Publications

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
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
conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.	the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ...	2014	24931479
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
conserved glycine 232 in the ligand channel of ba3 cytochrome oxidase from thermus thermophilus.	knowing how the protein environment modulates ligand pathways and redox centers in the respiratory heme-copper oxidases is fundamental for understanding the relationship between the structure and function of these enzymes. in this study, we investigated the reactions of o2 and no with the fully reduced g232v mutant of ba3 cytochrome c oxidase from thermus thermophilus (tt ba3) in which a conserved glycine residue in the o2 channel of the enzyme was replaced with a bulkier valine residue. previou ...	2014	24937405
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
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
synthesis of water-soluble dinuclear mn-porphyrin with multiple antioxidative activities.	superoxide dismutase (sod) and catalase activities of a drug are of great importance for its effective protection against reactive oxygen species (ros)-induced injury. achievement of catalase activity of a synthetic compound remains a challenge. water-soluble mn-porphyrins have high sod and peroxynitrite (onoo(-)) reducing activities, but not catalase-like activity. herein, we are able to retain the fair sod-like activity of a mononuclear mn-5-(n-methylpyridinium-4-yl)-10,15,20-triphenyl porphyr ...	2014	24944735
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
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
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
characterization of two homologous 2'-o-methyltransferases showing different specificities for their trna substrates.	the 2'-o-methylation of the nucleoside at position 32 of trna is found in organisms belonging to the three domains of life. unrelated enzymes catalyzing this modification in bacteria (trmj) and eukarya (trm7) have already been identified, but until now, no information is available for the archaeal enzyme. in this work we have identified the methyltransferase of the archaeon sulfolobus acidocaldarius responsible for the 2'-o-methylation at position 32. this enzyme is a homolog of the bacterial tr ...	2014	24951554
building a stable rna u-turn with a protonated cytidine.	the u-turn is a classical three-dimensional rna folding motif first identified in the anticodon and t-loops of trnas. it also occurs frequently as a building block in other functional rna structures in many different sequence and structural contexts. u-turns induce sharp changes in the direction of the rna backbone and often conform to the 3-nt consensus sequence 5'-unr-3' (n = any nucleotide, r = purine). the canonical u-turn motif is stabilized by a hydrogen bond between the n3 imino group of ...	2014	24951555
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-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
acetyl coenzyme a synthetase is acetylated on multiple lysine residues by a protein acetyltransferase with a single gcn5-type n-acetyltransferase (gnat) domain in saccharopolyspora erythraea.	reversible lysine acetylation (rla) is used by cells of all domains of life to modulate protein function. to date, bacterial acetylation/deacetylation systems have been studied in a few bacteria (e.g., salmonella enterica, bacillus subtilis, escherichia coli, erwinia amylovora, mycobacterium tuberculosis, and geobacillus kaustophilus), but little is known about rla in antibiotic-producing actinomycetes. here, we identify the gcn5-like protein acetyltransferase acua of saccharopolyspora erythraea ...	2014	24957627
linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry dft exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.	after a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear fe-a3-cub reaction center in this enzyme. a specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. a larger family of tautomers/protonation states is generate ...	2014	24960612
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
card integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria.	although the basic mechanisms of prokaryotic transcription are conserved, it has become evident that some bacteria require additional factors to allow for efficient gene transcription. card is an rna polymerase (rnap)-binding protein conserved in numerous bacterial species and essential in mycobacteria. despite the importance of card, its function at transcription complexes remains unclear. we have generated a panel of mutations that individually target three independent functional modules of ca ...	2014	24962732
the evolution of respiratory o2/no reductases: an out-of-the-phylogenetic-box perspective.	complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. however, the history of o2-levels in the atmosphere is complex and prior to the great oxidation event some 2.3 billion years ago, the amount of o2 in the biosphere is considered to have been extremely low as compared with present-day values. therefore the evolutionary histories of life and of o2-levels are likely intricately intertwined. the ...	2014	24968694
angling for uniqueness in enzymatic preparation of glycosides.	in the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. this is a general bird's-eye view and as such cannot be specific for articulated situations found in different classes of enzymes or for selected enzymatic processes. as far as the enzymatic preparation of glycosides is concerned, recent scientific literature is awash with examples of uniqueness related to the features ...	2013	24970171
improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis.	laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. the palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. a technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturatio ...	2013	24970191
misfolding of amyloidogenic proteins and their interactions with membranes.	in this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. many of these proteins are implicated in serious illnesses such as alzheimer's disease and parkinson's disease. misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membran ...	2013	24970204
misfolding of amyloidogenic proteins and their interactions with membranes.	in this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. many of these proteins are implicated in serious illnesses such as alzheimer's disease and parkinson's disease. misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membran ...	2013	24970204
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
magnesium-dependent processes are targets of bacterial manganese toxicity.	a bradyrhizobium japonicum mutant defective in the gene encoding the high-affinity mn(2+) transporter mnth has a severe growth phenotype under manganese limitation. here, we isolated suppressor mutants of an mnth strain that grew under manganese limitation, and activities of high-affinity mn(2+) transport and mn(2+) -dependent enzymes were partially rescued. the suppressor strains harbour gain-of-function mutations in the gene encoding the mg(2+) channel mgte. the mgte variants likely allow mn(2 ...	2014	24975873
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
veillonella, firmicutes: microbes disguised as gram negatives.	the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ...	2013	24976898
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
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
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
inhibition of the 4fe-4s proteins ispg and isph: an epr, endor and hyscore investigation.	ispg and isph are proteins that are involved in isoprenoid biosynthesis in most bacteria as well as in malaria parasites and are important drug targets. they contain cubane-type 4fe-4s clusters that are involved in unusual 2h(+)/2e(-) reductions. here, we report the results of electron paramagnetic resonance spectroscopic investigations of the binding of amino- and thiolo-hmbpp (hmbpp=e-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate) isph substrate-analog inhibitors to both proteins, as well as the ...	2014	24999381
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
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
evidence for a hexaheteromeric methylenetetrahydrofolate reductase in moorella thermoacetica.	moorella thermoacetica can grow with h₂ and co₂, forming acetic acid from 2 co₂ via the wood-ljungdahl pathway. all enzymes involved in this pathway have been characterized to date, except for methylenetetrahydrofolate reductase (metf). we report here that the m. thermoacetica gene that putatively encodes this enzyme, metf, is part of a transcription unit also containing the genes hdrcba, mvhd, and metv. metf copurified with the other five proteins encoded in the unit in a hexaheteromeric comple ...	2014	25002540
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
preliminary x-ray crystallographic analysis of an engineered glutamyl-trna synthetase from escherichia coli.	the nature of interaction between glutamyl-trna synthetase (glurs) and its trna substrate is unique in bacteria in that many bacterial glurs are capable of recognizing two trna substrates: trnaglu and trnagln. to properly understand this distinctive glurs-trna interaction it is important to pursue detailed structure-function studies; however, because of the fact that trna-glurs interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure-function correlation stud ...	2014	25005090
function and evolution of the sox multienzyme complex in the marine gammaproteobacterium congregibacter litoralis.	core sets of sox genes were detected in several genome sequenced members of the environmental important om60/nor5 clade of marine gammaproteobacteria. however, emendation of media with thiosulfate did not result in stimulation of growth in two of these strains and cultures of congregibacter litoralis dsm 17192(t) did not oxidize thiosulfate to sulfate in concentrations of one mmol l(-1) or above. on the other hand, a significant production of sulfate was detected upon growth with the organic sul ...	2014	25006520
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
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
inteins as indicators of gene flow in the halobacteria.	this research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the halobacteria. we surveyed 118 genomes representing 26 genera of halobacteria for intein sequences. we then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. we identified 24 proteins in the halobacteria that hav ...	2014	25018750
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
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
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
stability curve prediction of homologous proteins using temperature-dependent statistical potentials.	the unraveling and control of protein stability at different temperatures is a fundamental problem in biophysics that is substantially far from being quantitatively and accurately solved, as it requires a precise knowledge of the temperature dependence of amino acid interactions. in this paper we attempt to gain insight into the thermal stability of proteins by designing a tool to predict the full stability curve as a function of the temperature for a set of 45 proteins belonging to 11 homologou ...	2014	25032839
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
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
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
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
a bridge between the aminoacylation and editing domains of leucyl-trna synthetase is crucial for its synthetic activity.	leucyl-trna synthetases (leurss) catalyze the linkage of leucine with trna(leu). leurs contains a catalysis domain (aminoacylation) and a cp1 domain (editing). cp1 is inserted 35 å from the aminoacylation domain. aminoacylation and editing require cp1 to swing to the coordinated conformation. the neck between the cp1 domain and the aminoacylation domain is defined as the cp1 hairpin. the location of the cp1 hairpin suggests a crucial role in the cp1 swing and domain-domain interaction. here, the ...	2014	25051973
evidence for distinct electron transfer processes in terminal oxidases from different origin by means of protein film voltammetry.	cytochrome aa3 from paracoccus denitrificans and cytochrome ba3 from thermus thermophilus, two distinct members of the heme-copper oxidase superfamily, were immobilized on electrodes modified with gold nanoparticles. this procedure allowed us to achieve direct electron transfer between the enzyme and the gold nanoparticles and to obtain evidence for different electrocatalytic properties of the two enzymes. the ph dependence and thermostability reveal that the enzymes are highly adapted to their ...	2014	25054669
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
multiple regulatory mechanisms control the expression of the geobacillus stearothermophilus gene for extracellular xylanase.	geobacillus stearothermophilus t-6 produces a single extracellular xylanase (xyn10a) capable of producing short, decorated xylo-oligosaccharides from the naturally branched polysaccharide, xylan. gel retardation assays indicated that the master negative regulator, xylr, binds specifically to xylr operators in the promoters of xylose and xylan-utilization genes. this binding is efficiently prevented in vitro by xylose, the most likely molecular inducer. expression of the extracellular xylanase is ...	2014	25070894
evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease h active site.	ribonuclease h1 (rnase h) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. despite extensive study, especially of the e. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. in this work, we describe molecular dynamics simulations of the e. coli homolog in complex with ...	2014	25075292
afal: a web service for profiling amino acids surrounding ligands in proteins.	with advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. herein, a new web service is presented termed amino acid frequency around ligand (afal) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the protein data bank and for ...	2014	25085083
crystal structure of the full-length atpase gspe from the vibrio vulnificus type ii secretion system in complex with the cytoplasmic domain of gspl.	the type ii secretion system (t2ss) is present in many gram-negative bacteria and is responsible for secreting a large number of folded proteins, including major virulence factors, across the outer membrane. the t2ss consists of 11-15 different proteins most of which are present in multiple copies in the assembled secretion machinery. the atpase gspe, essential for the functioning of the t2ss, contains three domains (n1e, n2e and cte) of which the n1e domain is associated with the cytoplasmic do ...	2014	25092625
structural and functional basis of transcriptional regulation by tetr family protein cprb from s. coelicolor a3(2).	antibiotic production and resistance pathways in streptomyces are dictated by the interplay of transcriptional regulatory proteins that trigger downstream responses via binding to small diffusible molecules. to decipher the mode of dna binding and the associated allosteric mechanism in the sub-class of transcription factors that are induced by γ-butyrolactones, we present the crystal structure of cprb in complex with the consensus dna element to a resolution of 3.25 å. binding of the dna results ...	2014	25092919
comparative single-cell genomics reveals potential ecological niches for the freshwater aci actinobacteria lineage.	members of the aci lineage of actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. we obtained draft genome assemblies from 11 single cells representing three aci tribes (aci-a1, aci-a7, aci-b1) from four temperate lakes in the united states and europe. comparative analysis of aci sags and ...	2014	25093637
the interface between escherichia coli elongation factor tu and aminoacyl-trna.	nineteen of the highly conserved residues of escherichia coli (e. coli) elongation factor tu (ef-tu) that form the binding interface with aa-trna were mutated to alanine to better understand how modifying the thermodynamic properties of ef-tu-trna interaction can affect the decoding properties of the ribosome. comparison of δδg(o) values for binding ef-tu to aa-trna show that the majority of the interface residues stabilize the ternary complex and their thermodynamic contribution can depend on t ...	2014	25094027
nature's recipe for splitting inteins.	protein splicing in trans by split inteins has increasingly become a powerful protein-engineering tool for protein ligation, both in vivo and in vitro. over 100 naturally occurring and artificially engineered split inteins have been reported for protein ligation using protein trans-splicing. here, we review the current status of the reported split inteins in order to delineate an empirical or rational strategy for constructing new split inteins suitable for various applications in biotechnology ...	2014	25096198
l-lactic acid production from d-xylose with candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene.	bioplastics, like polylactic acid (pla), are renewable alternatives for petroleum-based plastics. lactic acid, the monomer of pla, has traditionally been produced biotechnologically with bacteria. with genetic engineering, yeast have the potential to replace bacteria in biotechnological lactic acid production, with the benefits of being acid tolerant and having simple nutritional requirements. lactate dehydrogenase genes have been introduced to various yeast to demonstrate this potential. import ...	2014	25104116
discovery and validation of novel and distinct rna regulators for ribosomal protein s15 in diverse bacterial phyla.	autogenous cis-regulators of ribosomal protein synthesis play a critical role in maintaining the stoichiometry of ribosome components. structured portions within an mrna transcript typically interact with specific ribosomal proteins to prevent expression of the entire operon, thus balancing levels of ribosomal proteins across transcriptional units. three distinct rna structures from different bacterial phyla have demonstrated interactions with s15 to regulate gene expression; however, these rnas ...	2014	25104606
molecular basis of rna polymerase promoter specificity switch revealed through studies of thermus bacteriophage transcription regulator.	transcription initiation is the central point of gene expression regulation. understanding of molecular mechanism of transcription regulation requires, ultimately, the structural understanding of consequences of transcription factors binding to dna-dependent rna polymerase (rnap), the enzyme of transcription. we recently determined a structure of a complex between transcription factor gp39 encoded by a thermus bacteriophage and thermus rnap holoenzyme. in this addendum to the original publicatio ...	2014	25105059
comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the red sea.	the bottom of the red sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (bsi), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the bsi. these features coupled with the deep-sea prevalence of ...	2014	25105904
comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the red sea.	the bottom of the red sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (bsi), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the bsi. these features coupled with the deep-sea prevalence of ...	2014	25105904
ndho, a subunit of nadph dehydrogenase, destabilizes medium size complex of the enzyme in synechocystis sp. strain pcc 6803.	two mutants that grew faster than the wild-type (wt) strain under high light conditions were isolated from synechocystis sp. strain pcc 6803 transformed with a transposon-bearing library. both mutants had a tag in ssl1690 encoding ndho. deletion of ndho increased the activity of nadph dehydrogenase (ndh-1)-dependent cyclic electron transport around photosystem i (ndh-cet), while overexpression decreased the activity. although deletion and overexpression of ndho did not have significant effects o ...	2014	25107904
molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix.	tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ...	2014	25108393
phylogenetic analysis and evolutionary origins of dna polymerase x-family members.	mammalian dna polymerase (pol) β is the founding member of a large group of dna polymerases now termed the x-family. dna polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the x-family of dna polymerases. the bacterial x-family dna polymerases, saccharomyces cerevisiae pol iv, and four mammalian x-fam ...	2014	25112931
dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.	microbial genomes encompass a sizable fraction of poorly characterized, narrowly spread fast-evolving genes. using sensitive methods for sequences comparison and protein structure prediction, we performed a detailed comparative analysis of clusters of such genes, which we denote "dark matter islands", in archaeal genomes. the dark matter islands comprise up to 20% of archaeal genomes and show remarkable heterogeneity and diversity. nevertheless, three classes of entities are common in these geno ...	2014	25113822
dna binding polarity, dimerization, and atpase ring remodeling in the cmg helicase of the eukaryotic replisome.	the cdc45/mcm2-7/gins (cmg) helicase separates dna strands during replication in eukaryotes. how the cmg is assembled and engages dna substrates remains unclear. using electron microscopy, we have determined the structure of the cmg in the presence of atpγs and a dna duplex bearing a 3' single-stranded tail. the structure shows that the mcm subunits of the cmg bind preferentially to single-stranded dna, establishes the polarity by which dna enters into the mcm2-7 pore, and explains how cdc45 hel ...	2014	25117490
discovery of a eukaryotic pyrroloquinoline quinone-dependent oxidoreductase belonging to a new auxiliary activity family in the database of carbohydrate-active enzymes.	pyrroloquinoline quinone (pqq) is a redox cofactor utilized by a number of prokaryotic dehydrogenases. not all prokaryotic organisms are capable of synthesizing pqq, even though it plays important roles in the growth and development of many organisms, including humans. the existence of pqq-dependent enzymes in eukaryotes has been suggested based on homology studies or the presence of pqq-binding motifs, but there has been no evidence that such enzymes utilize pqq as a redox cofactor. however, du ...	2014	25121592
structural biology. crystal structure of a crispr rna-guided surveillance complex bound to a ssdna target.	in prokaryotes, rna derived from type i and type iii crispr loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. in escherichia coli, this 405-kilodalton complex is called cascade. we report the crystal structure of cascade bound to a single-stranded dna (ssdna) target at a resolution of 3.03 angstroms. the structure reveals that the crispr rna and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. this noncan ...	2014	25123481
dead-box rna helicase domains exhibit a continuum between complete functional independence and high thermodynamic coupling in nucleotide and rna duplex recognition.	dead-box helicases catalyze the non-processive unwinding of double-stranded rna (dsrna) at the expense of adenosine triphosphate (atp) hydrolysis. nucleotide and rna binding and unwinding are mediated by the reca domains of the helicase core, but their cooperation in these processes remains poorly understood. we therefore investigated dsrna and nucleotide binding by the helicase cores and the isolated n- and c-terminal reca domains (reca_n, reca_c) of the dead-box proteins hera and yxin by stead ...	2014	25123660
allosteric regulation of a protein acetyltransferase in micromonospora aurantiaca by the amino acids cysteine and arginine.	act domains (amino acid-binding domains) are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. seventy proteins with act-gcn5-related n-acetyltransferase (gnat) domain organization were found in actinomycetales. in this study, we investigate the act-containing gnat acetyltransferase, micau_1670 (makat), from micromonospora aurantiaca atcc 27029. arginine and cysteine were identified as ligands by monitoring the conformational changes that occur upon amin ...	2014	25124041
structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops.	maintenance of the correct reading frame on the ribosome is essential for accurate protein synthesis. here, we report structures of the 70s ribosome bound to frameshift suppressor trna(sufa6) and n1-methylguanosine at position 37 (m(1)g37) modification-deficient anticodon stem loop(pro), both of which cause the ribosome to decode 4 rather than 3 nucleotides, resulting in a +1 reading frame. our results reveal that decoding at +1 suppressible codons causes suppressor trna(sufa6) to undergo a rear ...	2014	25128388
heteronuclear transverse and longitudinal relaxation in ax4 spin systems: application to (15)n relaxations in (15)nh4(+).	the equations that describe the time-evolution of transverse and longitudinal (15)n magnetisations in tetrahedral ammonium ions, (15)nh4(+), are derived from the bloch-wangsness-redfield density operator relaxation theory. it is assumed that the relaxation of the spin-states is dominated by (1) the intra-molecular (15)n-(1)h and (1)h-(1)h dipole-dipole interactions and (2) interactions of the ammonium protons with remote spins, which also include the contribution to the relaxations that arise fr ...	2014	25128779
a proton wire to couple aminoacyl-trna accommodation and peptide-bond formation on the ribosome.	during peptide-bond formation on the ribosome, the α-amine of an aminoacyl-trna attacks the ester carbonyl carbon of a peptidyl-trna to yield a peptide lengthened by one amino acid. although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. here, we present crystal structures of ...	2014	25132179
in vivo tmrna protection by smpb and pre-ribosome binding conformation in solution.	tmrna is an abundant rna in bacteria with trna and mrna features. it is specialized in trans-translation, a translation rescuing system. we demonstrate that its partner protein smpb binds the trna-like region (tld) in vivo and chaperones the fold of the tld-h2 region. we use an original approach combining the observation of tmrna degradation pathways in a heterologous system, the analysis of the tmrna digests by ms and nmr, and co-overproduction assays of tmrna and smpb. we study the conformatio ...	2014	25135523
formation and structures of groel:groes2 chaperonin footballs, the protein-folding functional form.	the groe chaperonins assist substrate protein (sp) folding by cycling through several conformational states. with each cycle the sp is, in turn, captured, unfolded, briefly encapsulated (t1/2 ∼ 1 s), and released by the chaperonin complex. the protein-folding functional form is the us-football-shaped groel:groes2 complex. we report structures of two such "football" complexes to ∼ 3.7-å resolution; one is empty whereas the other contains encapsulated sp in both chambers. although encapsulated sp ...	2014	25136110
investigating the thermostability of succinate: quinone oxidoreductase enzymes by direct electrochemistry at swnts-modified electrodes and ftir spectroscopy.	succinate: quinone reductases (sqrs) are the enzymes that couple the oxidation of succinate and the reduction of quinones in the respiratory chain of prokaryotes and eukaryotes. herein, we compare the temperature-dependent activity and structural stability of two sqrs, the first from the mesophilic bacterium escherichia coli and the second from the thermophilic bacterium thermus thermophilus, using a combined electrochemical and infrared spectroscopy approach. direct electron transfer was achiev ...	2014	25139263
dissection of the region of pseudomonas aeruginosa para that is important for dimerization and interactions with its partner parb.	pseudomonas aeruginosa para belongs to a large subfamily of walker-type atpases acting as partitioning proteins in bacteria. para has the ability to both self-associate and interact with its partner parb. analysis of the deletion mutants defined the part of the protein involved in dimerization and interactions with parb. here, a set of para alanine substitution mutants in the region between e67 and l85 was created and analysed in vivo and in vitro. all mutants impaired in dimerization (substitut ...	2014	25139949
structure analysis of free and bound states of an rna aptamer against ribosomal protein s8 from bacillus anthracis.	several protein-targeted rna aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. we examined the structural accommodation of an rna aptamer that binds bacterial r-protein s8. the core of the primary binding site for s8 on helix 21 of 16s rrna contains a pair of conserved base triples that mold the sugar-phosphate backbone to s8. ...	2014	25140011
dissection of structural and functional requirements that underlie the interaction of erdj3 protein with substrates in the endoplasmic reticulum.	erdj3, a mammalian endoplasmic reticulum (er) hsp40/dnaj family member, binds unfolded proteins, transfers them to bip, and concomitantly stimulates bip atpase activity. however, the requirements for erdj3 binding to and release from substrates in cells are not well understood. we found that erdj3 homodimers that cannot stimulate the atpase activity of bip (qpd mutants) bound to unfolded er proteins under steady state conditions in much greater amounts than wild-type erdj3. this was due to reduc ...	2014	25143379
dna binding properties of the small cascade subunit csa5.	crispr-cas systems provide immunity against viral attacks in archaeal and bacterial cells. type i systems employ a cas protein complex termed cascade, which utilizes small crispr rnas to detect and degrade the exogenic dna. a small sequence motif, the pam, marks the foreign substrates. previously, a recombinant type i-a cascade complex from the archaeon thermoproteus tenax was shown to target and degrade dna in vitro, dependent on a native pam sequence. here, we present the biochemical analysis ...	2014	25148031
how lamina-associated polypeptide 1 (lap1) activates torsin.	lamina-associated polypeptide 1 (lap1) resides at the nuclear envelope and interacts with torsins, poorly understood endoplasmic reticulum (er)-localized aaa+ atpases, through a conserved, perinuclear domain. we determined the crystal structure of the perinuclear domain of human lap1. lap1 possesses an atypical aaa+ fold. while lap1 lacks canonical nucleotide binding motifs, its strictly conserved arginine 563 is positioned exactly where the arginine finger of canonical aaa+ atpases is found. ba ...	2014	25149450
comparison of histidine recognition in human and trypanosomatid histidyl-trna synthetases.	as part of a project aimed at obtaining selective inhibitors and drug-like compounds targeting trna synthetases from trypanosomatids, we have elucidated the crystal structure of human cytosolic histidyl-trna synthetase (hs-chisrs) in complex with histidine in order to be able to compare human and parasite enzymes. the resultant structure of hs-chisrs•his represents the substrate-bound state (h-state) of the enzyme. it provides an interesting opportunity to compare with ligand-free and imidazole- ...	2014	25151410
interplay between oxygen and fe-s cluster biogenesis: insights from the suf pathway.	iron-sulfur (fe-s) cluster metalloproteins conduct essential functions in nearly all contemporary forms of life. the nearly ubiquitous presence of fe-s clusters and the fundamental requirement for fe-s clusters in both aerobic and anaerobic archaea, bacteria, and eukarya suggest that these clusters were likely integrated into central metabolic pathways early in the evolution of life prior to the widespread oxidation of earth's atmosphere. intriguingly, fe-s cluster-dependent metabolism is sensit ...	2014	25153801
phenotypic interactions among mutations in a thermus thermophilus 16s rrna gene detected with genetic selections and experimental evolution.	during protein synthesis, the ribosome undergoes conformational transitions between functional states, requiring communication between distant structural elements of the ribosome. despite advances in ribosome structural biology, identifying the protein and rrna residues governing these transitions remains a significant challenge. such residues can potentially be identified genetically, given the predicted deleterious effects of mutations stabilizing the ribosome in discrete conformations and the ...	2014	25157075
escherichia coli d-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway.	the enzymes of the β-decarboxylating dehydrogenase superfamily catalyze the oxidative decarboxylation of d-malate-based substrates with various specificities. here, we show that, in addition to its natural function affording bacterial growth on d-malate as a carbon source, the d-malate dehydrogenase of escherichia coli (ecdmla) naturally expressed from its chromosomal gene is capable of complementing leucine auxotrophy in a leub(-) strain lacking the paralogous isopropylmalate dehydrogenase enzy ...	2014	25160617
crisprstrand: predicting repeat orientations to determine the crrna-encoding strand at crispr loci.	the discovery of crispr-cas systems almost 20 years ago rapidly changed our perception of the bacterial and archaeal immune systems. crispr loci consist of several repetitive dna sequences called repeats, inter-spaced by stretches of variable length sequences called spacers. this crispr array is transcribed and processed into multiple mature rna species (crrnas). a single crrna is integrated into an interference complex, together with crispr-associated (cas) proteins, to bind and degrade invadin ...	2014	25161238
reco protein initiates dna recombination and strand annealing through two alternative dna binding mechanisms.	recombination mediator proteins (rmps) are important for genome stability in all organisms. several rmps support two alternative reactions: initiation of homologous recombination and dna annealing. we examined mechanisms of rmps in both reactions with mycobacterium smegmatis reco (msreco) and demonstrated that msreco interacts with ssdna by two distinct mechanisms. zinc stimulates msreco binding to ssdna during annealing, whereas the recombination function is zinc-independent and is regulated by ...	2014	25170075
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
re-evaluation of the near infrared spectra of mitochondrial cytochrome c oxidase: implications for non invasive in vivo monitoring of tissues.	we re-determined the near infrared (nir) spectral signatures (650-980nm) of the different cytochrome c oxidase redox centres, in the process separating them into their component species. we confirm that the primary contributor to the oxidase nir spectrum between 700 and 980nm is cupric cua, which in the beef heart enzyme has a maximum at 835nm. the 655nm band characterises the fully oxidised haem a3/cub binuclear centre; it is bleached either when one or more electrons are added to the binuclear ...	2014	25175349
replication slippage of the thermophilic dna polymerases b and d from the euryarchaeota pyrococcus abyssi.	replication slippage or slipped-strand mispairing involves the misalignment of dna strands during the replication of repeated dna sequences, and can lead to genetic rearrangements such as microsatellite instability. here, we show that polb and pold replicative dna polymerases from the archaeal model pyrococcus abyssi (pab) slip in vitro during replication of a single-stranded dna template carrying a hairpin structure and short direct repeats. we find that this occurs in both their wild-type (exo ...	2014	25177316
acetylome analysis reveals diverse functions of lysine acetylation in mycobacterium tuberculosis.	the lysine acetylation of proteins is a reversible post-translational modification that plays a critical regulatory role in both eukaryotes and prokaryotes. mycobacterium tuberculosis is a facultative intracellular pathogen and the causative agent of tuberculosis. increasing evidence shows that lysine acetylation may play an important role in the pathogenesis of m. tuberculosis. however, only a few acetylated proteins of m. tuberculosis are known, presenting a major obstacle to understanding the ...	2014	25180227