the emerging view of nε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (ptm) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. this ptm is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme a (accoa) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. here, we ...	2014	24756028
a new spanner in the works of bacterial transcription.	a promising molecular target that is unlikely to develop antibiotic resistance has been identified in bacteria.	2014	24755293
a role for [fe4s4] clusters in trna recognition--a theoretical study.	over the past several years, structural studies have led to the unexpected discovery of iron-sulfur clusters in enzymes that are involved in dna replication/repair and protein biosynthesis. although these clusters are generally well-studied cofactors, their significance in the new contexts often remains elusive. one fascinating example is a tryptophanyl-trna synthetase from the thermophilic bacterium thermotoga maritima, tmtrprs, that has recently been structurally characterized. it represents a ...	2014	24753428
controlling protein adsorption on graphene for cryo-em using low-energy hydrogen plasmas.	despite its many favorable properties as a sample support for biological electron microscopy, graphene is not widely used because its hydrophobicity precludes reliable protein deposition. we describe a method to modify graphene with a low-energy hydrogen plasma, which reduces hydrophobicity without degrading the graphene lattice. use of plasma-treated graphene enables better control of protein distribution in ice for electron cryo-microscopy and improves image quality by reducing radiation-induc ...	2014	24747813
cas6 specificity and crispr rna loading in a complex crispr-cas system.	crispr-cas is an adaptive prokaryotic immune system, providing protection against viruses and other mobile genetic elements. in type i and type iii crispr-cas systems, crispr rna (crrna) is generated by cleavage of a primary transcript by the cas6 endonuclease and loaded into multisubunit surveillance/effector complexes, allowing homology-directed detection and cleavage of invading elements. highly studied crispr-cas systems such as those in escherichia coli and pseudomonas aeruginosa have a sin ...	2014	24753403
biochemical and functional characterization of plasmodium falciparum gtp cyclohydrolase i.	antifolates are currently in clinical use for malaria preventive therapy and treatment. the drugs kill the parasites by targeting the enzymes in the de novo folate pathway. the use of antifolates has now been limited by the spread of drug-resistant mutations. gtp cyclohydrolase i (gch1) is the first and the rate-limiting enzyme in the folate pathway. the amplification of the gch1 gene found in certain plasmodium falciparum isolates can cause antifolate resistance and influence the course of anti ...	2014	24745605
casa mediates cas3-catalyzed target degradation during crispr rna-guided interference.	in bacteria, the clustered regularly interspaced short palindromic repeats (crispr)-associated (cas) dna-targeting complex cascade (crispr-associated complex for antiviral defense) uses crispr rna (crrna) guides to bind complementary dna targets at sites adjacent to a trinucleotide signature sequence called the protospacer adjacent motif (pam). the cascade complex then recruits cas3, a nuclease-helicase that catalyzes unwinding and cleavage of foreign double-stranded dna (dsdna) bearing a sequen ...	2014	24748111
mass spectrometry defines the c-terminal dimerization domain and enables modeling of the structure of full-length ompa.	the transmembrane domain of the outer membrane protein a (ompa) from escherichia coli is an excellent model for structural and folding studies of β-barrel membrane proteins. however, full-length ompa resists crystallographic efforts, and the link between its function and tertiary structure remains controversial. here we use site-directed mutagenesis and mass spectrometry of different constructs of ompa, released in the gas phase from detergent micelles, to define the minimal region encompassing ...	2014	24746938
structure determination of a sugar-binding protein from the phytopathogenic bacterium xanthomonas citri.	the uptake of maltose and related sugars in gram-negative bacteria is mediated by an abc transporter encompassing a periplasmic component (the maltose-binding protein or male), a pore-forming membrane protein (malf and malg) and a membrane-associated atpase (malk). in the present study, the structure determination of the apo form of the putative maltose/trehalose-binding protein (xac-male) from the citrus pathogen xanthomonas citri in space group p6522 is described. the crystals contained two pr ...	2014	24817711
functional substitution of a eukaryotic glycyl-trna synthetase with an evolutionarily unrelated bacterial cognate enzyme.	two oligomeric types of glycyl-trna synthetase (glyrs) are found in nature: a α2 type and a α2β2 type. the former has been identified in all three kingdoms of life and often pairs with trnagly that carries an a73 discriminator base, while the latter is found only in bacteria and chloroplasts and is almost always coupled with trnagly that contains u73. in the yeast saccharomyces cerevisiae, a single glyrs gene, grs1, provides both the cytoplasmic and mitochondrial functions, and trnagly isoaccept ...	2014	24743154
a technique for high-throughput protein crystallization in ionically cross-linked polysaccharide gel beads for x-ray diffraction experiments.	a simple technique for high-throughput protein crystallization in ionically cross-linked polysaccharide gel beads has been developed for contactless handling of crystals in x-ray crystallography. the method is designed to reduce mechanical damage to crystals caused by physical contact between crystal and mount tool and by osmotic shock during various manipulations including cryoprotection, heavy-atom derivatization, ligand soaking, and diffraction experiments. for this study, protein crystalliza ...	2014	24740192
a novel carbonyl reductase with anti-prelog stereospecificity from acetobacter sp. cctcc m209061: purification and characterization.	a novel carbonyl reductase (accr) catalyzing the asymmetric reduction of ketones to enantiopure alcohols with anti-prelog stereoselectivity was found in acetobacter sp. cctcc m209061 and enriched 27.5-fold with an overall yield of 0.4% by purification. the enzyme showed a homotetrameric structure with an apparent molecular mass of 104 kda and each subunit of 27 kda. the gene sequence of accr was cloned and sequenced, and a 762 bp gene fragment was obtained. either nad(h) or nadp(h) can be used a ...	2014	24740089