Publications

the mercury resistance operon: from an origin in a geothermal environment to an efficient detoxification machine.	mercuric mercury (hg[ii]) is a highly toxic and mobile element that is likely to have had a pronounced and adverse effect on biology since earth's oxygenation ∼2.4 billion years ago due to its high affinity for protein sulfhydryl groups, which upon binding destabilize protein structure and decrease enzyme activity, resulting in a decreased organismal fitness. the central enzyme in the microbial mercury detoxification system is the mercuric reductase (mera) protein, which catalyzes the reduction ...	2012	23087676
subunit-specific incorporation efficiency and kinetics in mitochondrial complex i homeostasis.	studies employing native page suggest that most ndna-encoded ci subunits form subassemblies before assembling into holo-ci. in addition, in vitro evidence suggests that some subunits can directly exchange in holo-ci. presently, data on the kinetics of these two incorporation modes for individual ci subunits during ci maintenance are sparse. here, we used inducible hek293 cell lines stably expressing acgfp1-tagged ci subunits and quantified the amount of tagged subunit in mitoplasts and holo-ci b ...	2012	23038253
thermal control of microbial development and virulence: molecular mechanisms of microbial temperature sensing.	temperature is a critical and ubiquitous environmental signal that governs the development and virulence of diverse microbial species, including viruses, archaea, bacteria, fungi, and parasites. microbial survival is contingent upon initiating appropriate responses to the cellular stress induced by severe environmental temperature change. in the case of microbial pathogens, development and virulence are often coupled to sensing host physiological temperatures. as such, microbes have developed di ...	2012	23033469
the 70s ribosome modulates the atpase activity of escherichia coli ychf.	ychf is one of two universally conserved gtpases with unknown cellular function. as a first step toward elucidating ychf's cellular role, we performed a detailed biochemical characterization of the protein from escherichia coli. our data from fluorescence titrations not only confirmed the surprising finding that ychfe.coli binds adenine nucleotides more efficiently than guanine nucleotides, but also provides the first evidence suggesting that ychf assumes two distinct conformational states (atp- ...	2012	22995830
mechanisms that impact microrna stability in plants.	micrornas (mirnas) are 20-24 nucleotide rnas that regulate a variety of developmental and metabolic processes. the accumulation of mirnas in vivo can be controlled at multiple levels. in addition to mirna biogenesis, mechanisms that lead to rna degradation, such as 3' uridylation and 3' truncation, also affect the steady-state levels of mirnas. on the other hand, 2'-o-methylation in plant mirnas protects their 3' ends from truncation and uridylation. the recent identification of heso1 as the key ...	2012	22995833
novel rapidly diversifiable antimicrobial rna polymerase switch region inhibitors with confirmed mode of action in haemophilus influenzae.	a series of inhibitors with a squaramide core was synthesized following its discovery in a high-throughput screen for novel inhibitors of a transcription-coupled translation assay using escherichia coli s30 extracts. the inhibitors were inactive when the plasmid substrate was replaced with mrna, suggesting they interfered with transcription. this was confirmed by their inhibition of purified e. coli rna polymerase. the series had antimicrobial activity against efflux-negative strains of e. coli ...	2012	22843845
characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria.	nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (pha)-degrading microorganisms were isolated from natural sources. from them, seven gram-positive and three gram-negative bacteria were identified. the ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) pha, poly(ε-caprolactone) (pcl), poly(ethylene succinate) (pes), and poly(l-lactide) (pla), has been studied. on the basis of the great ability to degrade different polyesters, str ...	2012	22865072
yeast trm7 interacts with distinct proteins for critical modifications of the trnaphe anticodon loop.	post-transcriptional modification of the trna anticodon loop is critical for translation. yeast trm7 is required for 2'-o-methylation of c(32) and n(34) of trna(phe), trna(trp), and trna(leu(uaa)) to form cm(32) and nm(34), and trm7-δ mutants have severe growth and translation defects, but the reasons for these defects are not known. we show here that overproduction of trna(phe) suppresses the growth defect of trm7-δ mutants, suggesting that the crucial biological role of trm7 is the modificatio ...	2012	22912484
analysis of the accessibility of clip bound sites reveals that nucleation of the mirna:mrna pairing occurs preferentially at the 3'-end of the seed match.	to find out whether the ago-mirna complex is more sensitive to the accessibility of a particular region inside the seed match, we analyze in detail the accessibility of a wide set of mirna binding sites validated by par-clip and hits-clip experiments. our analysis reveals that nucleotides at the 3'-end of bound seed matches are significantly more accessible than nucleotides at the 5'-end as well as nucleotides at any positions in the unbound seed matches. we show that the accessibility of a sing ...	2012	22915600
unusual c=c bond isomerization of an α,β-unsaturated γ-butyrolactone catalysed by flavoproteins from the old yellow enzyme family.	an unexpected, redox-neutral c=c bond isomerization of a γ-butyrolactone bearing an exo-methylene unit to the thermodynamically more favoured endo isomer (k(cat) =0.076 s(-1) ) catalysed by flavoproteins from the old yellow enzyme family was discovered. theoretical calculations and kinetic data support a mechanism through which the isomerization proceeds through fmn-mediated hydride addition onto exo-cβ, followed by hydride abstraction from endo-cβ', which is in line with the well-established c= ...	2012	23024004
functional analysis of three arabidopsis argonautes using slicer-defective mutants.	in rna-directed silencing pathways, ternary complexes result from small rna-guided argonaute (ago) associating with target transcripts. target transcripts are often silenced through direct cleavage (slicing), destabilization through slicer-independent turnover mechanisms, and translational repression. here, wild-type and active-site defective forms of several arabidopsis thaliana ago proteins involved in posttranscriptional silencing were used to examine several ago functions, including small rn ...	2012	23023169
recor complex including recr n-n dimer and reco monomer displays a high affinity for ssdna.	recr is an important recombination mediator protein in the recfor pathway. recr together with reco and recf facilitates reca nucleoprotein filament formation and homologous pairing. structural and biochemical studies of thermoanaerobacter tengcongensis recr (tterecr) and its series mutants revealed that tterecr uses the n-n dimer as a basic functional unit to interact with ttereco monomer. two tterecr n-n dimers form a ring-shaped tetramer via an interaction between their c-terminal regions. the ...	2012	23019218
convergent transmission of rnai guide-target mismatch information across argonaute internal allosteric network.	in rna interference, a guide strand derived from a short dsrna such as a microrna (mirna) is loaded into argonaute, the central protein in the rna induced silencing complex (risc) that silences messenger rnas on a sequence-specific basis. the positions of any mismatched base pairs in an mirna determine which argonaute subtype is used. subsequently, the argonaute-guide complex binds and silences complementary target mrnas; certain argonautes cleave the target. mismatches between guide strand and ...	2012	23028290
the crystal structure of the rv0301-rv0300 vapbc-3 toxin-antitoxin complex from m. tuberculosis reveals a mg²⁺ ion in the active site and a putative rna-binding site.	vapbc pairs account for 45 out of 88 identified toxin-antitoxin (ta) pairs in the mycobacterium tuberculosis (mtb) h37rv genome. a working model suggests that under times of stress, antitoxin molecules are degraded, releasing the toxins to slow the metabolism of the cell, which in the case of vapc toxins is via their rnase activity. otherwise the ta pairs remain bound to their promoters, autoinhibiting transcription. the crystal structure of rv0301-rv0300, an mtb vapbc ta complex determined at 1 ...	2012	23011806
mining the sinorhizobium meliloti transportome to develop fret biosensors for sugars, dicarboxylates and cyclic polyols.	förster resonance energy transfer (fret) biosensors are powerful tools to detect biologically important ligands in real time. currently fret bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens). to expand the number of available fret biosensors we used the induction profile of the sinorhizobium meliloti transportome to system ...	2012	23028462
enzyme redesign guided by cancer-derived idh1 mutations.	mutations in an enzyme can result in a neomorphic catalytic activity in cancers. we applied cancer-associated mutations from isocitrate dehydrogenases to homologous residues in the active sites of homoisocitrate dehydrogenases to derive enzymes that catalyze the conversion of 2-oxoadipate to (r)-2-hydroxyadipate, a critical step for adipic acid production. thus, we provide a prototypic example of how insights from cancer genome sequencing and functional studies can aid in enzyme redesign.	2012	23001033
stable cu(ii) and cu(i) mononuclear intermediates in the assembly of the cua center of thermus thermophilus cytochrome oxidase.	cua is a dinuclear mixed-valence center located in subunit 2 of the ba(3)-type cytochrome oxidase from thermus thermophilus. the assembly of this site within the periplasmic membrane is believed to be mediated by the copper chaperones sco and/or pcuac, but the biological mechanisms are still poorly understood, thereby stimulating interest in the mechanisms of cua formation from inorganic ions. the formulation of the cua center as an electron-delocalized cu(1.5)-cu(1.5) system implicates both cu( ...	2012	22946616
flexible connection of the n-terminal domain in clpb modulates substrate binding and the aggregate reactivation efficiency.	clpb reactivates aggregated proteins in cooperation with dnak/j. the clpb monomer contains two nucleotide-binding domains (d1, d2), a coiled-coil domain, and an n-terminal domain attached to d1 with a 17-residue-long unstructured linker containing a gly-gly motif. the clpb-mediated protein disaggregation is linked to translocation of substrates through the central channel in the hexameric clpb, but the events preceding the translocation are poorly understood. the n-terminal domains form a ring s ...	2012	22890624
identification of elongation factor g as the conserved cellular target of argyrin b.	argyrins, produced by myxobacteria and actinomycetes, are cyclic octapeptides with antibacterial and antitumor activity. here, we identify elongation factor g (ef-g) as the cellular target of argyrin b in bacteria, via resistant mutant selection and whole genome sequencing, biophysical binding studies and crystallography. argyrin b binds a novel allosteric pocket in ef-g, distinct from the known ef-g inhibitor antibiotic fusidic acid, revealing a new mode of protein synthesis inhibition. in euka ...	2012	22970117
common chaperone activity in the g-domain of trgtpase protects l11-l12 interaction on the ribosome.	translational gtpases (trgtpases) regulate all phases of protein synthesis. an early event in the interaction of a trgtpase with the ribosome is the contact of the g-domain with the c-terminal domain (ctd) of ribosomal protein l12 (l12-ctd) and subsequently interacts with the n-terminal domain of l11 (l11-ntd). however, the structural and functional relationships between l12-ctd and l11-ntd remain unclear. here, we performed mutagenesis, biochemical and structural studies to identify the interac ...	2012	22965132
protein-protein interactions in the β-oxidation part of the phenylacetate utilization pathway: crystal structure of the paaf-paag hydratase-isomerase complex.	microbial anaerobic and so-called hybrid pathways for degradation of aromatic compounds contain β-oxidation-like steps. these reactions convert the product of the opening of the aromatic ring to common metabolites. the hybrid phenylacetate degradation pathway is encoded in escherichia coli by the paa operon containing genes for 10 enzymes. previously, we have analyzed protein-protein interactions among the enzymes catalyzing the initial oxidation steps in the paa pathway (grishin, a. m., ajamian ...	2012	22961985
basic mechanism of transcription by rna polymerase ii.	rna polymerase ii-like enzymes carry out transcription of genomes in eukaryota, archaea, and some viruses. they also exhibit fundamental similarity to rna polymerases from bacteria, chloroplasts, and mitochondria. in this review we take an inventory of recent studies illuminating different steps of basic transcription mechanism, likely common for most multi-subunit rna polymerases. through the amalgamation of structural and computational chemistry data we attempt to highlight the most feasible r ...	2012	22982365
basic mechanism of transcription by rna polymerase ii.	rna polymerase ii-like enzymes carry out transcription of genomes in eukaryota, archaea, and some viruses. they also exhibit fundamental similarity to rna polymerases from bacteria, chloroplasts, and mitochondria. in this review we take an inventory of recent studies illuminating different steps of basic transcription mechanism, likely common for most multi-subunit rna polymerases. through the amalgamation of structural and computational chemistry data we attempt to highlight the most feasible r ...	2012	22982365
the spt4-spt5 complex: a multi-faceted regulator of transcription elongation.	in all domains of life, elongating rna polymerases require the assistance of accessory factors to maintain their processivity and regulate their rate. among these elongation factors, the spt5/nusg factors stand out. members of this protein family appear to be the only transcription accessory proteins that are universally conserved across all domains of life. in archaea and eukaryotes, spt5 associates with a second protein, spt4. in addition to regulating elongation, the eukaryotic spt4-spt5 comp ...	2012	22982195
the spt4-spt5 complex: a multi-faceted regulator of transcription elongation.	in all domains of life, elongating rna polymerases require the assistance of accessory factors to maintain their processivity and regulate their rate. among these elongation factors, the spt5/nusg factors stand out. members of this protein family appear to be the only transcription accessory proteins that are universally conserved across all domains of life. in archaea and eukaryotes, spt5 associates with a second protein, spt4. in addition to regulating elongation, the eukaryotic spt4-spt5 comp ...	2012	22982195
synthetic metabolic engineering-a novel, simple technology for designing a chimeric metabolic pathway.	the integration of biotechnology into chemical manufacturing has been recognized as a key technology to build a sustainable society. however, the practical applications of biocatalytic chemical conversions are often restricted due to their complexities involving the unpredictability of product yield and the troublesome controls in fermentation processes. one of the possible strategies to overcome these limitations is to eliminate the use of living microorganisms and to use only enzymes involved ...	2012	22950411
the b. subtilis mgte magnesium transporter can functionally compensate trpm7-deficiency in vertebrate b-cells.	recent studies have shown that the vertebrate magnesium transporters solute carrier family 41, members 1 and 2 (slc41a1, slc41a2) and magnesium transporter subtype 1 (magt1) can endow vertebrate b-cells lacking the ion-channel kinase transient receptor potential cation channel, subfamily m, member 7 (trpm7) with a capacity to grow and proliferate. slc41a1 and slc41a2 display distant homology to the prokaryotic family of mg(2+) transporters, mgte, first characterized in bacillus subtilis. these s ...	2012	22970223
benefits of using molecular structure and abundance in phylogenomic analysis.		2012	22973296
insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.	the hexameric purine nucleoside phosphorylase from bacillus subtilis (bspnp233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. in order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexame ...	2012	22957058
structure of the human mterf4-nsun4 protein complex that regulates mitochondrial ribosome biogenesis.	proteins crucial for the respiratory chain are translated by the mitochondrial ribosome. mitochondrial ribosome biogenesis is therefore critical for oxidative phosphorylation capacity and disturbances are known to cause human disease. this complex process is evolutionary conserved and involves several rna processing and modification steps required for correct ribosomal rna maturation. we recently showed that a member of the mitochondrial transcription termination factor (mterf) family of protein ...	2012	22949673
decoding properties of trna leave a detectable signal in codon usage bias.	the standard genetic code translates 61 codons into 20 amino acids using fewer than 61 transfer rnas (trnas). this is possible because of the trna's ability to 'wobble' at the third base to decode more than one codon. although the anticodon-codon mapping of trna to mrna is a prerequisite for certain codon usage indices and can contribute to the understanding of the evolution of alternative genetic codes, it is usually not determined experimentally because such assays are prohibitively expensive ...	2012	22962450
c16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the u6 snrna 3' end modification.	c16orf57 encodes a human protein of unknown function, and mutations in the gene occur in poikiloderma with neutropenia (pn), which is a rare, autosomal recessive disease. interestingly, mutations in c16orf57 were also observed among patients diagnosed with rothmund-thomson syndrome (rts) and dyskeratosis congenita (dc), which are caused by mutations in genes involved in dna repair and telomere maintenance. a genetic screen in saccharomyces cerevisiae revealed that the yeast ortholog of c16orf57, ...	2012	22899009
the chbg gene of the chitobiose (chb) operon of escherichia coli encodes a chitooligosaccharide deacetylase.	the chb operon of escherichia coli is involved in the utilization of the β-glucosides chitobiose and cellobiose. the function of chbg (ydjc), the sixth open reading frame of the operon that codes for an evolutionarily conserved protein is unknown. we show that chbg encodes a monodeacetylase that is essential for growth on the acetylated chitooligosaccharides chitobiose and chitotriose but is dispensable for growth on cellobiose and chitosan dimer, the deacetylated form of chitobiose. the predict ...	2012	22797760
single-molecule analysis of translational dynamics.	decades of extensive biochemical and biophysical research have outlined the mechanism of translation. rich structural studies have provided detailed snapshots of the translational machinery at all phases of the translation cycle. however, the relationship between structural dynamics, composition, and function remains unknown. the multistep nature of each stage of the translation cycle results in rapid desynchronization of individual ribosomes, thus hindering elucidation of the underlying mechani ...	2012	22798542
mercury resistance and mercuric reductase activities and expression among chemotrophic thermophilic aquificae.	mercury (hg) resistance (mer) by the reduction of mercuric to elemental hg is broadly distributed among the bacteria and archaea and plays an important role in hg detoxification and biogeochemical cycling. mera is the protein subunit of the homodimeric mercuric reductase (mr) enzyme, the central function of the mer system. mera sequences in the phylum aquificae form the deepest-branching lineage in bayesian phylogenetic reconstructions of all known mera homologs. we therefore hypothesized that t ...	2012	22773655
protection of bacillus pumilus spores by catalases.	bacillus pumilus safr-032, isolated at spacecraft assembly facilities of the national aeronautics and space administration jet propulsion laboratory, is difficult to kill by the sterilization method of choice, which uses liquid or vapor hydrogen peroxide. we identified two manganese catalases, yjqc and bpum_1305, in spore protein extracts of several b. pumilus strains by using page and mass spectrometric analyses. while the bpum_1305 catalase was present in six of the b. pumilus strains tested, ...	2012	22752169
multiple binding of repressed mrnas by the p-body protein rck/p54.	translational repression is achieved by protein complexes that typically bind 3' utr mrna motifs and interfere with the formation of the cap-dependent initiation complex, resulting in mrnps with a closed-loop conformation. we demonstrate here that the human dead-box protein rck/p54, which is a component of such complexes and central to p-body assembly, is in considerable molecular excess with respect to cellular mrnas and enriched to a concentration of 0.5 mm in p-bodies, where it is organized i ...	2012	22836354
transcriptional repression mediated by a tetr family protein, pfmr, from thermus thermophilus hb8.	pfmr is one of four tetr family transcriptional regulators found in the extremely thermophilic bacterium, thermus thermophilus hb8. we identified three promoters with strong negative regulation by pfmr, both in vivo and in vitro. pfmr binds pseudopalindromic sequences, with the consensus sequence of 5'-taccgaccgntnggtn-3' surrounding the promoters. according to the amino acid sequence and three-dimensional structure analyses of the pfmr-regulated gene products, they are predicted to be involved ...	2012	22753056
comparison of segger and other methods for segmentation and rigid-body docking of molecular components in cryo-em density maps.	segmentation and docking are useful methods for the discovery of molecular components in electron cryo-microscopy (cryo-em) density maps of macromolecular complexes. in this article, we describe the segmentation and docking methods implemented in segger. for 11 targets posted in the 2010 cryo-em challenge, we segmented the regions corresponding to individual molecular components using segger. we then used the segmented regions to guide rigid-body docking of individual components. docking results ...	2012	22696409
resolving the negative potential side (n-side) water-accessible proton pathway of f-type atp synthase by molecular dynamics simulations.	the rotation of f(1)f(o)-atp synthase is powered by the proton motive force across the energy-transducing membrane. the protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane f(o) domain, which is coupled to the atp-producing f(1) domain. the hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved asp/glu at the outer transmembrane helix (tmh). an open question is the proton transfer pat ...	2012	22942277
crystallization and preliminary x-ray crystallographic analysis of ygjg from escherichia coli.	putrescine, one of the polyamines that are found in virtually all living organisms, has been implicated as an important biological material. the protein ygjg is involved in the putrescine-degradation pathway in escherichia coli. the enzyme is a putrescine:2-oxoglutarate aminotransferase that belongs to the class iii aminotransferases. in this study, ygjg from e. coli was overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. diffraction data were collected to 2. ...	2012	22949197
cross-complementation study of the flagellar type iii export apparatus membrane protein flhb.	the bacterial type iii export apparatus is found in the flagellum and in the needle complex of some pathogenic gram-negative bacteria. in the needle complex its function is to secrete effector proteins for infection into eukaryotic cells. in the bacterial flagellum it exports specific proteins for the building of the flagellum during its assembly. the export apparatus is composed of about five membrane proteins and three soluble proteins. the mechanism of the export apparatus is not fully unders ...	2012	22952860
evolution of multiple, mutually orthogonal prolyl-trna synthetase/trna pairs for unnatural amino acid mutagenesis in escherichia coli.	the site-specific incorporation of unnatural amino acids (uaas) into proteins in living cells relies on an engineered trna/aminoacyl-trna synthetase (trna/aars) pair, orthogonal to the host cell, to deliver the uaa of choice in response to a unique nonsense or frameshift codon. here we report the generation of mutually orthogonal prolyl-trna/prolyl-trna synthase (prors) pairs derived from an archaebacterial ancestor for use in escherichia coli. by reprogramming the anticodon-binding pocket of py ...	2012	22927411
native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (crispr)-associated protein complexes from escherichia coli and pseudomonas aeruginosa.	the crispr/cas (clustered regularly interspaced short palindromic repeats/crispr-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to rna-interference. key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different crispr/cas subtypes. previous studies combined mass spectrometry, electron microscopy, and small angle x-ray scattering to demo ...	2012	22918228
biochemical and structural insights into xylan utilization by the thermophilic bacterium caldanaerobius polysaccharolyticus.	hemicellulose is the next most abundant plant cell wall component after cellulose. the abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. in an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium caldanaerobius polysaccharolyticus. analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and ...	2012	22918832
evolutionary mechanisms of microbial genomes 2012.		2012	22957300
allosteric control of the ribosome by small-molecule antibiotics.	protein synthesis is targeted by numerous, chemically distinct antibiotics that bind and inhibit key functional centers of the ribosome. using single-molecule imaging and x-ray crystallography, we show that the aminoglycoside neomycin blocks aminoacyl-transfer rna (aa-trna) selection and translocation as well as ribosome recycling by binding to helix 69 (h69) of 23s ribosomal rna within the large subunit of the escherichia coli ribosome. there, neomycin prevents the remodeling of intersubunit br ...	2012	22902368
structure of the prolyl-trna synthetase from the eukaryotic pathogen giardia lamblia.	the genome of the human intestinal parasite giardia lamblia contains only a single aminoacyl-trna synthetase gene for each amino acid. the giardia prolyl-trna synthetase gene product was originally misidentified as a dual-specificity pro/cys enzyme, in part owing to its unexpectedly high off-target activation of cysteine, but is now believed to be a normal representative of the class of archaeal/eukaryotic prolyl-trna synthetases. the 2.2 å resolution crystal structure of the g. lamblia enzyme p ...	2012	22948920
recfor proteins target reca protein to a dna gap with either dna or rna at the 5' terminus: implication for repair of stalled replication forks.	the repair of single-stranded gaps in duplex dna by homologous recombination requires the proteins of the recf pathway. the assembly of reca protein onto gapped dna (gdna) that is complexed with the single-stranded dna-binding protein is accelerated by the recf, reco, and recr (recfor) proteins. here, we show the recfor proteins specifically target reca protein to gdna even in the presence of a thousand-fold excess of single-stranded dna (ssdna). the binding constant of recf protein, in the pres ...	2012	22902627
distinct states of methionyl-trna synthetase indicate inhibitor binding by conformational selection.	to guide development of new drugs targeting methionyl-trna synthetase (metrs) for treatment of human african trypanosomiasis, crystal structure determinations of trypanosoma brucei metrs in complex with its substrate methionine and its intermediate product methionyl-adenylate were followed by those of the enzyme in complex with high-affinity aminoquinolone inhibitors via soaking experiments. drastic changes in conformation of one of the two enzymes in the asymmetric unit allowed these inhibitors ...	2012	22902861
post-translational oxidative modification and inactivation of mitochondrial complex i in epileptogenesis.	mitochondrial oxidative stress and damage have been implicated in the etiology of temporal lobe epilepsy, but whether or not they have a functional impact on mitochondrial processes during epilepsy development (epileptogenesis) is unknown. one consequence of increased steady-state mitochondrial reactive oxygen species levels is protein post-translational modification (ptm). we hypothesize that complex i (ci), a protein complex of the mitochondrial electron transport chain, is a target for oxidan ...	2012	22895709
cardiac mitochondrial matrix and respiratory complex protein phosphorylation.	it has become appreciated over the last several years that protein phosphorylation within the cardiac mitochondrial matrix and respiratory complexes is extensive. given the importance of oxidative phosphorylation and the balance of energy metabolism in the heart, the potential regulatory effect of these classical signaling events on mitochondrial function is of interest. however, the functional impact of protein phosphorylation and the kinase/phosphatase system responsible for it are relatively ...	2012	22886415
molecular dynamics simulations of ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.	to better understand the recognition mechanism of risc and the repertoire of guide-target interactions we introduced g:u wobbles and mismatches at various positions of the microrna (mirna) 'seed' region and performed all-atom molecular dynamics simulations of the resulting ago-mirna:mrna ternary complexes. our simulations reveal that many modifications, including combinations of multiple g:u wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuation ...	2012	22888400
functional expression of a penicillin acylase from the extreme thermophile thermus thermophilus hb27 in escherichia coli.	penicillin acylases (pacs) are enzymes of industrial relevance in the manufacture of β-lactam antibiotics. development of a pac with a longer half-life under the reaction conditions used is essential for the improvement of the operational stability of the process. a gene encoding a homologue to escherichia coli pac was found in the genome of the thermophilic bacterium thermus thermophilus (tth) hb27. because of the nature of this pac and its complex maturation that is crucial to reach its functi ...	2012	22876915
characterization of crispr rna processing in clostridium thermocellum and methanococcus maripaludis.	the crispr arrays found in many bacteria and most archaea are transcribed into a long precursor rna that is processed into small clustered regularly interspaced short palindromic repeats (crispr) rnas (crrnas). these rna molecules can contain fragments of viral genomes and mediate, together with a set of crispr-associated (cas) proteins, the prokaryotic immunity against viral attacks. crispr/cas systems are diverse and the cas6 enzymes that process crrnas vary between different subtypes. we anal ...	2012	22879377
structure of the rna claw of the dna packaging motor of bacteriophage φ29.	bacteriophage dna packaging motors translocate their genomic dna into viral heads, compacting it to near-crystalline density. the bacillus subtilis phage 29 has a unique ring of rna (prna) that is an essential component of its motor, serving as a scaffold for the packaging atpase. previously, deletion of a three-base bulge (18-cca-20) in the prna a-helix was shown to abolish packaging activity. here, we solved the structure of this crucial bulge by nuclear magnetic resonance (nmr) using a 27mer ...	2012	22879380
structural and catalytic differences between two fadh(2)-dependent monooxygenases: 2,4,5-tcp 4-monooxygenase (tftd) from burkholderia cepacia ac1100 and 2,4,6-tcp 4-monooxygenase (tcpa) from cupriavidus necator jmp134.	2,4,5-tcp 4-monooxygenase (tftd) and 2,4,6-tcp 4-monooxygenase (tcpa) have been discovered in the biodegradation of 2,4,5-trichlorophenol (2,4,5-tcp) and 2,4,6-trichlorophenol (2,4,6-tcp). tcpa and tftd belong to the reduced flavin adenine dinucleotide (fadh(2))-dependent monooxygenases and both use 2,4,6-tcp as a substrate; however, the two enzymes produce different end products. tftd catalyzes a typical monooxygenase reaction, while tcpa catalyzes a typical monooxygenase reaction followed by a ...	2012	22949829
cloning, expression and bioinformatics analysis of atp sulfurylase from acidithiobacillus ferrooxidans atcc 23270 in escherichia coli.	molecular studies of enzymes involved in sulfite oxidation in acidithiobacillus ferrooxidans have not yet been developed, especially in the atp sulfurylase (atps) of these acidophilus tiobacilli that have importance in biomining. this enzyme synthesizes atp and sulfate from adenosine phosphosulfate (aps) and pyrophosphate (ppi), final stage of the sulfite oxidation by these organisms in order to obtain energy. the atps gene (1674 bp) encoding the atps from acidithiobacillus ferrooxidans atcc 232 ...	2012	23055613
weakly antiferromagentic coupling via superexchange interaction between mn(ii)-mn(ii) atoms: a qm/mm study of the active site of human cytosolic x-propyl aminopeptidase p.	we investigate the dinuclear manganese, mn(ii)-mn(ii), active site of human cytosolic x-propyl aminopeptidase (xpnpep1) employing the qm/mm method. the optimized structure supports two manganese atoms at the active site and excludes the possibility of a single mn(ii) atom or other combination of divalent metal ions: ca(ii), fe(ii), mg(ii). a broken symmetry solution verifies an antiferromagnetically coupled state between the mn(ii)-mn(ii) pair, which is the ground state. from the energy differen ...	2012	23145216
the deactive form of respiratory complex i from mammalian mitochondria is a na+/h+ antiporter.	in mitochondria, complex i (nadh:ubiquinone oxidoreductase) uses the redox potential energy from nadh oxidation by ubiquinone to transport protons across the inner membrane, contributing to the proton-motive force. however, in some prokaryotes, complex i may transport sodium ions instead, and three subunits in the membrane domain of complex i are closely related to subunits from the mrp family of na(+)/h(+) antiporters. here, we define the relationship between complex i from bos taurus heart mit ...	2012	22854968
resistance to a novel antichlamydial compound is mediated through mutations in chlamydia trachomatis secy.	a novel and quantitative high-throughput screening approach was explored as a tool for the identification of novel compounds that inhibit chlamydial growth in mammalian cells. the assay is based on accumulation of a fluorescent marker by intracellular chlamydiae. its utility was demonstrated by screening 42,000 chemically defined compounds against chlamydia caviae gpic. this analysis led to the identification of 40 primary-hit compounds. five of these compounds were nontoxic to host cells and ha ...	2012	22644029
characterization of the pib-type atpases present in thermus thermophilus.	p(ib)-type atpases transport heavy metals (cu(2+), cu(+), ag(+), zn(2+), cd(2+), co(2+)) across biomembranes, playing a key role in homeostasis and in the mechanisms of biotolerance of these metals. three genes coding for putative p(ib)-type atpases are present in the genome of thermus thermophilus (hb8 and hb27): the ttc1358, ttc1371, and ttc0354 genes; these genes are annotated, respectively, as two copper transporter (copa and copb) genes and a zinc-cadmium transporter (zn(2+)/cd(2+)-atpase) ...	2012	22636781
phenylacetic acid catabolism and its transcriptional regulation in corynebacterium glutamicum.	the industrially important organism corynebacterium glutamicum has been characterized in recent years for its robust ability to assimilate aromatic compounds. in this study, c. glutamicum strain as 1.542 was investigated for its ability to catabolize phenylacetic acid (paa). the paa genes were identified; they are organized as a continuous paa gene cluster. the type strain of c. glutamicum, atcc 13032, is not able to catabolize paa, but the recombinant strain atcc 13032/pec-k18mob2::paa gained t ...	2012	22685150
structural insights into the function of 23s rrna methyltransferase rlmg (m²g1835) from escherichia coli.	rlmg is a specific adomet-dependent methyltransferase (mtase) responsible for n²-methylation of g1835 in 23s rrna of escherichia coli. methylation of m²g1835 specifically enhances association of ribosomal subunits and provides a significant advantage for bacteria in osmotic and oxidative stress. here, the crystal structure of rlmg in complex with adomet and its structure in solution were determined. the structure of rlmg is similar to that of the mtase rsmc, consisting of two homologous domains: ...	2012	22753782
fidaxomicin is an inhibitor of the initiation of bacterial rna synthesis.	fidaxomicin was recently approved for the treatment of clostridium difficile infection. it inhibits transcription by bacterial rna polymerase. because transcription is a multistep process, experiments were conducted in which fidaxomicin was added at different stages of transcriptional initiation to identify the blocked step. dna footprinting experiments were also conducted to further elucidate the stage inhibited. fidaxomicin blocks initiation only if added before the formation of the "open prom ...	2012	22752861
membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes.	the crystal structure of the β(2)-adrenergic receptor in complex with an agonist and its cognate g protein has just recently been determined. it is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signaling event across the membrane, and sets in motion a series of g protein-directed intracellular responses. the structure was determined using crystals of the ternary complex grown in a rationally desi ...	2012	22783824
crystallization and preliminary x-ray diffraction analysis of a fatty-acid metabolism regulatory protein, fadr, from bacillus halodurans.	fadr is an acyl-coa-dependent transcription factor which regulates genes encoding proteins involved in fatty-acid degradation and synthesis in order to maintain lipid homeostasis. fadr from the alkaliphilic bacterium bacillus halodurans was cloned and overexpressed in escherichia coli. the fadr (bh3102) protein from b. halodurans is composed of 195 amino-acid residues with a molecular mass of 22 378 da. crystals were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.05 å r ...	2012	22869136
crystallization and preliminary x-ray analysis of pac17 from the pacidamycin-biosynthetic cluster of streptomyces coeruleorubidus.	pac17 is an uncharacterized protein from the pacidamycin gene cluster of the soil bacterium streptomyces coeruleorubidus. it is implicated in the biosynthesis of the core diaminobutyric acid residue of the antibiotic, although its precise role is uncertain at present. given that pacidamycins inhibit translocase i of pseudomonas aeruginosa, a clinically unexploited antibiotic target, they offer new hope in the search for antibacterial agents directed against this important pathogen. crystals of p ...	2012	22869135
crystallization and preliminary crystallographic analysis of the c-terminal domain of mamm, a magnetosome-associated protein from magnetospirillum gryphiswaldense msr-1.	mamm is a unique magnetosome-associated protein that shares substantial homology with cation diffusion facilitator (cdf) proteins, a group of heavy-metal-ion efflux transporters that participate in metal-ion homeostasis in all domains of life. magnetotactic bacteria utilize cdf proteins in iron-oxide biomineralization and in magnetosome formation. here, the crystallization and preliminary x-ray analysis of recombinant magnetospirillum gryphiswaldense mamm is reported. the c-terminal domain of ma ...	2012	22869124
crystal structure of xenotropic murine leukaemia virus-related virus (xmrv) ribonuclease h.	rnase h (retroviral ribonuclease h) cleaves the phosphate backbone of the rna template within an rna/dna hybrid to complete the synthesis of double-stranded viral dna. in the present study we have determined the complete structure of the rnase h domain from xmrv (xenotropic murine leukaemia virus-related virus) rt (reverse transcriptase). the basic protrusion motif of the xmrv rnase h domain is folded as a short helix and an adjacent highly bent loop. structural superposition and subsequent muta ...	2012	22724525
nuclear rnase p of trypanosoma brucei: a single protein in place of the multicomponent rna-protein complex.	rnase p is the endonuclease that removes 5' extensions from trna precursors. in its best-known form, the enzyme is composed of a catalytic rna and a protein moiety variable in number and mass. this ribonucleoprotein enzyme is widely considered ubiquitous and apparently reached its highest complexity in the eukaryal nucleus, where it is typically composed of at least ten subunits. here, we show that in the protist trypanosoma brucei, two proteins are the sole forms of rnase p. they localize to th ...	2012	22840392
structural insights into electron transfer in caa3-type cytochrome oxidase.	cytochrome c oxidase is a member of the haem copper oxidase superfamily (hco). hcos function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. integral to the enzyme's function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. electron entry and exit are proposed to occur from the same site on cytochrome c. here we report the cr ...	2012	22763450
go hybrid: em, crystallography, and beyond.	a mechanistic understanding of the molecular transactions that govern cellular function requires knowledge of the dynamic organization of the macromolecular machines involved in these processes. structural biologists employ a variety of biophysical methods to study large macromolecular complexes, but no single technique is likely to provide a complete description of the structure-function relationship of all the constituent components. since structural studies generally only provide snapshots of ...	2012	22835744
evolution and diversification of the organellar release factor family.	translation termination is accomplished by proteins of the class i release factor family (rf) that recognize stop codons and catalyze the ribosomal release of the newly synthesized peptide. bacteria have two canonical rfs: rf1 recognizes uaa and uag, rf2 recognizes uaa and uga. despite that these two release factor proteins are sufficient for de facto translation termination, the eukaryotic organellar rf protein family, which has evolved from bacterial release factors, has expanded considerably, ...	2012	22688947
the complete genome sequence of natrinema sp. j7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements.	natrinema sp. j7-2 is an extreme haloarchaeon capable of growing on synthetic media without amino acid supplements. here we report the complete genome sequence of natrinema sp. j7-2 which is composed of a 3,697,626-bp chromosome and a 95,989-bp plasmid pj7-i. this is the first complete genome sequence of a member of the genus natrinema. we demonstrate that natrinema sp. j7-2 can use gluconate, glycerol, or acetate as the sole carbon source and that its genome encodes complete metabolic pathways ...	2012	22911826
protein l5 is crucial for in vivo assembly of the bacterial 50s ribosomal subunit central protuberance.	in the present work, ribosomes assembled in bacterial cells in the absence of essential ribosomal protein l5 were obtained. after arresting l5 synthesis, escherichia coli cells divide a limited number of times. during this time, accumulation of defective large ribosomal subunits occurs. these 45s particles lack most of the central protuberance (cp) components (5s rrna and proteins l5, l16, l18, l25, l27, l31, l33 and l35) and are not able to associate with the small ribosomal subunit. at the sam ...	2012	22821559
mechanisms of secm-mediated stalling in the ribosome.	nascent-peptide modulation of translation is a common regulatory mechanism of gene expression. in this mechanism, while the nascent peptide is still in the exit tunnel of the ribosome, it induces translational pausing, thereby controlling the expression of downstream genes. one example is secm, which inhibits peptide-bond formation in the ribosome's peptidyl transferase center (ptc) during its own translation, upregulating the expression of the protein translocase seca. although biochemical expe ...	2012	22853911
re-visiting protein-centric two-tier classification of existing dna-protein complexes.	precise dna-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. earlier in 2000, a systematic classification of dna-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namel ...	2012	22800292
structural basis for intersubunit signaling in a protein disaggregating machine.	clpb is a ring-forming, atp-dependent protein disaggregase that cooperates with the cognate hsp70 system to recover functional protein from aggregates. how clpb harnesses the energy of atp binding and hydrolysis to facilitate the mechanical unfolding of previously aggregated, stress-damaged proteins remains unclear. here, we present crystal structures of the clpb d2 domain in the nucleotide-bound and -free states, and the fitted cryoem structure of the d2 hexamer ring, which provide a structural ...	2012	22802670
structural characterization of neutral and acidic glycolipids from thermus thermophilus hb8.	the structural characterization of glycolipids from thermus thermophilus hb8 was performed in this study. two neutral and one acidic glycolipids were extracted and purified by the modified tlc-blotting method, after which their chemical structures were determined by chemical composition analysis, mass spectrometry (ms) and nuclear magnetic resonance (nmr) spectroscopy. the structure of one of the neutral glycolipids, ngl-a, was galp(α1-6)glcpnacyl(β1-2)glcp(α1-)acyl(2)gro, and the other, ngl-c, ...	2012	22815675
molecular characterization of nad+-dependent dna ligase from wolbachia endosymbiont of lymphatic filarial parasite brugia malayi.	the lymphatic filarial parasite, brugia malayi contains wolbachia endobacteria that are essential for development, viability and fertility of the parasite. therefore, wolbachial proteins have been currently seen as the potential antifilarial drug targets. nad(+)-dependent dna ligase is characterized as a promising drug target in several organisms due to its crucial, indispensable role in dna replication, recombination and dna repair. we report here the cloning, expression and purification of nad ...	2012	22815933
piecing together how a prokaryotic vov1-atpase works}: reconstitution of vacuolar-type rotary h+-atpase/synthase from thermus thermophilus.		2012	22798549
structural basis of biological nitrile reduction.	the enzyme quef catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preq(0)) to 7-aminomethyl-7-deazaguanine (preq(1)), the only nitrile reduction reaction known in biology. we describe here two crystal structures of bacillus subtilis quef, one of the wild-type enzyme in complex with the substrate preq(0), trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the c55a mutant in complex with the substrate preq(0) bound noncovalently. the q ...	2012	22787148
molecular dynamics of a thermostable multicopper oxidase from thermus thermophilus hb27: structural differences between the apo and holo forms.	molecular dynamic (md) simulations have been performed on tth-mco, a hyperthermophilic multicopper oxidase from thermus thermophilus hb27, in the apo as well as the holo form, with the aim of exploring the structural dynamic properties common to the two conformational states. according to structural comparison between this enzyme and other mcos, the substrate in process to electron transfer in an outer-sphere event seems to transiently occupy a shallow and overall hydrophobic cavity near the cu ...	2012	22808237
a lon-like protease with no atp-powered unfolding activity.	lon proteases are a family of atp-dependent proteases involved in protein quality control, with a unique proteolytic domain and an aaa(+) (atpases associated with various cellular activities) module accommodated within a single polypeptide chain. they were classified into two types as either the ubiquitous soluble lona or membrane-inserted archaeal lonb. in addition to the energy-dependent forms, a number of medically and ecologically important groups of bacteria encode a third type of lon-like ...	2012	22792246
mechanism of elongation factor-g-mediated fusidic acid resistance and fitness compensation in staphylococcus aureus.	antibiotic resistance in bacteria is often associated with fitness loss, which is compensated by secondary mutations. fusidic acid (fa), an antibiotic used against pathogenic bacteria staphylococcus aureus, locks elongation factor-g (ef-g) to the ribosome after gtp hydrolysis. to clarify the mechanism of fitness loss and compensation in relation to fa resistance, we have characterized three s. aureus ef-g mutants with fast kinetics and crystal structures. our results show that a significantly sl ...	2012	22767604
oxidants and not alkylating agents induce rapid mtdna loss and mitochondrial dysfunction.	mitochondrial dna (mtdna) is essential for proper mitochondrial function and encodes 22 trnas, 2 rrnas and 13 polypeptides that make up subunits of complex i, iii, iv, in the electron transport chain and complex v, the atp synthase. although mitochondrial dysfunction has been implicated in processes such as premature aging, neurodegeneration, and cancer, it has not been shown whether persistent mtdna damage causes a loss of oxidative phosphorylation. we addressed this question by treating mouse ...	2012	22766155
the scoi homologue senc is a copper binding protein that interacts directly with the cbb₃-type cytochrome oxidase in rhodobacter capsulatus.	sco proteins are widespread assembly factors for the cu(a) centre of aa₃-type cytochrome oxidases in eukaryotic and prokaryotic organisms. however, sco homologues are also found in bacteria like rhodobacter capsulatus which lack aa₃-type cytochrome oxidases and instead use a cbb₃-type cytochrome oxidase (cbb₃ cox) without a cu(a) centre as a terminal oxidase. in the current study, we have analyzed the role of sco (senc) during cbb₃ cox assembly in r. capsulatus. in agreement with earlier works, ...	2012	22771512
stoichiometry of proton pumping by the cbb3-type oxygen reductase in whole cells of rhodobacter capsulatus at ph 7 is about 0.5 h+ per electron.		2012	22761318
arrangement of subunits in intact mammalian mitochondrial atp synthase determined by cryo-em.	mitochondrial atp synthase is responsible for the synthesis of atp, a universal energy currency in cells. whereas x-ray crystallography has revealed the structure of the soluble region of the complex and the membrane-intrinsic c-subunits, little is known about the structure of the six other proteins (a, b, f, a6l, e, and g) that comprise the membrane-bound region of the complex in animal mitochondria. here, we present the structure of intact bovine mitochondrial atp synthase at ∼18 å resolution ...	2012	22753497
the elongation, termination, and recycling phases of translation in eukaryotes.	this work summarizes our current understanding of the elongation and termination/recycling phases of eukaryotic protein synthesis. we focus here on recent advances in the field. in addition to an overview of translation elongation, we discuss unique aspects of eukaryotic translation elongation including eef1 recycling, eef2 modification, and eef3 and eif5a function. likewise, we highlight the function of the eukaryotic release factors erf1 and erf3 in translation termination, and the functions o ...	2012	22751155
mass spectrometry--from peripheral proteins to membrane motors.	that membrane protein complexes could survive in the gas phase had always seemed impossible. the lack of chargeable residues, high hydrophobicity, and poor solubility and the vast excess of detergent contributed to the view that it would not be possible to obtain mass spectra of intact membrane complexes. with the recent success in recording mass spectra of these complexes, first from recombinant sources and later from the cellular environment, many surprising properties of these gas phase membr ...	2012	22750574
molecular evolution of dihydrouridine synthases.	dihydrouridine (d) is a modified base found in conserved positions in the d-loop of trna in bacteria, eukaryota, and some archaea. despite the abundant occurrence of d, little is known about its biochemical roles in mediating trna function. it is assumed that d may destabilize the structure of trna and thus enhance its conformational flexibility. d is generated post-transcriptionally by the reduction of the 5,6-double bond of a uridine residue in rna transcripts. the reaction is carried out by d ...	2012	22741570
dnak chaperone-dependent disaggregation by caseinolytic peptidase b (clpb) mutants reveals functional overlap in the n-terminal domain and nucleotide-binding domain-1 pore tyrosine.	protein disaggregation in escherichia coli is carried out by clpb, an aaa(+) (atpases associated with various cellular activities) molecular chaperone, together with the dnak chaperone system. conformational changes in clpb driven by atp binding and hydrolysis promote substrate binding, unfolding, and translocation. conserved pore tyrosines in both nucleotide-binding domain-1 (nbd-1) and -2 (nbd-2), which reside in flexible loops extending into the central pore of the clpb hexamer, bind substrat ...	2012	22745126
single-molecule analysis of inhibitory pausing states of v1-atpase.	v(1)-atpase, the hydrophilic v-atpase domain, is a rotary motor fueled by atp hydrolysis. here, we found that thermus thermophilus v(1)-atpase shows two types of inhibitory pauses interrupting continuous rotation: a short pause (sp, 4.2 s) that occurred frequently during rotation, and a long inhibitory pause (lp, >30 min) that terminated all active rotations. both pauses occurred at the same angle for atp binding and hydrolysis. kinetic analysis revealed that the time constants of inactivation i ...	2012	22736762
structural study on the architecture of the bacterial atp synthase fo motor.	we purified the f(o) complex from the ilyobacter tartaricus na(+)-translocating f(1)f(o)-atp synthase and performed a biochemical and structural study. laser-induced liquid bead ion desorption ms analysis demonstrates that all three subunits of the isolated f(o) complex were present and in native stoichiometry (ab(2)c(11)). cryoelectron microscopy of 2d crystals yielded a projection map at a resolution of 7.0 å showing electron densities from the c(11) rotor ring and up to seven adjacent helices ...	2012	22736796
control of electron transport routes through redox-regulated redistribution of respiratory complexes.	in cyanobacteria, respiratory electron transport takes place in close proximity to photosynthetic electron transport, because the complexes required for both processes are located within the thylakoid membranes. the balance of electron transport routes is crucial for cell physiology, yet the factors that control the predominance of particular pathways are poorly understood. here we use a combination of tagging with green fluorescent protein and confocal fluorescence microscopy in live cells of t ...	2012	22733774
structure of the signal transduction protein trap (target of rnaiii-activating protein).	the crystal structure of the signal transduction protein trap is reported at 1.85 å resolution. the structure of trap consists of a central eight-stranded β-barrel flanked asymmetrically by helices and is monomeric both in solution and in the crystal structure. a formate ion was found bound to trap identically in all four molecules in the asymmetric unit.	2012	22750855
the fragmented mitochondrial ribosomal rnas of plasmodium falciparum.	the mitochondrial genome in the human malaria parasite plasmodium falciparum is most unusual. over half the genome is composed of the genes for three classic mitochondrial proteins: cytochrome oxidase subunits i and iii and apocytochrome b. the remainder encodes numerous small rnas, ranging in size from 23 to 190 nt. previous analysis revealed that some of these transcripts have significant sequence identity with highly conserved regions of large and small subunit rrnas, and can form the expecte ...	2012	22761677
thermodynamic characterization of rna 2 × 3 nucleotide internal loops.	to better elucidate rna structure-function relationships and to improve the design of pharmaceutical agents that target specific rna motifs, an understanding of rna primary, secondary, and tertiary structure is necessary. the prediction of rna secondary structure from sequence is an intermediate step in predicting rna three-dimensional structure. rna secondary structure is typically predicted using a nearest neighbor model based on free energy parameters. the current free energy parameters for 2 ...	2012	22720720