Publications

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
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
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
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
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
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
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
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
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
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
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
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
structural basis for translation termination by archaeal rf1 and gtp-bound ef1α complex.	when a stop codon appears at the ribosomal a site, the class i and ii release factors (rfs) terminate translation. in eukaryotes and archaea, the class i and ii rfs form a heterodimeric complex, and complete the overall translation termination process in a gtp-dependent manner. however, the structural mechanism of the translation termination by the class i and ii rf complex remains unresolved. in archaea, archaeal elongation factor 1 alpha (aef1α), a carrier gtpase for trna, acts as a class ii r ...	2012	22772989
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
site-directed mutagenesis of a family 42 β-galactosidase from an antarctic bacterium.	site directed mutagenesis was used to modify the active site of a cold active beta-galactosidase taken from an antarctic psychrotolerant planococcus bacterial isolate. the goal was to modify the active site such that there would be an increase in activity on certain substrates which showed little to no activity with the wild type enzyme. a total of 5 mutant enzymes were constructed with amino acid changes based on an analysis done via homology modeling. all 5 modified enzymes were assayed using ...	2012	22773960
capreomycin susceptibility is increased by tlya-directed 2'-o-methylation on both ribosomal subunits.	the binding site of the cyclic peptide antibiotics capreomycin and viomycin is located on the ribosomal subunit interface close to nucleotides c1409 in 16s rrna and c1920 in 23s rrna. in mycobacterium tuberculosis, the 2'-hydroxyls of both nucleotides are methylated by the enzyme tlya. loss of these methylations through inactivation of tlya confers resistance to capreomycin and viomycin. we report here that tlya orthologues occur in diverse bacteria and fall into two distinct groups. one group, ...	2012	22779429
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
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
the porphyrias: advances in diagnosis and treatment.	the inborn errors of heme biosynthesis, the porphyrias, are 8 genetically distinct metabolic disorders that can be classified as "acute hepatic," "hepatic cutaneous," and "erythropoietic cutaneous" diseases. recent advances in understanding their pathogenesis and molecular genetic heterogeneity have led to improved diagnosis and treatment. these advances include dna-based diagnoses for all the porphyrias, new understanding of the pathogenesis of the acute hepatic porphyrias, identification of th ...	2012	22791288
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
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
piecing together how a prokaryotic vov1-atpase works}: reconstitution of vacuolar-type rotary h+-atpase/synthase from thermus thermophilus.		2012	22798549
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
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
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
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
from static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility.	crystallographic structure and deuterium accessibility comparisons of cco in different redox states have suggested conformational changes of mechanistic significance. to predict the intrinsic flexibility and low energy motions in cco, this work has analyzed available high-resolution crystallographic structures with proflex and elnémo computational methods. the results identify flexible regions and potential conformational changes in cco that correlate well with published structural and biochemic ...	2012	22824280
role of elongation and secondary pathways in s6 amyloid fibril growth.	the concerted action of a large number of individual molecular level events in the formation and growth of fibrillar protein structures creates a significant challenge for differentiating between the relative contributions of different self-assembly steps to the overall kinetics of this process. the characterization of the individual steps is, however, an important requirement for achieving a quantitative understanding of this general phenomenon which underlies many crucial functional and pathol ...	2012	22824281
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
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
structural analysis of hypothetical proteins from helicobacter pylori: an approach to estimate functions of unknown or hypothetical proteins.	helicobacter pylori (h. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. it can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (malt) lymphoma, gastric cancer, etc. based on genomic research of h. pylori, over 1600 genes have been functionally identified so far. however, h. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the f ...	2012	22837682
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
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
functional characterization of the role of the chromosome i partitioning system in genome segregation in deinococcus radiodurans.	deinococcus radiodurans, a radiation-resistant bacterium, harbors a multipartite genome. chromosome i contains three putative centromeres (segs1, segs2, and segs3), and para (para1) and parb (parb1) homologues. the parb1 interaction with segs was sequence specific, and para1 was shown to be a dna binding atpase. the atpase activity of para1 was stimulated when segs elements were coincubated with parb1, but the greatest increase was observed with segs3. para1 incubated with the segs-parb1 complex ...	2012	22843847
dna stabilization at the bacillus subtilis polx core--a binding model to coordinate polymerase, ap-endonuclease and 3'-5' exonuclease activities.	family x dna polymerases (polxs) are involved in dna repair. their binding to gapped dnas relies on two conserved helix-hairpin-helix motifs, one located at the 8-kda domain and the other at the fingers subdomain. bacterial/archaeal polxs have a specifically conserved third helix-hairpin-helix motif (gfgxk) at the fingers subdomain whose putative role in dna binding had not been established. here, mutagenesis at the corresponding residues of bacillus subtilis polx (polxbs), gly130, gly132 and ly ...	2012	22844091
phylogenetic position of aquificales based on the whole genome sequences of six aquificales species.	species belonging to the order aquificales are believed to be an early branching lineage within the bacteria. however, the branching order of this group in single-gene phylogenetic trees is highly variable; for example, it has also been proposed that the aquificales should be grouped with ε-proteobacteria. to investigate the phylogenetic position of aquificales at the whole-genome level, here we reconstructed the phylogenetic trees of 18 bacteria including six aquificales species based on the co ...	2012	22844640
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
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
a three-dimensional topology of complex i inferred from evolutionary correlations.	the quaternary structure of eukaryotic nadh:ubiquinone oxidoreductase (complex i), the largest complex of the oxidative phosphorylation, is still mostly unresolved. furthermore, it is unknown where transiently bound assembly factors interact with complex i. we therefore asked whether the evolution of complex i contains information about its 3d topology and the binding positions of its assembly factors. we approached these questions by correlating the evolutionary rates of eukaryotic complex i su ...	2012	22857522
altered large-ring cyclodextrin product profile due to a mutation at tyr-172 in the amylomaltase of corynebacterium glutamicum.	corynebacterium glutamicum amylomaltase (cgam) catalyzes the formation of large-ring cyclodextrins (lr-cds) with a degree of polymerization of 19 and higher. the cloned cgam gene was ligated into the pet-17b vector and used to transform escherichia coli bl21(de3). site-directed mutagenesis of tyr-172 in cgam to alanine (y172a) was performed to determine its role in the control of lr-cd production. both the recombinant wild-type (wt) and y172a enzymes were purified to apparent homogeneity and cha ...	2012	22865069
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
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
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 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
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
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
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
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
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
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
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
interaction of card with rna polymerase mediates mycobacterium tuberculosis viability, rifampin resistance, and pathogenesis.	mycobacterium tuberculosis infection continues to cause substantial human suffering. new chemotherapeutic strategies, which require insight into the pathways essential for m. tuberculosis pathogenesis, are imperative. we previously reported that depletion of the card protein in mycobacteria compromises viability, resistance to oxidative stress and fluoroquinolones, and pathogenesis. card associates with the rna polymerase (rnap), but it has been unknown which of the diverse functions of card are ...	2012	22904282
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
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
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
crystal structure of rlmm, the 2'o-ribose methyltransferase for c2498 of escherichia coli 23s rrna.	rlmm (ygde) catalyzes the s-adenosyl methionine (adomet)-dependent 2'o methylation of c2498 in 23s ribosomal rna (rrna) of escherichia coli. previous experiments have shown that rlmm is active on 23s rrna from an rlmm knockout strain but not on mature 50s subunits from the same strain. here, we demonstrate rlmm methyltransferase (mtase) activity on in vitro transcribed 23s rrna and its domain v. we have solved crystal structures of e. coli rlmm at 1.9 å resolution and of an rlmm-adomet complex a ...	2012	22923526
inhibition of protein synthesis on the ribosome by tildipirosin compared with other veterinary macrolides.	tildipirosin is a 16-membered-ring macrolide developed to treat bacterial pathogens, including mannheimia haemolytica and pasteurella multocida, that cause respiratory tract infections in cattle and swine. here we evaluated the efficacy of tildipirosin at inhibiting protein synthesis on the ribosome (50% inhibitory concentration [ic(50)], 0.23 ± 0.01 μm) and compared it with the established veterinary macrolides tylosin, tilmicosin, and tulathromycin. mutation and methylation at key rrna nucleot ...	2012	22926570
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
spectroscopic and kinetic investigation of the fully reduced and mixed valence states of ba3-cytochrome c oxidase from thermus thermophilus: a fourier transform infrared (ftir) and time-resolved step-scan ftir study.	the complete understanding of a molecular mechanism of action requires the thermodynamic and kinetic characterization of different states and intermediates. cytochrome c oxidase reduces o(2) to h(2)o, a reaction coupled to proton translocation across the membrane. therefore, it is necessary to undertake a thorough characterization of the reduced form of the enzyme and the determination of the electron transfer processes and pathways between the redox-active centers. in this study fourier transfo ...	2012	22927441
the role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription.	bacterial enhancer binding proteins (bebps) are transcriptional activators that assemble as hexameric rings in their active forms and utilize atp hydrolysis to remodel the conformation of rna polymerase containing the alternative sigma factor σ(54). we present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. the review is structured by introducing each of the three domains in turn: the central catalytic domain, the ...	2012	22933558
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
double-stranded endonuclease activity in bacillus halodurans clustered regularly interspaced short palindromic repeats (crispr)-associated cas2 protein.	the crispr (clustered regularly interspaced short palindromic repeats) system is a prokaryotic rna-based adaptive immune system against extrachromosomal genetic elements. cas2 is a universally conserved core crispr-associated protein required for the acquisition of new spacers for crispr adaptation. it was previously characterized as an endoribonuclease with preference for single-stranded (ss)rna. here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the bac ...	2012	22942283
a blueprint for a mutationist theory of replicative strand asymmetries formation.	in the present review, we summarized current knowledge on replicative strand asymmetries in prokaryotic genomes. a cornerstone for the creation of a theory of their formation has been overviewed. according to our recent works, the probability of nonsense mutation caused by replication-associated mutational pressure is higher for genes from lagging strands than for genes from leading strands of both bacterial and archaeal genomes. lower density of open reading frames in lagging strands can be exp ...	2012	22942675
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
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
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
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
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
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
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
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
evolutionary mechanisms of microbial genomes 2012.		2012	22957300
insights into glycogen metabolism in chemolithoautotrophic bacteria from distinctive kinetic and regulatory properties of adp-glucose pyrophosphorylase from nitrosomonas europaea.	nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes co(2) via the benson-calvin cycle. despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in n. europaea, adp-glucose pyrophosphorylase and ...	2012	22961847
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
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
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
naxd is a deacetylase required for lipid a modification and francisella pathogenesis.	modification of specific gram-negative bacterial cell envelope components, such as capsule, o-antigen and lipid a, are often essential for the successful establishment of infection. francisella species express lipid a molecules with unique characteristics involved in circumventing host defences, which significantly contribute to their virulence. in this study, we show that naxd, a member of the highly conserved ydjc superfamily, is a deacetylase required for an important modification of the oute ...	2012	22966934
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
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
specific metal recognition in nickel trafficking.	nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. as with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. because there are few enzymes (targets) that require nickel for activi ...	2012	22970729
archaeal jab1/mpn/mov34 metalloenzyme (hvjamm1) cleaves ubiquitin-like small archaeal modifier proteins (samps) from protein-conjugates.	proteins with jab1/mpn/mov34 metalloenzyme (jamm/mpn+) domains are widespread among all domains of life, yet poorly understood. here we report the purification and characterization of an archaeal jamm/mpn+ domain protein (hvjamm1) from haloferax volcanii that cleaves ubiquitin-like small archaeal modifier proteins (samp1/2) from protein conjugates. hvjamm1 cleaved samp1/2 conjugates generated in h. volcanii as well as isopeptide- and linear-linked samp1-moae in purified form. cleavage of linear ...	2012	22970855
oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways.	in the universe, oxygen is the third most widespread element, while on earth it is the most abundant one. moreover, oxygen is a major constituent of all biopolymers fundamental to living organisms. besides o(2), reactive oxygen species (ros), among them hydrogen peroxide (h(2)o(2)), are also important reactants in the present aerobic metabolism. according to a widely accepted hypothesis, aerobic metabolism and many other reactions/pathways involving o(2) appeared after the evolution of oxygenic ...	2012	22970865
characterization of the genome, proteome, and structure of yersiniophage ϕr1-37.	the bacteriophage vb_yecm-ϕr1-37 (ϕr1-37) is a lytic yersiniophage that can propagate naturally in different yersinia species carrying the correct lipopolysaccharide receptor. this large-tailed phage has deoxyuridine (du) instead of thymidine in its dna. in this study, we determined the genomic sequence of phage ϕr1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. t ...	2012	22973030
benefits of using molecular structure and abundance in phylogenomic analysis.		2012	22973296
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
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
crystal structures of complexes of the branched-chain aminotransferase from deinococcus radiodurans with α-ketoisocaproate and l-glutamate suggest the radiation resistance of this enzyme for catalysis.	branched-chain aminotransferases (bcat), which utilize pyridoxal 5'-phosphate (plp) as a cofactor, reversibly catalyze the transfer of the α-amino groups of three of the most hydrophobic branched-chain amino acids (bcaa), leucine, isoleucine, and valine, to α-ketoglutarate to form the respective branched-chain α-keto acids and glutamate. the bcat from deinococcus radiodurans (drbcat), an extremophile, was cloned and expressed in escherichia coli for structure and functional studies. the crystal ...	2012	22984263
a multicenter blinded analysis indicates no association between chronic fatigue syndrome/myalgic encephalomyelitis and either xenotropic murine leukemia virus-related virus or polytropic murine leukemia virus.	the disabling disorder known as chronic fatigue syndrome or myalgic encephalomyelitis (cfs/me) has been linked in two independent studies to infection with xenotropic murine leukemia virus-related virus (xmrv) and polytropic murine leukemia virus (pmlv). although the associations were not confirmed in subsequent studies by other investigators, patients continue to question the consensus of the scientific community in rejecting the validity of the association. here we report blinded analysis of p ...	2012	22991430
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