Publications

product-controlled steady-state kinetics between cytochrome aa(3) from rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach.	cytochrome c oxidase (cco) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. in this study, the oxidation of horse cyt c(2+) by cco from rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. a novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) ...	2012	22516686
comparative analyses of homocitrate synthase genes of ascomycetous yeasts.	most ascomycetous yeasts have 2 homocitrate synthases (hcss). among the fungal lysine biosynthesis-related genes, only the hcs gene was duplicated in the course of evolution. it was recently reported that hcs of saccharomyces cerevisiae has an additional function in nuclear activities involving chromatin regulation related to dna damage repair, which is not related to lysine biosynthesis. thus, it is possible that the bifunctionality is associated with hcs gene duplication. phylogenetic analysis ...	2012	22518332
crispr immunity relies on the consecutive binding and degradation of negatively supercoiled invader dna by cascade and cas3.	the prokaryotic crispr/cas immune system is based on genomic loci that contain incorporated sequence tags from viruses and plasmids. using small guide rna molecules, these sequences act as a memory to reject returning invaders. both the cascade ribonucleoprotein complex and the cas3 nuclease/helicase are required for crispr interference in escherichia coli, but it is unknown how natural target dna molecules are recognized and neutralized by their combined action. here we show that cascade effici ...	2012	22521689
mechanism of foreign dna selection in a bacterial adaptive immune system.	in bacterial and archaeal crispr immune pathways, dna sequences from invading bacteriophage or plasmids are integrated into crispr loci within the host genome, conferring immunity against subsequent infections. the ribonucleoprotein complex cascade utilizes rnas generated from these loci to target complementary "nonself" dna sequences for destruction, while avoiding binding to "self" sequences within the crispr locus. here we show that casa, the largest protein subunit of cascade, is required fo ...	2012	22521690
ribosome engineering to promote new crystal forms.	crystallographic studies of the ribosome have provided molecular details of protein synthesis. however, the crystallization of functional complexes of ribosomes with gtpase translation factors proved to be elusive for a decade after the first ribosome structures were determined. analysis of the packing in different 70s ribosome crystal forms revealed that regardless of the species or space group, a contact between ribosomal protein l9 from the large subunit and 16s rrna in the shoulder of a neig ...	2012	22525755
mechanistic stoichiometry of proton translocation by cytochrome cbb3.	cytochrome cbb(3) belongs to the superfamily of respiratory heme-copper oxidases that couple the reduction of molecular oxygen to proton translocation across the bacterial or mitochondrial membrane. the cbb(3)-type enzymes are found only in bacteria, and are both structurally and functionally the most distant from their mitochondrial counterparts. the mechanistic h(+)/e(-) stoichiometry of proton translocation in these cbb(3)-type cytochrome c oxidases has remained controversial. a stoichiometri ...	2012	22529361
hd-rnas: an automated hierarchical database of rna structures.	one of the important goals of most biological investigations is to classify and organize the experimental findings so that they are readily useful for deriving generalized rules. although there is a huge amount of information on rna structures in pdb, there are redundant files, ambiguous synthetic sequences etc. moreover, a systematic hierarchical organization, reflecting rna classification, is missing in pdb. in this investigation, we have classified all the available rna structures from pdb th ...	2012	22529851
biological applications of hybrid quantum mechanics/molecular mechanics calculation.	since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. accordingly, qm calculations that are jointed with mm calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. a unix-shell-based interface program connecting the quantum mechanics ...	2012	22536015
identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.	the identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. here we describe a knowledge-based method exploiting the observation that unrelated binding sites share small structural motifs that bind the same chemical fragments irrespective of the nature of the ligand as a whole.	2012	22536963
structure and folding of a rare, natural kink turn in rna with an aa pair at the 2b2n position.	the kink turn (k-turn) is a frequently occurring motif, comprising a bulge followed by g•a and a•g pairs that introduces a sharp axial bend in duplex rna. natural k-turn sequences exhibit significant departures from the consensus, including the a•g pairs that form critical interactions stabilizing the core of the structure. kt-23 found in the small ribosomal subunit differs from the consensus in many organisms, particularly in the second a•g pair distal to the bulge (2b•2n). analysis of many kt- ...	2012	22539525
mycobacterium thermoresistibile as a source of thermostable orthologs of mycobacterium tuberculosis proteins.	the genus mycobacterium comprises major human pathogens such as the causative agent of tuberculosis, mycobacterium tuberculosis (mtb), and many environmental species. tuberculosis claims ~1.5 million lives every year, and drug resistant strains of mtb are rapidly emerging. to aid the development of new tuberculosis drugs, major efforts are currently under way to determine crystal structures of mtb drug targets and proteins involved in pathogenicity. however, a major obstacle to obtaining crystal ...	2012	22544630
crystal structure of dnak protein complexed with nucleotide exchange factor grpe in dnak chaperone system: insight into intermolecular communication.	the conserved, atp-dependent bacterial dnak chaperones process client substrates with the aid of the co-chaperones dnaj and grpe. however, in the absence of structural information, how these proteins communicate with each other cannot be fully delineated. for the study reported here, we solved the crystal structure of a full-length geobacillus kaustophilus hta426 grpe homodimer in complex with a nearly full-length g. kaustophilus hta426 dnak that contains the interdomain linker (acting as a pseu ...	2012	22544739
characterization of multi-functional properties and conformational analysis of muts2 from thermotoga maritima msb8.	the muts2 homologues have received attention because of their unusual activities that differ from those of muts. in this work, we report on the functional characteristics and conformational diversities of thermotoga maritima muts2 (tmmuts2). various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (spm), atpase assays, analytical ultracentrifugation, dna binding assays, size chromatography, and limited proteolytic analysis. dimeric tm ...	2012	22545085
bacterial toxin-antitoxin systems: translation inhibitors everywhere.	toxin-antitoxin (ta) systems are composed of two elements: a toxic protein and an antitoxin which is either an rna (type i and iii) or a protein (type ii). type ii systems are abundant in bacterial genomes in which they move via horizontal gene transfer. they are generally composed of two genes organized in an operon, encoding a toxin and a labile antitoxin. when carried by mobile genetic elements, these small modules contribute to their stability by a phenomenon denoted as addiction. recently, ...	2011	22545240
the structure and function of the eukaryotic ribosome.	structures of the bacterial ribosome have provided a framework for understanding universal mechanisms of protein synthesis. however, the eukaryotic ribosome is much larger than it is in bacteria, and its activity is fundamentally different in many key ways. recent cryo-electron microscopy reconstructions and x-ray crystal structures of eukaryotic ribosomes and ribosomal subunits now provide an unprecedented opportunity to explore mechanisms of eukaryotic translation and its regulation in atomic ...	2012	22550233
when ribonucleases come into play in pathogens: a survey of gram-positive bacteria.	it is widely acknowledged that rna stability plays critical roles in bacterial adaptation and survival in different environments like those encountered when bacteria infect a host. bacterial ribonucleases acting alone or in concert with regulatory rnas or rna binding proteins are the mediators of the regulatory outcome on rna stability. we will give a current update of what is known about ribonucleases in the model gram-positive organism bacillus subtilis and will describe their established role ...	2012	22550495
structure, function, and assembly of heme centers in mitochondrial respiratory complexes.	the sequential flow of electrons in the respiratory chain, from a low reduction potential substrate to o(2), is mediated by protein-bound redox cofactors. in mitochondria, hemes-together with flavin, iron-sulfur, and copper cofactors-mediate this multi-electron transfer. hemes, in three different forms, are used as a protein-bound prosthetic group in succinate dehydrogenase (complex ii), in bc(1) complex (complex iii) and in cytochrome c oxidase (complex iv). the exact function of heme b in comp ...	2012	22554985
stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability.	understanding the determinants of protein stability remains one of protein science's greatest challenges. there are still no computational solutions that calculate the stability effects of even point mutations with sufficient reliability for practical use. amino acid substitutions rarely increase the stability of native proteins; hence, large libraries and high-throughput screens or selections are needed to stabilize proteins using directed evolution. consensus mutations have proven effective fo ...	2012	22555051
cellular function and molecular structure of ecto-nucleotidases.	ecto-nucleotidases play a pivotal role in purinergic signal transmission. they hydrolyze extracellular nucleotides and thus can control their availability at purinergic p2 receptors. they generate extracellular nucleosides for cellular reuptake and salvage via nucleoside transporters of the plasma membrane. the extracellular adenosine formed acts as an agonist of purinergic p1 receptors. they also can produce and hydrolyze extracellular inorganic pyrophosphate that is of major relevance in the c ...	2012	22555564
comparing the similarity of different groups of bacteria to the human proteome.	numerous aspects of the relationship between bacteria and human have been investigated. one aspect that has recently received attention is sequence overlap at the proteomic level. however, there has not yet been a study that comprehensively characterizes the level of sequence overlap between bacteria and human, especially as it relates to bacterial characteristics like pathogenicity, g-c content, and proteome size. in this study, we began by performing a general characterization of the range of ...	2012	22558081
metallation state of human manganese superoxide dismutase expressed in saccharomyces cerevisiae.	human manganese superoxide dismutase (sod2p) has been expressed in yeast and the protein purified from isolated yeast mitochondria, yielding both the metallated protein and the less stable apoprotein in a single chromatographic step. at 30 °c growth temperature, more than half of the purified enzyme is apoprotein that can be fully activated following reconstitution, while the remainder contains a mixture of manganese and iron. in contrast, only fully metallated enzyme was isolated from a similar ...	2012	22561997
ispe inhibitors identified by a combination of in silico and in vitro high-throughput screening.	cdp-me kinase (ispe) contributes to the non-mevalonate or deoxy-xylulose phosphate (doxp) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. ispe has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substr ...	2012	22563402
structure based hypothesis of a mitochondrial ribosome rescue mechanism.	mtrf1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtrf1a. to elucidate the function of mtrf1, we determined the positions that are conserved among mtrf1 sequences but that are different in their mtrf1a paralogs. we subsequently modeled the 3d structure of mtrf1a and mtrf1 bound to the ribosome, highlighting the structural implications of these differences to derive a hypothesis for the function of mtrf1.	2012	22569235
active site opening and closure control translocation of multisubunit rna polymerase.	multisubunit rna polymerase (rnap) is the central information-processing enzyme in all cellular life forms, yet its mechanism of translocation along the dna molecule remains conjectural. here, we report direct monitoring of bacterial rnap translocation following the addition of a single nucleotide. time-resolved measurements demonstrated that translocation is delayed relative to nucleotide incorporation and occurs shortly after or concurrently with pyrophosphate release. an investigation of tran ...	2012	22570421
mycobacterium tuberculosis rbpa protein is a new type of transcriptional activator that stabilizes the σ a-containing rna polymerase holoenzyme.	rbpa is an rna polymerase (rnap)-binding protein whose presence increases the tolerance levels of mycobacteria to the first-line anti-tuberculosis drug rifampicin by an unknown mechanism. here, we show that the role of mycobacterium tuberculosis rbpa in resistance is indirect because it does not affect the sensitivity of rnap to rifampicin while it stimulates transcription controlled by the housekeeping σ(a)-factor. the transcription regulated by the stress-related σ(f) was not affected by rbpa. ...	2012	22570422
one ring to rule them all: trafficking of heme and heme synthesis intermediates in the metazoans.	the appearance of heme, an organic ring surrounding an iron atom, in evolution forever changed the efficiency with which organisms were able to generate energy, utilize gasses and catalyze numerous reactions. because of this, heme has become a near ubiquitous compound among living organisms. in this review we have attempted to assess the current state of heme synthesis and trafficking with a goal of identifying crucial missing information, and propose hypotheses related to trafficking that may g ...	2012	22575458
staphylococcus aureus fabi: inhibition, substrate recognition, and potential implications for in vivo essentiality.	methicillin-resistant staphylococcus aureus (mrsa) infections constitute a serious health threat worldwide, and novel antibiotics are therefore urgently needed. the enoyl-acp reductase (safabi) is essential for the s. aureus fatty acid biosynthesis and, hence, serves as an attractive drug target. we have obtained a series of snapshots of this enzyme that provide a mechanistic picture of ligand and inhibitor binding, including a dimer-tetramer transition combined with extensive conformational cha ...	2012	22579249
codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids.	synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. we find a bias pattern linked to the degeneracy of the encode ...	2012	22581775
reconstitution of vacuolar-type rotary h+-atpase/synthase from thermus thermophilus.	vacuolar-type rotary h(+)-atpase/synthase (v(o)v(1)) from thermus thermophilus, composed of nine subunits, a, b, d, f, c, e, g, i, and l, has been reconstituted from individually isolated v(1) (a(3)b(3)d(1)f(1)) and v(o) (c(1)e(2)g(2)i(1)l(12)) subcomplexes in vitro. a(3)b(3)d and a(3)b(3) also reconstituted with v(o), resulting in a holoenzyme-like complexes. however, a(3)b(3)d-v(o) and a(3)b(3)-v(o) did not show atp synthesis and dicyclohexylcarbodiimide-sensitive atpase activity. the reconsti ...	2012	22582389
corallopyronin a specifically targets and depletes essential obligate wolbachia endobacteria from filarial nematodes in vivo.	doxycycline and rifampicin deplete essential wolbachia from filarial nematodes that cause lymphatic filariasis or onchocerciasis, resulting in blocked worm development and death. however, doxycycline is contraindicated for children and pregnant/breastfeeding women, as is rifampicin in the latter group with the additional specter of possible resistance development in mycobacterium spp. novel antibiotics with a narrower spectrum would aid in eliminating filarial diseases. corallococcus coralloides ...	2012	22586066
structure, function and inhibition of the two- and three-domain 4fe-4s ispg proteins.	ispg is a 4fe4s protein involved in isoprenoid biosynthesis. most bacterial ispgs contain two domains: a tim barrel (a) and a 4fe4s domain (b), but in plants and malaria parasites, there is a large insert domain (a*) whose structure and function are unknown. we show that bacterial ispgs function in solution as (ab)(2) dimers and that mutations in either both a or both b domains block activity. chimeras harboring an a-mutation in one chain and a b-mutation in the other have 50% of the activity se ...	2012	22586085
structural insights into the substrate specificity of streptococcus pneumoniae β(1,3)-galactosidase bgac.	the surface-exposed β-galactosidase bgac from streptococcus pneumoniae was reported to be a virulence factor because of its specific hydrolysis activity toward the β(1,3)-linked galactose and n-acetylglucosamine (galβ(1,3)nag) moiety of oligosaccharides on the host molecules. here we report the crystal structure of bgac at 1.8 å and its complex with galactose at 1.95 å. at ph 5.5-8.0, bgac exists as a stable homodimer, each subunit of which consists of three distinct domains: a catalytic domain ...	2012	22593580
structure and conservation of the periplasmic targeting factor tic22 protein from plants and cyanobacteria.	mitochondria and chloroplasts are of endosymbiotic origin. their integration into cells entailed the development of protein translocons, partially by recycling bacterial proteins. we demonstrate the evolutionary conservation of the translocon component tic22 between cyanobacteria and chloroplasts. tic22 in anabaena sp. pcc 7120 is essential. the protein is localized in the thylakoids and in the periplasm and can be functionally replaced by a plant orthologue. tic22 physically interacts with the ...	2012	22593581
role of apoptosis-inducing factor, proline dehydrogenase, and nadph oxidase in apoptosis and oxidative stress.	flavoproteins catalyze a variety of reactions utilizing flavin mononucleotide or flavin adenine dinucleotide as cofactors. the oxidoreductase properties of flavoenzymes implicate them in redox homeostasis, oxidative stress, and various cellular processes, including programmed cell death. here we explore three critical flavoproteins involved in apoptosis and redox signaling, ie, apoptosis-inducing factor (aif), proline dehydrogenase, and nadph oxidase. these proteins have diverse biochemical func ...	2012	22593641
absence of helicobacter pylori high tetracycline resistant 16s rdna aga926-928ttc genotype in gastric biopsy specimens from dyspeptic patients of a city in the interior of são paulo, brazil.	treatment effectiveness of helicobacter pylori varies regionally and is decreasing worldwide, principally as a result of antibiotic resistant bacterium. tetracycline is generally included in second line h. pylori eradication regimens. in brazil, a high level of tetracycline resistance (tetr) is mainly associated with aga926-928ttc 16 s rdna nucleotide substitutions. as h. pylori culture is fastidious, we investigated the primary occurrence of h. pylori 16 s rdna high level tetr genotype using a ...	2012	22594560
distinct functions of regions 1.1 and 1.2 of rna polymerase σ subunits from escherichia coli and thermus aquaticus in transcription initiation.	rna polymerase (rnap) from thermophilic thermus aquaticus is characterized by higher temperature of promoter opening, lower promoter complex stability, and higher promoter escape efficiency than rnap from mesophilic escherichia coli. we demonstrate that these differences are in part explained by differences in the structures of the n-terminal regions 1.1 and 1.2 of the e. coli σ(70) and t. aquaticus σ(a) subunits. in particular, region 1.1 and, to a lesser extent, region 1.2 of the e. coli σ(70) ...	2012	22605342
how hibernation factors rmf, hpf, and yfia turn off protein synthesis.	eubacteria inactivate their ribosomes as 100s dimers or 70s monomers upon entry into stationary phase. in escherichia coli, 100s dimer formation is mediated by ribosome modulation factor (rmf) and hibernation promoting factor (hpf), or alternatively, the yfia protein inactivates ribosomes as 70s monomers. here, we present high-resolution crystal structures of the thermus thermophilus 70s ribosome in complex with each of these stationary-phase factors. the binding site of rmf overlaps with that o ...	2012	22605777
mobility of xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase.	we use a form of "freeze-trap, kinetic crystallography" to explore the migration of xe atoms away from the dinuclear heme a(3)/cu(b) center in thermus thermophilus cytochrome ba(3) oxidase. this enzyme is a member of the heme-copper oxidase superfamily and is thus crucial for dioxygen-dependent life. the mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. pressuriz ...	2012	22607023
proline oxidase promotes tumor cell survival in hypoxic tumor microenvironments.	proline is a readily released stress substrate that can be metabolized by proline oxidase (pox) to generate either reactive oxygen species (ros) to induce apoptosis or autophagy or atp during times of nutrient stress. however, the contribution of proline metabolism to tumorigenesis in hypoxic microenvironments has not been explored. in this study, we investigated the different functions of pox under hypoxia and glucose depletion. we found that hypoxia induced pox expression in cancer cells in vi ...	2012	22609800
phylogenomics of prokaryotic ribosomal proteins.	archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. we developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 arch ...	2012	22615861
a study on l-asparaginase of nocardia levis mk-vl_113.	an enzyme-based drug, l-asparaginase, was produced by nocardia levis mk-vl_113 isolated from laterite soils of guntur region. cultural parameters affecting the production of l-asparaginase by the strain were optimized. maximal yields of l-asparaginase were recorded from 3-day-old culture grown in modified asparagine-glycerol salts broth with initial ph 7.0 at temperature 30°c. glycerol (2%) and yeast extract (1.5%) served as good carbon and nitrogen sources for l-asparaginase production, respect ...	2012	22619604
crystal structure of the largest subunit of a bacterial rna-guided immune complex and its role in dna target binding.	prokaryotes make use of small rnas encoded by crispr (clustered regularly interspaced short palindromic repeat) loci to provide immunity against bacteriophage or plasmid invasion. in escherichia coli, the crispr-associated complex for antiviral defense (cascade) utilizes these rnas to target foreign dna for destruction. casa, the largest subunit of cascade, is essential for its function. here we report the crystal structure of thermus thermophilus casa. the structure is composed of two domains t ...	2012	22621933
engineering rotor ring stoichiometries in the atp synthase.	atp synthase membrane rotors consist of a ring of c-subunits whose stoichiometry is constant for a given species but variable across different ones. we investigated the importance of c/c-subunit contacts by site-directed mutagenesis of a conserved stretch of glycines (gxgxgxgxg) in a bacterial c(11) ring. structural and biochemical studies show a direct, specific influence on the c-subunit stoichiometry, revealing c(<11), c(12), c(13), c(14), and c(>14) rings. molecular dynamics simulations rati ...	2012	22628564
real-time evidence for ef-g-induced dynamics of helix 44 in 16s rrna.	the penultimate stem-loop of 16s ribosomal rna (rrna), helix 44, plays a central role in ribosome function. using time-resolved dimethyl sulfate (dms) probing, we have analyzed time-dependent modifications that occur at specific bases in this helix near the decoding region, resulting from the binding of elongation factor g (ef-g) in various forms. when ef-g-gtp is bound to 70s ribosomes, bases a1492 and a1493 are immediately protected, while other bases in the region show either no change or enh ...	2012	22634282
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
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
flexibility of the metal-binding region in apo-cupredoxins.	protein-mediated electron transfer is an essential event in many biochemical processes. efficient electron transfer requires the reorganization energy of the redox event to be minimized, which is ensured by the presence of rigid donor and acceptor sites. electron transfer copper sites are present in the ubiquitous cupredoxin fold, able to bind one or two copper ions. the low reorganization energy in these metal centers has been accounted for by assuming that the protein scaffold creates an entat ...	2012	22645370
structure and function of fusb: an elongation factor g-binding fusidic acid resistance protein active in ribosomal translocation and recycling.	fusidic acid (fa) is a bacteriostatic antibiotic that locks elongation factor g (ef-g) to the ribosome after gtp hydrolysis during elongation and ribosome recycling. the plasmid pub101-encoded protein fusb causes fa resistance in clinical isolates of staphylococcus aureus through an interaction with ef-g. here, we report 1.6 and 2.3 å crystal structures of fusb. we show that fusb is a two-domain protein lacking homology to known structures, where the n-terminal domain is a four-helix bundle and ...	2012	22645663
evolution of lysine biosynthesis in the phylum deinococcus-thermus.	thermus thermophilus biosynthesizes lysine through the α-aminoadipate (aaa) pathway: this observation was the first discovery of lysine biosynthesis through the aaa pathway in archaea and bacteria. genes homologous to the t. thermophilus lysine biosynthetic genes are widely distributed in bacteria of the deinococcus-thermus phylum. our phylogenetic analyses strongly suggest that a common ancestor of the deinococcus-thermus phylum had the ancestral genes for bacterial lysine biosynthesis through ...	2012	22645699
lessons from high-throughput protein crystallization screening: 10 years of practical experience.	x-ray crystallography provides the majority of our structural biological knowledge at a molecular level and, in terms of pharmaceutical design, is a valuable tool to accelerate discovery. it is the premier technique in the field, but its usefulness is significantly limited by the need to grow well-diffracting crystals. it is for this reason that high-throughput crystallization has become a key technology that has matured over the past 10 years through the field of structural genomics. areas cove ...	2011	22646073
an iron-sulfur cluster loop motif in the archaeoglobus fulgidus uracil-dna glycosylase mediates efficient uracil recognition and removal.	the family 4 uracil-dna glycosylase from the hyperthermophilic organism archaeoglobus fulgidus (afudg) is responsible for the removal of uracil in dna as the first step in the base excision repair (ber) pathway. afudg contains a large solvent-exposed peptide region containing an α helix and loop anchored on each end via ligation of two cysteine thiolates to a [4fe-4s](2+) cluster. we propose that this region plays a similar role in dna damage recognition as a smaller iron-sulfur cluster loop (fc ...	2012	22646210
steric restrictions of risc in rna interference identified with size-expanded rna nucleobases.	understanding the interactions between small interfering rnas (sirnas) and the rna-induced silencing complex (risc), the key protein complex of rna interference (rnai), is of great importance to the development of sirnas with improved biological and potentially therapeutic function. although various chemically modified sirnas have been reported, relatively few studies with modified nucleobases exist. here we describe the synthesis and hybridization properties of sirnas bearing size-expanded rna ...	2012	22646660
a thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels.	generation of biofuels from sugars in lignocellulosic biomass is a promising alternative to liquid fossil fuels, but efficient and inexpensive bioprocessing configurations must be developed to make this technology commercially viable. one of the major barriers to commercialization is the recalcitrance of plant cell wall polysaccharides to enzymatic hydrolysis. biomass pretreatment with ionic liquids (ils) enables efficient saccharification of biomass, but residual ils inhibit both saccharificati ...	2012	22649505
a predictive model of intein insertion site for use in the engineering of molecular switches.	inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. by analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant ...	2012	22649521
glycines: role in α-helical membrane protein structures and a potential indicator of native conformation.	among the growing number of membrane protein structures in the protein data bank, there are many transmembrane domains that appear to be native-like; at the same time, there are others that appear to have less than complete native-like character. hence, there is an increasing need for validation tools that distinguish native-like from non-native-like structures. membrane mimetics used in protein structural characterizations differ in numerous physicochemical properties from native membranes and ...	2012	22650985
a computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.	assembly of the ribosome from its protein and rna constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. however, to date, no studies have attempted to elucidate these conformational changes. the present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of t ...	2012	22654657
rational design and directed evolution of a bacterial-type glutaminyl-trna synthetase precursor.	protein biosynthesis requires aminoacyl-transfer rna (trna) synthetases to provide aminoacyl-trna substrates for the ribosome. most bacteria and all archaea lack a glutaminyl-trna synthetase (glnrs); instead, gln-trna(gln) is produced via an indirect pathway: a glutamyl-trna synthetase (glurs) first attaches glutamate (glu) to trna(gln), and an amidotransferase converts glu-trna(gln) to gln-trna(gln). the human pathogen helicobacter pylori encodes two glurs enzymes, with glurs2 specifically amin ...	2012	22661575
stable isotope peptide mass spectrometry to decipher amino acid metabolism in dehalococcoides strain cbdb1.	dehalococcoides species are key players in the anaerobic transformation of halogenated solvents at contaminated sites. here, we analyze isotopologue distributions in amino acid pools from peptides of dehalococcoides strain cbdb1 after incubation with (13)c-labeled acetate or bicarbonate as a carbon source. the resulting data were interpreted with regard to genome annotations to identify amino acid biosynthesis pathways. in addition to using gas chromatography-mass spectrometry (gc-ms) for analyz ...	2012	22661690
the c-terminal domain of 4-hydroxyphenylacetate 3-hydroxylase from acinetobacter baumannii is an autoinhibitory domain.	p-hydroxyphenylacetate (hpa) 3-hydroxylase from acinetobacter baumannii consists of a reductase component (c(1)) and an oxygenase component (c(2)). c(1) catalyzes the reduction of fmn by nadh to provide fmnh(-) as a substrate for c(2). the rate of reduction of flavin is enhanced ∼20-fold by binding hpa. the n-terminal domain of c(1) is homologous to other flavin reductases, whereas the c-terminal domain (residues 192-315) is similar to marr, a repressor protein involved in bacterial antibiotic r ...	2012	22661720
phage-induced expression of crispr-associated proteins is revealed by shotgun proteomics in streptococcus thermophilus.	the crispr/cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. while the mechanism of action for this acquired immunity is currently under investigation, the response of cas protein expression to phage infection has yet to be elucidated. in this study, we employed shotgun proteomics to measure the global proteome expression in a model system fo ...	2012	22666452
suppression of premature termination codons as a therapeutic approach.	in this review, we describe our current understanding of translation termination and pharmacological agents that influence the accuracy of this process. a number of drugs have been identified that induce suppression of translation termination at in-frame premature termination codons (ptcs; also known as nonsense mutations) in mammalian cells. we discuss efforts to utilize these drugs to suppress disease-causing ptcs that result in the loss of protein expression and function. in-frame ptcs repres ...	2012	22672057
structural mechanism of atp-induced polymerization of the partition factor parf: implications for dna segregation.	segregation of the bacterial multidrug resistance plasmid tp228 requires the centromere-binding protein parg, the parh centromere, and the walker box atpase parf. the cycling of parf between adp- and atp-bound states drives tp228 partition; atp binding stimulates parf polymerization, which is essential for segregation, whereas adp binding antagonizes polymerization and inhibits dna partition. the molecular mechanism involved in this adenine nucleotide switch is unclear. moreover, it is unknown h ...	2012	22674577
characterization of a conserved interaction between dna glycosylase and para in mycobacterium smegmatis and m. tuberculosis.	the chromosome partitioning proteins, parab, ensure accurate segregation of genetic materials into daughter cells and most bacterial species contain their homologs. however, little is known about the regulation of parab proteins. in this study, we found that 3-methyladenine dna glycosylase i mstag(ms5082) regulates bacterial growth and cell morphology by directly interacting with mspara (ms6939) and inhibiting its atpase activity in mycobacterium smegmatis. using bacterial two-hybrid and pull-do ...	2012	22675536
thermostable dna polymerase from a viral metagenome is a potent rt-pcr enzyme.	viral metagenomic libraries are a promising but previously untapped source of new reagent enzymes. deep sequencing and functional screening of viral metagenomic dna from a near-boiling thermal pool identified clones expressing thermostable dna polymerase (pol) activity. among these, 3173 pol demonstrated both high thermostability and innate reverse transcriptase (rt) activity. we describe the biochemistry of 3173 pol and report its use in single-enzyme reverse transcription pcr (rt-pcr). wild-ty ...	2012	22675552
complete genome sequence of the aerobic, heterotroph marinithermus hydrothermalis type strain (t1(t)) from a deep-sea hydrothermal vent chimney.	marinithermus hydrothermalis sako et al. 2003 is the type species of the monotypic genus marinithermus. m. hydrothermalis t1(t) was the first isolate within the phylum "thermus-deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for nacl for growth. m. hydrothermalis t1(t) is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organi ...	2012	22675595
comparative analysis of two phenotypically-similar but genomically-distinct burkholderia cenocepacia-specific bacteriophages.	genomic analysis of bacteriophages infecting the burkholderia cepacia complex (bcc) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. the objective of this study was to characterize kl1 (vb_bces_kl1) and ah2 (vb_bces_ah2), two novel burkholderia cenocepacia-specific siphoviruses isolated from environmental samples.	2012	22676492
molecular dynamics and mutational analysis of the catalytic and translocation cycle of rna polymerase.		2012	22676913
the structure of human argonaute-2 in complex with mir-20a.	argonaute proteins lie at the heart of the rna-induced silencing complex (risc), wherein they use small rna guides to recognize targets. initial insight into the architecture of argonautes came from studies of prokaryotic proteins, revealing a crescent-shaped base made up of the amino-terminal, paz, middle, and piwi domains. the recently reported crystal structure of human argonaute-2 (hago2), the "slicer" in rna interference, in complex with a mixed population of rnas derived from insect cells ...	2012	22682761
structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-trna synthetase.	leucyl-trna synthetase (leurs) produces error-free leucyl-trna(leu) by coordinating translocation of the 3' end of (mis-)charged trnas from its synthetic site to a separate proofreading site for editing. here we report cocrystal structures of the escherichia coli leurs-trna(leu) complex in the aminoacylation or editing conformations, showing that translocation involves correlated rotations of four flexibly linked leurs domains. this pivots the trna to guide its charged 3' end from the closed ami ...	2012	22683997
crystallization and preliminary x-ray analysis of the reductase component of p-hydroxyphenylacetate 3-hydroxylase from acinetobacter baumannii.	p-hydroxyphenylacetate 3-hydroxylase (hpah) from acinetobacter baumannii catalyzes the hydroxylation of p-hydroxyphenylacetate (hpa) at the ortho position to yield 3,4-dihydroxyphenylacetate (dhpa). hpah from a. baumannii is a two-component flavoprotein consisting of a smaller reductase (c(1)) component and a larger oxygenase (c(2)) component. the c(1) component supplies a reduced flavin in its free form to the c(2) counterpart for hydroxylation. in addition, hpa can bind to c(1) and enhance the ...	2012	22684080
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
diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.	the yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. sensitivity and selectivity have improved because of various technical tricks and experimental designs. here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment comp ...	2012	22688816
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
draft genome sequence of thermus sp. strain rl, isolated from a hot water spring located atop the himalayan ranges at manikaran, india.	thermus sp. strain rl was isolated from a hot water spring (90°c to 98°c) at manikaran, himachal pradesh, india. here we report the draft genome sequence (20,36,600 bp) of this strain. the draft genome sequence consists of 17 contigs and 1,986 protein-coding sequences and has an average g+c content of 68.77%.	2012	22689228
preliminary crystallographic analysis of two hypothetical ribose-5-phosphate isomerases from streptococcus mutans.	study of the enzymes from sugar metabolic pathways may provide a better understanding of the pathogenesis of the human oral pathogen streptococcus mutans. bioinformatics, biochemical and crystallization methods were used to characterize and understand the function of two putative ribose-5-phosphate isomerases: smu1234 and smu2142. the proteins were cloned and constructed with n-terminal his tags. protein purification was performed by ni(2+)-chelating and size-exclusion chromatography. the crysta ...	2012	22691789
crystallization and preliminary crystallographic analysis of the major capsid proteins vp16 and vp17 of bacteriophage p23-77.	members of the diverse double-β-barrel lineage of viruses are identified by the conserved structure of their major coat protein. new members of this lineage have been discovered based on structural analysis and we are interested in identifying relatives that utilize unusual versions of the double-β-barrel fold. one candidate for such studies is p23-77, an icosahedral dsdna bacteriophage that infects the extremophile thermus thermophilus. p23-77 has two major coat proteins, namely vp16 and vp17, ...	2012	22691792
a comparison of the crystal structures of eukaryotic and bacterial ssu ribosomal rnas reveals common structural features in the hypervariable regions.	while the majority of the ribosomal rna structure is conserved in the three major domains of life--archaea, bacteria, and eukaryotes, specific regions of the rrna structure are unique to at least one of these three primary forms of life. in particular, the comparative secondary structure for the eukaryotic ssu rrna contains several regions that are different from the analogous regions in the bacteria. our detailed analysis of two recently determined eukaryotic 40s ribosomal crystal structures, t ...	2012	22693601
ancient origin of the divergent forms of leucyl-trna synthetases in the halobacteriales.	horizontal gene transfer (hgt) has greatly impacted the genealogical history of many lineages, particularly for prokaryotes, with genes frequently moving in and out of a line of descent. many genes that were acquired by a lineage in the past likely originated from ancestral relatives that have since gone extinct. during the course of evolution, hgt has played an essential role in the origin and dissemination of genetic and metabolic novelty.	2012	22694720
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
thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics.	thermodynamic stability, configurational motions and internal forces of haemoglobin (hb) of three endotherms (platypus, ornithorhynchus anatinus; domestic chicken, gallus gallus domesticus and human, homo sapiens) and an ectotherm (salt water crocodile, crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained brownian dynamics simulations. the experimental results from hb solutions revealed a direct correlation between protein resil ...	2012	22696485
dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin.	aminoglycosides are potent antibacterials, but therapy is compromised by substantial toxicity causing, in particular, irreversible hearing loss. aminoglycoside ototoxicity occurs both in a sporadic dose-dependent and in a genetically predisposed fashion. we recently have developed a mechanistic concept that postulates a key role for the mitochondrial ribosome (mitoribosome) in aminoglycoside ototoxicity. we now report on the surprising finding that apramycin, a structurally unique aminoglycoside ...	2012	22699498
identification and characterization of the thermus thermophilus 5-methylcytidine (m5c) methyltransferase modifying 23 s ribosomal rna (rrna) base c1942.	methylation of cytidines at carbon-5 is a common posttranscriptional rna modification encountered across all domains of life. here, we characterize the modifications of c1942 and c1962 in thermus thermophilus 23 s rrna as 5-methylcytidines (m(5)c) and identify the two associated methyltransferases. the methyltransferase modifying c1942, named rlmo, has not been characterized previously. rlmo modifies naked 23 s rrna, but not the assembled 50 s subunit or 70 s ribosomes. the x-ray crystal structu ...	2012	22711535
reverse structural genomics: an unusual flavin-binding site in a putative protease from bacteroides thetaiotaomicron.	the structure of a putative protease from bacteroides thetaiotaomicron features an unprecedented binding site for flavin mononucleotide. the flavin isoalloxazine ring is sandwiched between two tryptophan residues in the interface of the dimeric protein. we characterized the recombinant protein with regard to its affinity for naturally occurring flavin derivatives and several chemically modified flavin analogs. dissociation constants were determined by isothermal titration calorimetry. the protei ...	2012	22718753
polymorphisms in the mitochondrial ribosome recycling factor ef-g2mt/mef2 compromise cell respiratory function and increase atorvastatin toxicity.	mitochondrial translation, essential for synthesis of the electron transport chain complexes in the mitochondria, is governed by nuclear encoded genes. polymorphisms within these genes are increasingly being implicated in disease and may also trigger adverse drug reactions. statins, a class of hmg-coa reductase inhibitors used to treat hypercholesterolemia, are among the most widely prescribed drugs in the world. however, a significant proportion of users suffer side effects of varying severity ...	2012	22719265
glutamine versus ammonia utilization in the nad synthetase family.	nad is a ubiquitous and essential metabolic redox cofactor which also functions as a substrate in certain regulatory pathways. the last step of nad synthesis is the atp-dependent amidation of deamido-nad by nad synthetase (nads). members of the nads family are present in nearly all species across the three kingdoms of life. in eukaryotic nads, the core synthetase domain is fused with a nitrilase-like glutaminase domain supplying ammonia for the reaction. this two-domain nads arrangement enabling ...	2012	22720044
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
structure of yeast argonaute with guide rna.	the rna-induced silencing complex, comprising argonaute and guide rna, mediates rna interference. here we report the 3.2 å crystal structure of kluyveromyces polysporus argonaute (kpago) fortuitously complexed with guide rna originating from small-rna duplexes autonomously loaded by recombinant kpago. despite their diverse sequences, guide-rna nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nu ...	2012	22722195
reconstitution of translation from thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components.	thermus thermophilus is a thermophilic model organism distantly related to the mesophilic model organism e. coli. we reconstituted protein translation of thermus thermophilus in vitro from purified ribosomes, transfer ribonucleic acids (trnas) and 33 recombinant proteins. this reconstituted system was fully functional, capable of translating natural messenger rna (mrna) into active full-length proteins at temperatures up to 65°c and with yields up to 60 μg/ml. surprisingly, the synthesis of acti ...	2012	22723376
structural constraints identified with covariation analysis in ribosomal rna.	covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of rna sequences. these constraints on the evolution of two positions are usually associated with a base pair in a helix. while mutual information (mi) has been used to accurately predict an rna secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the predictio ...	2012	22724009
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
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
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
simulation of the opening and closing of hsp70 chaperones by coarse-grained molecular dynamics.	heat-shock proteins 70 (hsp70s) are key molecular chaperones which assist in the folding and refolding/disaggregation of proteins. hsp70s, which consist of a nucleotide-binding domain (nbd, consisting of nbd-i and nbd-ii subdomains) and a substrate-binding domain [sbd, further split into the β-sheet (sbd-β) and α-helical (sbd-α) subdomains], occur in two major conformations having (a) a closed sbd, in which the sbd and nbd domains do not interact, (b) an open sbd, in which sbd-α interacts with n ...	2012	22737044
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
structural determinants of the β-selectivity of a bacterial aminotransferase.	chiral β-amino acids occur as constituents of various natural and synthetic compounds with potentially useful bioactivities. the pyridoxal 5'-phosphate (plp)-dependent s-selective transaminase from mesorhizobium sp. strain luk (mesat) is a fold type i aminotransferase that can be used for the preparation of enantiopure β-phe and derivatives thereof. using x-ray crystallography, we solved structures of mesat in complex with (s)-β-phe, (r)-3-amino-5-methylhexanoic acid, 2-oxoglutarate, and the inh ...	2012	22745123
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
the fpg/nei family of dna glycosylases: substrates, structures, and search for damage.	during the initial stages of the base excision dna repair pathway, dna glycosylases are responsible for locating and removing the majority of endogenous oxidative base lesions. the bifunctional formamidopyrimidine dna glycosylase (fpg) and endonuclease viii (nei) are members of the fpg/nei family, one of the two families of glycosylases that recognize oxidized dna bases, the other being the hhh/gpd (or nth) superfamily. structural and biochemical developments over the past decades have led to no ...	2012	22749143
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
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