| structural dynamics of human argonaute2 and its interaction with sirnas designed to target mutant tdp43. | the human argonaute2 protein (ago2) is a key player in rna interference pathway and small rna recognition by ago2 is the crucial step in sirna mediated gene silencing mechanism. the present study highlights the structural and functional dynamics of human ago2 and the interaction mechanism of ago2 with a set of seven sirnas for the first time. the human ago2 protein adopts two conformations such as "open" and "close" during the simulation of 25 ns. one of the domains named as paz, which is respon ... | 2016 | 27110240 |
| genomic and transcriptomic analysis of the streptomycin-dependent mycobacterium tuberculosis strain 18b. | the ability of mycobacterium tuberculosis to establish a latent infection (ltbi) in humans confounds the treatment of tuberculosis. consequently, there is a need to discover new therapeutic agents that can kill m. tuberculosis both during active disease and ltbi. the streptomycin-dependent strain of m. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (str) it enters a non-replicating state that mimics latency both in vitro and in animal models. | 2016 | 26944551 |
| structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. | throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trgtpase). although the structural basis for trgtpase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trgtpase, initiation factor 2 (if2), complexed with the ribosome, remains elusive. we determine t ... | 2016 | 26973877 |
| structural basis for the endoribonuclease activity of the type iii-a crispr-associated protein csm6. | prokaryotic crispr-cas systems provide an rna-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. in type iii-a crispr-cas systems, the rna-guided multisubunit csm effector complex targets both single-stranded rnas and double-stranded dnas. in addition to the csm complex, efficient anti-plasmid immunity mediated by type iii-a systems also requires the crispr-associated protein csm6. here we report the crystal structure of csm6 from thermus thermophil ... | 2016 | 26763118 |
| impact of different target sequences on type iii crispr-cas immunity. | clustered regularly interspaced short palindromic repeat (crispr) loci encode an adaptive immune system of prokaryotes. within these loci, sequences intercalated between repeats known as "spacers" specify the targets of crispr immunity. the majority of spacers match sequences present in phages and plasmids; however, it is not known whether there are differences in the immunity provided against these diverse invaders. we studied this issue using the staphylococcus epidermidis crispr system, which ... | 2016 | 26755632 |
| cooperation between two periplasmic copper chaperones is required for full activity of the cbb3 -type cytochrome c oxidase and copper homeostasis in rhodobacter capsulatus. | copper (cu) is an essential micronutrient that functions as a cofactor in several important enzymes, such as respiratory heme-copper oxygen reductases. yet, cu is also toxic and therefore cells engage a highly coordinated cu uptake and delivery system to prevent the accumulation of toxic cu concentrations. in this study, we analyzed cu delivery to the cbb3 -type cytochrome c oxidase (cbb3 -cox) of rhodobacter capsulatus. we identified the pcua c-like periplasmic chaperone pcca and analyzed its c ... | 2016 | 26718481 |
| the kink turn, a key architectural element in rna structure. | kink turns (k-turns) are widespread structural elements that introduce an axial bend into duplex rna with an included angle of 50°. these mediate key tertiary interactions and bind specific proteins including members of the l7ae family. the standard k-turn comprises a three-nucleotide bulge followed by g·a and a·g pairs. the rna kinks by an association of the two minor grooves, stabilized by the formation of a number of key cross-strand hydrogen bonds mostly involving the adenine bases of the g· ... | 2016 | 26522935 |
| naturally occurring isoleucyl-trna synthetase without trna-dependent pre-transfer editing. | isoleucyl-trna synthetase (ilers) is unusual among aminoacyl-trna synthetases in having a trna-dependent pre-transfer editing activity. alongside the typical bacterial ilers (such as escherichia coli ilers), some bacteria also have the enzymes (eukaryote-like) that cluster with eukaryotic ilerss and exhibit low sensitivity to the antibiotic mupirocin. our phylogenetic analysis suggests that the iles1 and iles2 genes of contemporary bacteria are the descendants of genes that might have arisen by ... | 2016 | 26921320 |
| in-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth. | precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. we developed a system for producing high-quality protein crystals with high throughput. using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. in addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. ... | 2016 | 26916802 |
| atp binding by the p-loop ntpase osychf1 (an unconventional g protein) contributes to biotic but not abiotic stress responses. | g proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze gtp. the ychf subfamily, interestingly, possesses the unique ability to bind both atp and gtp, and is possibly an ancestral form of g proteins based on phylogenetic studies and is present in all kingdoms of life. however, the biological significance of such a relaxed ligand specificity has long eluded researchers. here, we have elucidated the different conformational chan ... | 2016 | 26912459 |
| systematic evolution and study of uagn decoding trnas in a genomically recoded bacteria. | we report the first systematic evolution and study of trna variants that are able to read a set of uagn (n = a, g, u, c) codons in a genomically recoded e. coli strain that lacks any endogenous in-frame uagn sequences and release factor 1. through randomizing bases in anticodon stem-loop followed by a functional selection, we identified trna mutants with significantly improved uagn decoding efficiency, which will augment the current efforts on genetic code expansion through quadruplet decoding. ... | 2016 | 26906548 |
| substrate recognition and cleavage-site selection by a single-subunit protein-only rnase p. | rnase p is the enzyme that removes 5' extensions from trna precursors. with its diversity of enzyme forms-either protein- or rna-based, ranging from single polypeptides to multi-subunit ribonucleoproteins-the rnase p enzyme family represents a unique model system to compare the evolution of enzymatic mechanisms. here we present a comprehensive study of substrate recognition and cleavage-site selection by the nuclear single-subunit proteinaceous rnase p prorp3 from arabidopsis thaliana. compared ... | 2016 | 26896801 |
| the trade-off of availability and growth inhibition through copper for the production of copper-dependent enzymes by pichia pastoris. | copper is an essential chemical element for life as it is a part of prosthetic groups of enzymes including super oxide dismutase and cytochrome c oxidase; however, it is also toxic at high concentrations. here, we present the trade-off of copper availability and growth inhibition of a common host used for copper-dependent protein production, pichia pastoris. | 2016 | 26897180 |
| curing the megaplasmid ptt27 from thermus thermophilus hb27 and maintaining exogenous plasmids in the plasmid-free strain. | stepwise deletions in the only plasmid in thermus thermophilus hb27, megaplasmid ptt27, showed that two distantly located loci were important for maintenance of the plasmid. one is a minimum replicon including one gene, rept, coding a replication initiator, and the other encodes subunits of class i ribonucleotide reductase (rnr) for deoxynucleoside triphosphate (dntp) synthesis. since the initiator protein, rept, bound to direct repeats downstream from its own gene, it was speculated that a more ... | 2016 | 26712540 |
| aerobic and anaerobic thiosulfate oxidation by a cold-adapted, subglacial chemoautotroph. | geochemical data indicate that protons released during pyrite (fes2) oxidation are important drivers of mineral weathering in oxic and anoxic zones of many aquatic environments, including those beneath glaciers. oxidation of fes2 under oxic, circumneutral conditions proceeds through the metastable intermediate thiosulfate (s2o3 (2-)), which represents an electron donor capable of supporting microbial metabolism. subglacial meltwaters sampled from robertson glacier (rg), canada, over a seasonal m ... | 2016 | 26712544 |
| all the o2 consumed by thermus thermophilus cytochrome ba3 is delivered to the active site through a long, open hydrophobic tunnel with entrances within the lipid bilayer. | cytochrome ba3 is a proton-pumping heme-copper oxygen reductase from the extreme thermophile thermus thermophilus. despite the fact that the enzyme's active site is buried deep within the protein, the apparent second order rate constant for the initial binding of o2 to the active-site heme has been experimentally found to be 10(9) m(-1) s(-1) at 298 k, at or near the diffusion limit, and 2 orders of magnitude faster than for o2 binding to myoglobin. to provide quantitative and microscopic descri ... | 2016 | 26845082 |
| purification and characterization of glutaminase free asparaginase from enterobacter cloacae: in-vitro evaluation of cytotoxic potential against human myeloid leukemia hl-60 cells. | asparaginase is an important antileukemic agent extensively used worldwide but the intrinsic glutaminase activity of this enzymatic drug is responsible for serious life threatening side effects. hence, glutaminase free asparaginase is much needed for upgradation of therapeutic index of asparaginase therapy. in the present study, glutaminase free asparaginase produced from enterobacter cloacae was purified to apparent homogeneity. the purified enzyme was found to be homodimer of approximately 106 ... | 2016 | 26891220 |
| chemical control of xylem differentiation by thermospermine, xylemin, and auxin. | the xylem conducts water and minerals from the root to the shoot and provides mechanical strength to the plant body. the vascular precursor cells of the procambium differentiate to form continuous vascular strands, from which xylem and phloem cells are generated in the proper spatiotemporal pattern. procambium formation and xylem differentiation are directed by auxin. in angiosperms, thermospermine, a structural isomer of spermine, suppresses xylem differentiation by limiting auxin signalling. h ... | 2016 | 26879262 |
| role of protein phosphorylation in the regulation of cell cycle and dna-related processes in bacteria. | in all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. in eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. protein phosphorylation is also involved in the global control of dna replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. similar to eukaryotes, bacteria use hanks-type kinases and phosphatases for signal transductio ... | 2016 | 26909079 |
| ribosomal small subunit domains radiate from a central core. | the domain architecture of a large rna can help explain and/or predict folding, function, biogenesis and evolution. we offer a formal and general definition of an rna domain and use that definition to experimentally characterize the rrna of the ribosomal small subunit. here the rrna comprising a domain is compact, with a self-contained system of molecular interactions. a given rrna helix or stem-loop must be allocated uniquely to a single domain. local changes such as mutations can give domain-w ... | 2016 | 26876483 |
| isc, a novel group of bacterial and archaeal dna transposons that encode cas9 homologs. | bacterial genomes encode numerous homologs of cas9, the effector protein of the type ii crispr-cas systems. the homology region includes the arginine-rich helix and the hnh nuclease domain that is inserted into the ruvc-like nuclease domain. these genes, however, are not linked to cas genes or crispr. here, we show that cas9 homologs represent a distinct group of nonautonomous transposons, which we denote isc (insertion sequences cas9-like). we identify many diverse families of full-length isc t ... | 2016 | 26712934 |
| kinetic mechanism and fidelity of nick sealing by escherichia coli nad+-dependent dna ligase (liga). | escherichia coli dna ligase (ecoliga) repairs 3'-oh/5'-po4 nicks in duplex dna via reaction of liga with nad(+) to form a covalent liga-(lysyl-nζ)-amp intermediate (step 1); transfer of amp to the nick 5'-po4 to form an appdna intermediate (step 2); and attack of the nick 3'-oh on appdna to form a 3'-5' phosphodiester (step 3). a distinctive feature of ecoliga is its stimulation by ammonium ion. here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealin ... | 2016 | 26857547 |
| biofuel production based on carbohydrates from both brown and red macroalgae: recent developments in key biotechnologies. | marine macroalgae (green, red and brown macroalgae) have attracted attention as an alternative source of renewable biomass for producing both fuels and chemicals due to their high content of suitable carbohydrates and to their advantages over terrestrial biomass. however, except for green macroalgae, which contain relatively easily-fermentable glucans as their major carbohydrates, practical utilization of red and brown macroalgae has been regarded as difficult due to the major carbohydrates (alg ... | 2016 | 26861307 |
| markerless gene deletion with cytosine deaminase in thermus thermophilus strain hb27. | we developed a counterselectable deletion system for thermus thermophilus hb27 based on cytosine deaminase (encoded by coda) from thermaerobacter marianensis dsm 12885 and the sensitivity of t. thermophilus hb27 to the antimetabolite 5-fluorocytosine (5-fc). the deletion vector comprises the puc18 origin of replication, a thermostable kanamycin resistance marker functional in t. thermophilus hb27, and coda under the control of a constitutive putative trehalose promoter from t. thermophilus hb27. ... | 2016 | 26655764 |
| cytoplasmic copz-like protein and periplasmic rusticyanin and acop proteins as possible copper resistance determinants in acidithiobacillus ferrooxidans atcc 23270. | acidophilic organisms, such as acidithiobacillus ferrooxidans, possess high-level resistance to copper and other metals. a. ferrooxidans contains canonical copper resistance determinants present in other bacteria, such as copa atpases and rnd efflux pumps, but these components do not entirely explain its high metal tolerance. the aim of this study was to find other possible copper resistance determinants in this bacterium. transcriptional expression of a. ferrooxidans genes coding for a cytoplas ... | 2016 | 26637599 |
| interaction network of tobacco etch potyvirus nia protein with the host proteome during infection. | the genomes of plant viruses have limited coding capacity, and to complete their infectious cycles, viral factors must target, direct or indirectly, many host elements. however, the interaction networks between viruses and host factors are poorly understood. the genus potyvirus is the largest group of plus-strand rna viruses infecting plants. potyviral nuclear inclusion a (nia) plays many roles during infection. nia is a polyprotein consisting of two domains, viral protein genome-linked (vpg) an ... | 2016 | 26830344 |
| structural similarities and differences between two functionally distinct seca proteins, mycobacterium tuberculosis seca1 and seca2. | while seca is the atpase component of the major bacterial secretory (sec) system, mycobacteria and some gram-positive pathogens have a second paralog, seca2. in bacteria with two seca paralogs, each seca is functionally distinct, and they cannot compensate for one another. compared to seca1, seca2 exports a distinct and smaller set of substrates, some of which have roles in virulence. in the mycobacterial system, some seca2-dependent substrates lack a signal peptide, while others contain a signa ... | 2016 | 26668263 |
| acetylome analysis reveals the involvement of lysine acetylation in biosynthesis of antibiotics in bacillus amyloliquefaciens. | lysine acetylation is a major post-translational modification that plays an important regulatory role in almost every aspects in both eukaryotes and prokaryotes. bacillus amyloliquefaciens, a gram-positive bacterium, is very effective for the control of plant pathogens. however, very little is known about the function of lysine acetylation in this organism. here, we conducted the first lysine acetylome in b. amyloliquefaciens through a combination of highly sensitive immune-affinity purification ... | 2016 | 26822828 |
| a structural view of microrna-target recognition. | it is well established that the correct identification of the messenger rna targeted by a given microrna (mirna) is a difficult problem, and that available methods all suffer from low specificity. we hypothesize that the correct identification of the pairing should take into account the effect of the argonaute protein (ago), an essential catalyst of the recognition process. therefore, we developed a strategy named miren for building and scoring three-dimensional models of the ternary complex for ... | 2016 | 26825463 |
| systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5'-phosphate production in e. coli. | recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. understanding the role of such enzymes is an important open question in biology. here we develop a genome-wide method, proper, that uses a permissive psi-blast approach to predict promiscuous activities of metabolic genes. enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous 'replacer' gene rescues lethality caused by ina ... | 2016 | 26821166 |
| biological nanomotors with a revolution, linear, or rotation motion mechanism. | the ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. in 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded dna (dsdna) bacteriophages. this review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and en ... | 2016 | 26819321 |
| structural insights into the quaternary catalytic mechanism of hexameric human quinolinate phosphoribosyltransferase, a key enzyme in de novo nad biosynthesis. | quinolinate phosphoribosyltransferase (qprt) catalyses the production of nicotinic acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous coenzyme nicotinamide adenine dinucleotide. qprt is also essential for maintaining the homeostasis of quinolinic acid in the brain, a possible neurotoxin causing various neurodegenerative diseases. although qprt has been extensively analysed, the molecular basis of the reaction catalysed by human qprt remains unclear. here, we present the c ... | 2016 | 26805589 |
| structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. | with bacterial resistance becoming a serious threat to global public health, antimicrobial peptides (amps) have become a promising area of focus in antibiotic research. amps are derived from a diverse range of species, from prokaryotes to humans, with a mechanism of action that often involves disruption of the bacterial cell membrane. proline-rich antimicrobial peptides (pramps) are instead actively transported inside the bacterial cell where they bind and inactivate specific targets. recently, ... | 2016 | 26809677 |
| multiple nucleic acid cleavage modes in divergent type iii crispr systems. | crispr-cas is an rna-guided adaptive immune system that protects bacteria and archaea from invading nucleic acids. type iii systems (cmr, csm) have been shown to cleave rna targets in vitro and some are capable of transcription-dependent dna targeting. the crenarchaeon sulfolobus solfataricus has two divergent subtypes of the type iii system (sso-iiid and a cmr7-containing variant of sso-iiib). here, we report that both the sso-iiid and sso-iiib complexes cleave cognate rna targets with a ruler ... | 2016 | 26801642 |
| novel base-pairing interactions at the trna wobble position crucial for accurate reading of the genetic code. | posttranscriptional modifications at the wobble position of transfer rnas play a substantial role in deciphering the degenerate genetic code on the ribosome. the number and variety of modifications suggest different mechanisms of action during messenger rna decoding, of which only a few were described so far. here, on the basis of several 70s ribosome complex x-ray structures, we demonstrate how escherichia coli trna(lys)(uuu) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)u) at ... | 2016 | 26791911 |
| structure of the mammalian antimicrobial peptide bac7(1-16) bound within the exit tunnel of a bacterial ribosome. | proline-rich antimicrobial peptides (pramps) produced as part of the innate immune response of animals, insects and plants represent a vast, untapped resource for the treatment of multidrug-resistant bacterial infections. pramps such as oncocin or bactenecin-7 (bac7) interact with the bacterial ribosome to inhibit translation, but their supposed specificity as inhibitors of bacterial rather than mammalian protein synthesis remains unclear, despite being key to developing drugs with low toxicity. ... | 2016 | 26792896 |
| centers of motion associated with ef-tu binding to the ribosome. | structural centers of motion (pivot points) in the ribosome have recently been identified by measurement of conformational changes in rrna resulting from ef-g gtp hydrolysis. this series of measurements is extended here to the ribosome's interactions with the cofactor ef-tu. four recent ef-tu bound ribosome structures were compared to unbound structures. a total of 16 pivots were identified, of which 4 are unique to the ef-tu interaction. pivots in the gtpase associated center and the sarcin-ric ... | 2016 | 26786136 |
| a target-protection mechanism of antibiotic resistance at atomic resolution: insights into fusb-type fusidic acid resistance. | antibiotic resistance in clinically important bacteria can be mediated by proteins that physically associate with the drug target and act to protect it from the inhibitory effects of an antibiotic. we present here the first detailed structural characterization of such a target protection mechanism mediated through a protein-protein interaction, revealing the architecture of the complex formed between the fusb fusidic acid resistance protein and the drug target (ef-g) it acts to protect. binding ... | 2016 | 26781961 |
| the dna polymerase iii holoenzyme contains γ and is not a trimeric polymerase. | there is widespread agreement that the clamp loader of the escherichia coli replicase has the composition dnax3δδ'χψ. two dnax proteins exist in e. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds dna polymerase iii tightly; γ does not. there is a controversy as to whether or not dna polymerase iii holoenzyme (pol iii he) contains γ. a three-τ form of pol iii he would contain three pol iiis. proponents of the three-τ hypothesis have claimed that γ found i ... | 2016 | 26786318 |
| n(6)-methyladenosine in mrna disrupts trna selection and translation-elongation dynamics. | n(6)-methylation of adenosine (forming m(6)a) is the most abundant post-transcriptional modification within the coding region of mrna, but its role during translation remains unknown. here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)a in mrna decoding. although m(6)a base-pairs with uridine during decoding, as shown by x-ray crystallographic analyses of thermus thermophilus ribosomal complexes, our measurements in an escherichia coli translation system revealed t ... | 2016 | 26751643 |
| two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes. | mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. direct structural evidence on the transient cytochrome c oxidase-cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. here, we report on the 2d crystallization of monomeric bovine cytochrome c oxidase with tightly bound c ... | 2016 | 26754561 |
| the bioactive secondary metabolites from talaromyces species. | the focus of this review is placed on the chemical structures from the species of the genus talaromyces reported with reference to their biological activities. 221 secondary metabolites, including 43 alkaloids and peptides, 88 esters, 31 polyketides, 19 quinones, 15 steroid and terpenoids, and 25 other structure type compounds, have been included, and 66 references are cited. | 2016 | 26746215 |
| a model for genesis of transcription systems. | repeating sequences generated from rna gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. a simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-ψ-β-barrel (dpbb) type rna polymerases (rnaps), general transcription factors (gtfs), and promoters. a general rule that emerges is that biological complexity that arises through generation of repea ... | 2016 | 26735411 |
| redirection of the reaction specificity of a thermophilic acetolactate synthase toward acetaldehyde formation. | acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. in this study, the reaction specificity of acetolactate synthase from thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxyla ... | 2016 | 26731734 |
| watson-crick-like pairs in ccug repeats: evidence for tautomeric shifts or protonation. | rna transcripts that include expanded ccug repeats are associated with myotonic dystrophy type 2. crystal structures of two ccug-containing oligomers show that the rna strands associate into slipped duplexes that contain noncanonical c-u pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual watson-crick-like pairing. the overhanging ends of the duplexes interact forming u-u pairs, which also show tautomerism. duplexes consisting of ccug repeats are the ... | 2016 | 26543073 |
| complete kinetic mechanism for recycling of the bacterial ribosome. | how ef-g and rrf act together to split a post-termination ribosomal complex into its subunits has remained obscure. here, using stopped-flow experiments with rayleigh light scattering detection and quench-flow experiments with radio-detection of gtp hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. ribosome splitting requires that ef-g binds to an already rrf-containing ribosome. ef-g binding to rrf-free ribosomes ... | 2016 | 26527791 |
| an ambiguity principle for assigning protein structural domains. | ambiguity is the quality of being open to several interpretations. for an image, it arises when the contained elements can be delimited in two or more distinct ways, which may cause confusion. we postulate that it also applies to the analysis of protein three-dimensional structure, which consists in dividing the molecule into subunits called domains. because different definitions of what constitutes a domain can be used to partition a given structure, the same protein may have different but equa ... | 2017 | 28097215 |
| integrating mass spectrometry with md simulations reveals the role of lipids in na(+)/h(+) antiporters. | na(+)/h(+) antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the na(+)/h(+) exchanger napa from thermus thermophilus and compare this to the prototypical antiporter nhaa from escherichia coli and the human homologue nha2. we find that napa and nha2, but ... | 2017 | 28071645 |
| exploring conformational equilibria of a heterodimeric abc transporter. | abc exporters pump substrates across the membrane by coupling atp-driven movements of nucleotide binding domains (nbds) to the transmembrane domains (tmds), which switch between inward- and outward-facing (if, of) orientations. deer measurements on the heterodimeric abc exporter tm287/288 from thermotoga maritima, which contains a non-canonical atp binding site, revealed that in the presence of nucleotides the transporter exists in an if/of equilibrium. while atp binding was sufficient to partia ... | 2017 | 28051765 |
| thermophilic bacteria are potential sources of novel rieske non-heme iron oxygenases. | rieske non-heme iron oxygenases, which have a rieske-type [2fe-2s] cluster and a non-heme catalytic iron center, are an important family of oxidoreductases involved mainly in regio- and stereoselective transformation of a wide array of aromatic hydrocarbons. though present in all domains of life, the most widely studied rieske non-heme iron oxygenases are found in mesophilic bacteria. the present study explores the potential for isolating novel rieske non-heme iron oxygenases from thermophilic s ... | 2017 | 28050858 |
| activation of respiratory complex i from escherichia coli studied by fluorescent probes. | respiratory complex i from e. coli may exist in two interconverting forms: resting (r) and active (a). the r/a transition of purified, solubilized complex i occurring upon turnover was studied employing two different fluorescent probes, annine 6+, and ndb-acetogenin. nadh-induced fluorescent changes of both dyes bound to solubilized complex i from e. coli were characterized as a function of the protein:dye ratio, temperature, ubiquinone redox state and the enzyme activity. analysis of this data ... | 2017 | 28070565 |