Publications

structural dissection of the maltodextrin disproportionation cycle of the arabidopsis plastidial disproportionating enzyme 1 (dpe1).	the degradation of transitory starch in the chloroplast to provide fuel for the plant during the night requires a suite of enzymes that generate a series of short chain linear glucans. however, glucans of less than four glucose units are no longer substrates for these enzymes, whereas export from the plastid is only possible in the form of either maltose or glucose. in order to make use of maltotriose, which would otherwise accumulate, disproportionating enzyme 1 (dpe1; a 4-α-glucanotransferase) ...	2015	26504082
complete genome sequence of thermus aquaticus y51mc23.	thermus aquaticus y51mc23 was isolated from a boiling spring in the lower geyser basin of yellowstone national park. remarkably, this t. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. y51mc23 is a gram-negative, rod-shaped organism that grows well between 50°c and 80°c with maximum growth rate at 65°c to 70°c. growth studies suggest that y51mc23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular ...	2015	26465632
complete genome sequence of the thermophilic thermus sp. ccb_us3_uf1 from a hot spring in malaysia.	thermus sp. strain ccb_us3_uf1 is a thermophilic bacterium of the genus thermus, a member of the family thermaceae. members of the genus thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. here, we present the complete genome sequence of thermus sp. ccb_us3_uf1 isolated from a hot spring in malaysia, which is the fifth member of the genus thermus with a completely sequenced and publ ...	2015	26457128
from structure-function analyses to protein engineering for practical applications of dna ligase.	dna ligases are indispensable in all living cells and ubiquitous in all organs. dna ligases are broadly utilized in molecular biology research fields, such as genetic engineering and dna sequencing technologies. here we review the utilization of dna ligases in a variety of in vitro gene manipulations, developed over the past several decades. during this period, fewer protein engineering attempts for dna ligases have been made, as compared to those for dna polymerases. we summarize the recent pro ...	2015	26508902
mismatch repair.	highly conserved muts homologs (msh) and mutl homologs (mlh/pms) are the fundamental components of mismatch repair (mmr). after decades of debate, it appears clear that the msh proteins initiate mmr by recognizing a mismatch and forming multiple extremely stable atp-bound sliding clamps that diffuse without hydrolysis along the adjacent dna. the function(s) of mlh/pms proteins is less clear, although they too bind atp and are targeted to mmr by msh sliding clamps. structural analysis combined wi ...	2015	26354434
cbr antimicrobials inhibit rna polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.	rna polymerase inhibitors like the cbr class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. catalysis by rna polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound ntp and two mg(2+) ions from a preinsertion state to a reactive configuration. cbr inhibitors target a crevice between the n-terminal portion of the bridge helix and a surrounding cap region within ...	2015	26195788
structural basis for the interconversion of maltodextrins by malq, the amylomaltase of escherichia coli.	amylomaltase malq is essential for the metabolism of maltose and maltodextrins in escherichia coli. it catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. to elucidate the molecular basis of transglycosylation by malq, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine- ...	2015	26139606
thermus parvatiensis rl(t) sp. nov., isolated from a hot water spring, located atop the himalayan ranges at manikaran, india.	a gram negative, yellow pigmented, rod shaped bacterium designated as rl(t) was isolated from a hot water spring (90-98 °c) located at manikaran in northern india. the isolate grows at 60-80 °c (optimum, 70 °c) and at ph 7.0-9.0 (optimum ph 7.2). phylogenetic analysis of 16s rrna gene sequences and levels of dna-dna relatedness together indicate that the new isolate represents a novel species of the genus thermus with closest affinity to thermus thermophilus hb8(t) (99.5 %) followed by thermus a ...	2015	26543260
protein synthesis during cellular quiescence is inhibited by phosphorylation of a translational elongation factor.	in nature, most organisms experience conditions that are suboptimal for growth. to survive, cells must fine-tune energy-demanding metabolic processes in response to nutrient availability. here, we describe a novel mechanism by which protein synthesis in starved cells is down-regulated by phosphorylation of the universally conserved elongation factor tu (ef-tu). phosphorylation impairs the essential gtpase activity of ef-tu, thereby preventing its release from the ribosome. as a consequence, phos ...	2015	26056311
first glycoside hydrolase family 2 enzymes from thermus antranikianii and thermus brockianus with β-glucosidase activity.	two glycoside hydrolase encoding genes (tagh2 and tbgh2) were identified from different thermus species using functional screening. based on amino acid similarities, the enzymes were predicted to belong to glycoside hydrolase (gh) family 2. surprisingly, both enzymes (tagh2 and tbgh2) showed twofold higher activities for the hydrolysis of nitrophenol-linked β-d-glucopyranoside than of -galactopyranoside. specific activities of 3,966 u/mg for tagh2 and 660 u/mg for tbgh2 were observed. in accorda ...	2015	26090361
draft genome sequence of the thermophile thermus filiformis atcc 43280, producer of carotenoid-(di)glucoside-branched fatty acid (di)esters and source of hyperthermostable enzymes of biotechnological interest.	here, we present the draft genome sequence of thermus ﬁliformis strain atcc 43280, a thermophile bacterium capable of producing glycosylated carotenoids acylated with branched fatty acids and enzymes of biotechnological potential.	2015	25977443
role of a ribosomal rna phosphate oxygen during the ef-g-triggered gtp hydrolysis.	elongation factor-catalyzed gtp hydrolysis is a key reaction during the ribosomal elongation cycle. recent crystal structures of g proteins, such as elongation factor g (ef-g) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational gtpases (trgtpases) with the sarcin-ricin loop (srl) of ribosomal rna (rrna) is pivotal for hydrolysis. however, the precise mechanism remains elusive and is intensively debated. based on the close prox ...	2015	25941362
salinity regulation of the interaction of halovirus snj1 with its host and alteration of the halovirus replication strategy to adapt to the variable ecosystem.	halovirus is a major force that affects the evolution of extreme halophiles and the biogeochemistry of hypersaline environments. however, until now, the systematic studies on the halovirus ecology and the effects of salt concentration on virus-host systems are lacking. to provide more valuable information for understanding ecological strategies of a virus-host system in the hypersaline ecosystem, we studied the interaction between halovirus snj1 and its host natrinema sp.j7-2 under various nacl ...	2015	25853566
molecular analysis of codon 548 in the rpob gene involved in mycobacterium tuberculosis resistance to rifampin.	most mycobacterium tuberculosis rifampin-resistant strains have been associated with mutations in an 81-bp rifampin resistance-determining region (rrdr) in the gene rpob. however, if this region alone were targeted, rifampin-resistant strains with mutations outside the rrdr would not be detected. in this study, among 51 rifampin-resistant clinical isolates analyzed by sequencing 1,681-bp-long dna fragments containing the rrdr, 47 isolates contained mutations within the rrdr, three isolates conta ...	2015	25534743
a selb/ef-tu/aif2γ-like protein from methanosarcina mazei in the gtp-bound form binds cysteinyl-trna(cys.).	the putative translation elongation factor mbar_a0971 from the methanogenic archaeon methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of ef-tu ("ef-pyl"). in the present study, the crystal structures of its homologue from methanosarcina mazei (mm1309) were determined in the gmppnp-bound, gdp-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. the three mm1309 structures are quite similar (r.m.s.d. < 0.1 å). the three domains, correspond ...	2015	25618148
long-range pcr amplification of dna by dna polymerase iii holoenzyme from thermus thermophilus.	dna replication in bacteria is accomplished by a multicomponent replicase, the dna polymerase iii holoenzyme (pol iii he). the three essential components of the pol iii he are the α polymerase, the β sliding clamp processivity factor, and the dnax clamp-loader complex. we report here the assembly of the functional holoenzyme from thermus thermophilus (tth), an extreme thermophile. the minimal holoenzyme capable of dna synthesis consists of α, β and dnax (τ and γ), δ and δ' components of the clam ...	2015	25688300
draft genome sequence of thermus sp. isolate 2.9, obtained from a hot water spring located in salta, argentina.	thermus sp. isolate 2.9 was obtained from a hot water spring in salta, argentina. here, we report the draft genome sequence (2,485,434 bp) of this isolate, which consists of 11 scaffolds of >10 kbp and 2,719 protein-coding sequences.	2015	25593256
fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?	the determination of a protein's folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. in this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain brownian dynamics simulations. the resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, wh ...	2015	26577596
binuclear cu(a) formation in biosynthetic models of cu(a) in azurin proceeds via a novel cu(cys)2his mononuclear copper intermediate.	cu(a) is a binuclear electron transfer (et) center found in cytochrome c oxidases (ccos), nitrous oxide reductases (n₂ors), and nitric oxide reductase (nor). in these proteins, the cu(a) centers facilitate efficient et (ket > 10⁴s⁻¹) under low thermodynamic driving forces (10-90 mv). while the structure and functional properties of cu(a) are well understood, a detailed mechanism of the incorporation of copper into the protein and the identity of the intermediates formed during the cu(a) maturati ...	2015	26352296
characterization of clinically identified mutations in ndufv1, the flavin-binding subunit of respiratory complex i, using a yeast model system.	dysfunctions in mitochondrial complex i (nadh:ubiquinone oxidoreductase) are both genetically and clinically highly diverse and a major cause of human mitochondrial diseases. the genetic determinants of individual clinical cases are increasingly being described, but how these genetic defects affect complex i on the molecular and cellular level, and have different clinical consequences in different individuals, is little understood. furthermore, without molecular-level information innocent geneti ...	2015	26345448
broken symmetry dft calculations/analysis for oxidized and reduced dinuclear center in cytochrome c oxidase: relating structures, protonation states, energies, and mössbauer properties in ba3 thermus thermophilus.	the fea3(3+)···cub(2+) dinuclear center (dnc) structure of the as-isolated oxidized ba3 cytochrome c oxidase (cco) from thermus thermophilus (tt) is still not fully understood. when the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through x-ray irradiation. several x-ray crystal structures of reduced ba3 cco from tt are available. however, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent ...	2015	26192749
during cytochrome c maturation ccmi chaperones the class i apocytochromes until the formation of their b-type cytochrome intermediates.	the c-type cytochromes are electron transfer proteins involved in energy transduction. they have heme-binding (cxxch) sites that covalently ligate heme b via thioether bonds and are classified into different classes based on their protein folds and the locations and properties of their cofactors. rhodobacter capsulatus produces various c-type cytochromes using the cytochrome c maturation (ccm) system i, formed from the ccmabcdefghi proteins. ccmi, a component of the heme ligation complex ccmfhi, ...	2015	25979338
reassessment of the transhydrogenase/malate shunt pathway in clostridium thermocellum atcc 27405 through kinetic characterization of malic enzyme and malate dehydrogenase.	clostridium thermocellum produces ethanol as one of its major end products from direct fermentation of cellulosic biomass. therefore, it is viewed as an attractive model for the production of biofuels via consolidated bioprocessing. however, a better understanding of the metabolic pathways, along with their putative regulation, could lead to improved strategies for increasing the production of ethanol. in the absence of an annotated pyruvate kinase in the genome, alternate means of generating py ...	2015	25616802
mutation of a single residue in the ba3 oxidase specifically impairs protonation of the pump site.	the ba3-type cytochrome c oxidase from thermus thermophilus is a membrane-bound protein complex that couples electron transfer to o2 to proton translocation across the membrane. to elucidate the mechanism of the redox-driven proton pumping, we investigated the kinetics of electron and proton transfer in a structural variant of the ba3 oxidase where a putative "pump site" was modified by replacement of asp372 by ile. in this structural variant, proton pumping was uncoupled from internal electron ...	2015	25733886
the class iii cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways.	photolyases are proteins with an fad chromophore that repair uv-induced pyrimidine dimers on the dna in a light-dependent manner. the cyclobutane pyrimidine dimer class iii photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. here we present the crystal structure of a class iii photolyase termed photolyase-related protein a (phra) of agrobacterium tumefaciens at 1.67-å resolution. phra contains 5,10-methenyltetrahydrofolate (m ...	2015	25784552
a novel family of integrases associated with prophages and genomic islands integrated within the trna-dihydrouridine synthase a (dusa) gene.	genomic islands play a key role in prokaryotic genome plasticity. genomic islands integrate into chromosomal loci such as transfer rna genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. a gene encoding a putative integrase was identified at a single site within the 5' end of the dusa gene in the genomes of over 200 bacteria. this integrase was discovered to be a component of numerous genomic islands, which appear to ...	2015	25883135
cold and hot extremozymes: industrial relevance and current trends.	the development of enzymes for industrial applications relies heavily on the use of microorganisms. the intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. these microorganisms have developed unique mechanisms and molecular means to cope with extreme ...	2015	26539430
marine extremophiles: a source of hydrolases for biotechnological applications.	the marine environment covers almost three quarters of the planet and is where evolution took its first steps. extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. the ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. hydrolases including amylases, cellulases, peptidases and lipases from hyper ...	2015	25854643
cpf1 is a single rna-guided endonuclease of a class 2 crispr-cas system.	the microbial adaptive immune system crispr mediates defense against foreign genetic elements through two classes of rna-guided nuclease effectors. class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized cas9. here, we report characterization of cpf1, a putative class 2 crispr effector. we demonstrate that cpf1 mediates robust dna interference with features distinct from cas9. cpf1 is a single rna-guid ...	2015	26422227
essentiality of threonylcarbamoyladenosine (t(6)a), a universal trna modification, in bacteria.	threonylcarbamoyladenosine (t(6)a) is a modified nucleoside universally conserved in trnas in all three kingdoms of life. the recently discovered genes for t(6)a synthesis, including tsac and tsad, are essential in model prokaryotes but not essential in yeast. these genes had been identified as antibacterial targets even before their functions were known. however, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. here, we show that t(6)a is a strong positive ...	2015	26337258
structure principles of crispr-cas surveillance and effector complexes.	the pathway of crispr-cas immunity redefines the roles of rna in the flow of genetic information and ignites excitement for next-generation gene therapy tools. crispr-cas machineries offer a fascinating set of new enzyme assemblies from which one can learn principles of molecular interactions and chemical activities. the interference step of the crispr-cas immunity pathway congregates proteins, rna, and dna into a single molecular entity that selectively destroys invading nucleic acids. although ...	2015	26048003
applications of cas9 as an rna-programmed rna-binding protein.	the streptococcus pyogenes crispr-cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the cas9 protein and guide rnas enables recognition of specific dna sequences. the recent discovery that cas9 can also bind and cleave rna in an rna-programmable manner indicates the potential utility of this system as a universal nucleic acid-recognition technology. rna-targeted cas9 (rcas9) could allow identification and manipulation o ...	2015	25880497
evaluation and directed evolution for thermostability improvement of a gh 13 thermostable α-glucosidase from thermus thermophilus tc11.	thermal stable α-glucosidases with transglycosylation activity could be applied to the industrial production of oligosaccharides as well as conjugation of sugars to biologically useful materials. therefore, α-glucosidases isolated from thermophiles have gained attention over the past decade. in this study, the characterization of a highly thermostable α-glucosidase and its thermostability improved mutant from newly isolated strain thermus thermophilus tc11 were investigated.	2015	26490269
x-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and o2-reduction states.	during x-ray data collection from a multicopper oxidase (mco) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the x-ray-induced reduction of o2 to 2h2o at the trinuclear copper cluster (tnc) of the enzyme. in this work, 12 crystallographic structures of thermus thermophilus hb27 multicopper oxidase (tth-mco) in holo, apo and hg-bound forms and with different x-ray absorbed doses have been determined. in holo tth-mco structures w ...	2015	26627648
colombos v3.0: leveraging gene expression compendia for cross-species analyses.	colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ...	2015	26586805
colombos v3.0: leveraging gene expression compendia for cross-species analyses.	colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ...	2015	26586805
high-resolution structures of lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate.	probiotic bacterial strains have been shown to enhance the health of the host through a range of mechanisms including colonization, resistance against pathogens, secretion of antimicrobial compounds and modulation of the activity of the innate immune system. lactobacillus salivarius ucc118 is a well characterized probiotic strain which survives intestinal transit and has many desirable host-interaction properties. probiotic bacteria display a wide range of catabolic activities, which determine t ...	2015	26457526
structural basis of transcription inhibition by cbr hydroxamidines and cbr pyrazoles.	cbr hydroxamidines are small-molecule inhibitors of bacterial rna polymerase (rnap) discovered through high-throughput screening of synthetic-compound libraries. cbr pyrazoles are structurally related rnap inhibitors discovered through scaffold hopping from cbr hydroxamidines. cbr hydroxamidines and pyrazoles selectively inhibit gram-negative bacterial rnap and exhibit selective antibacterial activity against gram-negative bacteria. here, we report crystal structures of the prototype cbr hydroxa ...	2015	26190576
structural biology of bacterial rna polymerase.	since its discovery and characterization in the early 1960s (hurwitz, j. the discovery of rna polymerase. j. biol. chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial rna polymerase (rnap). in the late 1990s, structural information pertaining to bacterial rnap has emerged that provided unprecedented insights into the function and mechanism of rna transcription. in this review, i list all structures related to bacterial rn ...	2015	25970587
gbtools: interactive visualization of metagenome bins in r.	improvements in dna sequencing technology have increased the amount and quality of sequences that can be obtained from metagenomic samples, making it practical to extract individual microbial genomes from metagenomic assemblies ("binning"). however, while many tools and methods exist for unsupervised binning with various statistical algorithms, there are few options for visualizing the results, even though visualization is vital to exploratory data analysis. we have developed gbtools, a software ...	2015	26732662
crystallographic characterization of the ribosomal binding site and molecular mechanism of action of hygromycin a.	hygromycin a (hyga) binds to the large ribosomal subunit and inhibits its peptidyl transferase (pt) activity. the presented structural and biochemical data indicate that hyga does not interfere with the initial binding of aminoacyl-trna to the a site, but prevents its subsequent adjustment such that it fails to act as a substrate in the pt reaction. structurally we demonstrate that hyga binds within the peptidyl transferase center (ptc) and induces a unique conformation. specifically in its ribo ...	2015	26464437
distinct trna accommodation intermediates observed on the ribosome with the antibiotics hygromycin a and a201a.	the increase in multi-drug-resistant bacteria is limiting the effectiveness of currently approved antibiotics, leading to a renewed interest in antibiotics with distinct chemical scaffolds. we have solved the structures of the thermus thermophilus 70s ribosome with a-, p-, and e-site trnas bound and in complex with either the aminocyclitol-containing antibiotic hygromycin a (hyga) or the nucleoside antibiotic a201a. both antibiotics bind at the peptidyl transferase center and sterically occlude ...	2015	26028538
16s rrna gene mutations associated with decreased susceptibility to tetracycline in mycoplasma bovis.	mycoplasma bovis isolates with decreased susceptibilities to tetracyclines are increasingly reported worldwide. the acquired molecular mechanisms associated with this phenomenon were investigated in 70 clinical isolates of m. bovis. sequence analysis of the two 16s rrna-encoding genes (rrs3 and rrs4 alleles) containing the primary binding pocket for tetracycline (tet-1 site) was performed on isolates with tetracycline hydrochloride mics of 0.125 to 16 μg/ml. mutations at positions a965t, a967t/c ...	2015	25403668
card uses a minor groove wedge mechanism to stabilize the rna polymerase open promoter complex.	a key point to regulate gene expression is at transcription initiation, and activators play a major role. card, an essential activator in mycobacterium tuberculosis, is found in many bacteria, including thermus species, but absent in escherichia coli. to delineate the molecular mechanism of card, we determined crystal structures of thermus transcription initiation complexes containing card. the structures show card interacts with the unique dna topology presented by the upstream double-stranded/ ...	2015	26349034
structural basis for methyl-donor-dependent and sequence-specific binding to trna substrates by knotted methyltransferase trmd.	the deep trefoil knot architecture is unique to the spou and trna methyltransferase d (trmd) (spout) family of methyltransferases (mtases) in all three domains of life. in bacteria, trmd catalyzes the n(1)-methylguanosine (m(1)g) modification at position 37 in transfer rnas (trnas) with the (36)gg(37) sequence, using s-adenosyl-l-methionine (adomet) as the methyl donor. the m(1)g37-modified trna functions properly to prevent +1 frameshift errors on the ribosome. here we report the crystal struct ...	2015	26183229
recent functional insights into the role of (p)ppgpp in bacterial physiology.	the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppgpp) are involved in regulating growth and several different stress responses in bacteria. in recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppgpp metabolism and (p)ppgpp-mediated regulation. in this review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the rela/spot homologue (rsh) ...	2015	25853779
determination of rna polymerase binding surfaces of transcription factors by nmr spectroscopy.	in bacteria, rna polymerase (rnap), the central enzyme of transcription, is regulated by n-utilization substance (nus) transcription factors. several of these factors interact directly, and only transiently, with rnap to modulate its function. as details of these interactions are largely unknown, we probed the rnap binding surfaces of escherichia coli (e. coli) nus factors by nuclear magnetic resonance (nmr) spectroscopy. perdeuterated factors with [(1)h,(13)c]-labeled methyl groups of val, leu, ...	2015	26560741
the eukaryotic translation initiation regulator cdc123 defines a divergent clade of atp-grasp enzymes with a predicted role in novel protein modifications.	deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. one such feature is the highly conserved, but poorly understood, eukaryotic protein cdc123, which regulates the abundance of the eukaryotic translation initiation eif2 complex and binds one of its components eif2γ. we show that the eukaryotic protein cdc123 defines a novel clade of atp-grasp enzymes distinguished from all other members o ...	2015	25976611
a comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes.	the lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. the uptake of the method is such that it is experiencing what can only be described as explosive growth. this timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. a model of how crystallization comes about mechanistically is presented for a more rational approach ...	2015	25615961
bacterial transfer rnas.	transfer rna is an essential adapter molecule that is found across all three domains of life. the primary role of transfer rna resides in its critical involvement in the accurate translation of messenger rna codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. this review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer rn ...	2015	25796611
novel type ii and monomeric nad+ specific isocitrate dehydrogenases: phylogenetic affinity, enzymatic characterization, and evolutionary implication.	nad(+) use is an ancestral trait of isocitrate dehydrogenase (idh), and the nadp(+) phenotype arose through evolution as an ancient adaptation event. however, no nad(+)-specific idhs have been found among type ii idhs and monomeric idhs. in this study, novel type ii homodimeric nad-idhs from ostreococcus lucimarinus cce9901 idh (olidh) and micromonas sp. rcc299 (miidh), and novel monomeric nad-idhs from campylobacter sp. fobrc14 idh (caidh) and campylobacter curvus (ccidh) were reported for the ...	2015	25775177
time-dependent transcriptional changes in axenic giardia duodenalis trophozoites.	giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. although g. duodenalis can be cultured axenically, significant gaps exist in our understanding of the molecular biology and metabolism of this pathogen. the present study employed rna sequencing to characterize the mrna transcriptome of g. duodenalis trophozoites in axenic culture, at log (48 h of g ...	2015	26636323
a conserved histidine in switch-ii of ef-g moderates release of inorganic phosphate.	elongation factor g (ef-g), a translational gtpase responsible for trna-mrna translocation possesses a conserved histidine (h91 in escherichia coli) at the apex of switch-ii, which has been implicated in gtpase activation and gtp hydrolysis. while h91a, h91r and h91e mutants showed different degrees of defect in ribosome associated gtp hydrolysis, h91q behaved like the wt. however, all these mutants, including h91q, are much more defective in inorganic phosphate (pi) release, thereby suggesting ...	2015	26264741
low temperature adaptation is not the opposite process of high temperature adaptation in terms of changes in amino acid composition.	previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. however, the relationship between high and low temperature adaptations remains unclear. to investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substit ...	2015	26614525
structural basis for gene regulation by a b12-dependent photoreceptor.	photoreceptor proteins enable organisms to sense and respond to light. the newly discovered carh-type photoreceptors use a vitamin b12 derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. here we present crystal structures of thermus thermophilus carh in all three relevant states: in the dark, both free and bound to operator dna, and after light exposure. these structures provide visualizations of how adenosylcobalamin mediates carh tetramer ...	2015	26416754
identification of middle chain fatty acyl-coa ligase responsible for the biosynthesis of 2-alkylmalonyl-coas for polyketide extender unit.	understanding the biosynthetic mechanism of the atypical polyketide extender unit is important for the development of bioactive natural products. reveromycin (rm) derivatives produced by streptomyces sp. sn-593 possess several aliphatic extender units. here, we studied the molecular basis of 2-alkylmalonyl-coa formation by analyzing the revr and revs genes, which form a transcriptional unit with the revt gene, a crotonyl-coa carboxylase/reductase homolog. we mainly focused on the uncharacterized ...	2015	26378232
the photochemical mechanism of a b12-dependent photoreceptor protein.	the coenzyme b12-dependent photoreceptor protein, carh, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. on binding of coenzyme b12 the monomeric apoprotein forms tetramers in the dark, which bind operator dna thus blocking transcription. under illumination the carh tetramer dissociates, weakening its affinity for dna and allowing transcription. the mechanism by which this occurs is unknown. here we describe the photochemistry in carh t ...	2015	26264192
the transcription factor carh safeguards use of adenosylcobalamin as a light sensor by altering the photolysis products.	the newly discovered light-dependent transcription factor carh uses adenosylcobalamin as a light sensor to regulate expression of protective genes in bacteria upon exposure to sunlight. this use of adenosylcobalamin is a clever adaptation of a classic enzyme cofactor, taking advantage of its photolabile co-c bond. however, it is also puzzling in that photolysis of adenosylcobalamin generates the 5'-deoxyadenosyl radical that could damage dna. here, using liquid chromatography and spectroscopic t ...	2015	25966286
role and function of litr, an adenosyl b12-bound light-sensitive regulator of bacillus megaterium qm b1551, in regulation of carotenoid production.	the litr/carh family of proteins is a light-sensitive merr family of transcriptional regulators that contain an adenosyl b12 (coenzyme b12 or adob12)-binding domain at the c terminus. the genes encoding these proteins are found in phylogenetically diverse bacterial genera; however, the biochemical properties of these proteins from gram-positive bacteria remain poorly understood. we performed genetic and biochemical analyses of a homolog of the litr protein from bacillus megaterium qm b1551, a gr ...	2015	25917914
ubiquitous transcription factors display structural plasticity and diverse functions: nusg proteins - shifting shapes and paradigms.	numerous accessory factors modulate rna polymerase response to regulatory signals and cellular cues and establish communications with co-transcriptional rna processing. transcription regulators are astonishingly diverse, with similar mechanisms arising via convergent evolution. nusg/spt5 elongation factors comprise the only universally conserved and ancient family of regulators. they bind to the conserved clamp helices domain of rna polymerase, which also interacts with non-homologous initiation ...	2015	25640595
intrastrand triplex dna repeats in bacteria: a source of genomic instability.	repetitive nucleic acid sequences are often prone to form secondary structures distinct from b-dna. prominent examples of such structures are dna triplexes. we observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. a systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the itxf database available online at http://bioinformatics.uni-konstanz.de/utils/itxf/ ...	2015	26450966
molecular mechanism and evolution of guanylate kinase regulation by (p)ppgpp.	the nucleotide (p)ppgpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. here, we characterize the molecular interaction between (p)ppgpp and guanylate kinase (gmk), revealing the importance of this interaction in adaptation to starvation. combining structural and kinetic analyses, we show that (p)ppgpp binds the gmk active site and competitively inhibits the enzyme. the (p)ppgpp-gmk interact ...	2015	25661490
the 29(th) annual symposium of the protein society, barcelona, spain, july 22-25, 2015.		2015	26452528
multiple conversion between the genes encoding bacterial class-i release factors.	bacteria require two class-i release factors, rf1 and rf2, that recognize stop codons and promote peptide release from the ribosome. rf1 and rf2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. this scenario expects that the two rf gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. however, we here report two independent cases of conversion b ...	2015	26257102
long-term survival of borrelia burgdorferi lacking the hibernation promotion factor homolog in the unfed tick vector.	borrelia burgdorferi, a causative agent of lyme borreliosis, is a zoonotic pathogen that survives in nutrient-limited environments within a tick, prior to transmission to its mammalian host. survival under these prolonged nutrient-limited conditions is thought to be similar to survival during stationary phase, which is characterized by growth cessation and decreased protein production. multiple ribosome-associated proteins are implicated in stationary-phase survival of escherichia coli. these pr ...	2015	26438790
the borrelia afzelii outer membrane protein bapko_0422 binds human factor-h and is predicted to form a membrane-spanning β-barrel.	the deep evolutionary history of the spirochetes places their branch point early in the evolution of the diderms, before the divergence of the present day proteobacteria. as a spirochete, the morphology of the borrelia cell envelope shares characteristics of both gram-positive and gram-negative bacteria. a thin layer of peptidoglycan, tightly associated with the cytoplasmic membrane, is surrounded by a more labile outer membrane (om). this om is rich in lipoproteins but with few known integral m ...	2015	26181365
acylation of biomolecules in prokaryotes: a widespread strategy for the control of biological function and metabolic stress.	acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic aci ...	2015	26179745
structure-function dissection of myxococcus xanthus card n-terminal domain, a defining member of the card_cdnl_trcf family of rna polymerase interacting proteins.	two prototypes of the large card_cdnl_trcf family of bacterial rna polymerase (rnap)-binding proteins, myxococcus xanthus card and cdnl, have distinct functions whose molecular basis remain elusive. card, a global regulator linked to the action of several extracytoplasmic function (ecf) σ-factors, binds to the rnap β subunit (rnap-β) and to protein carg via an n-terminal domain, cardnt, and to dna via an intrinsically unfolded c-terminal domain resembling eukaryotic high-mobility-group a (hmga) ...	2015	25811865
complete genome sequence and description of salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat.	during a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of lake 21 on the kiritimati atoll (kiribati republic, central pacific) strain l21-rpul-d2(t) was isolated. the closest phylogenetic neighbor was spirochaeta africana z-7692(t) that shared a 16s rrna gene sequence identity value of 90% with the novel strain and thus was only distantly related. a comprehensive polyphasic study including determination of the complete genome sequence was initiated to chara ...	2015	26203324
detecting conformational differences between rna 3d structures.	a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ...	2015	27330250
detecting conformational differences between rna 3d structures.	a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ...	2015	27330250
short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations.	mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ...	2015	26721932
short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations.	mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ...	2015	26721932
structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome.	during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ...	2015	26715760
structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome.	during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ...	2015	26715760
novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2.	the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ...	2015	26712743
novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2.	the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ...	2015	26712743
human holliday junction resolvase gen1 uses a chromodomain for efficient dna recognition and cleavage.	holliday junctions (hjs) are key dna intermediates in homologous recombination. they link homologous dna strands and have to be faithfully removed for proper dna segregation and genome integrity. here, we present the crystal structure of human hj resolvase gen1 complexed with dna at 3.0 å resolution. the gen1 core is similar to other rad2/xpg nucleases. however, unlike other members of the superfamily, gen1 contains a chromodomain as an additional dna interaction site. chromodomains are known fo ...	2015	26682650
resveratrol directly binds to mitochondrial complex i and increases oxidative stress in brain mitochondria of aged mice.	resveratrol is often described as a promising therapeutic molecule for numerous diseases, especially in metabolic and neurodegenerative disorders. while the mechanism of action is still debated, an increasing literature reports that resveratrol regulates the mitochondrial respiratory chain function. in a recent study we have identified mitochondrial complex i as a direct target of this molecule. nevertheless, the mechanisms and consequences of such an interaction still require further investigat ...	2015	26684010
co-evolution of bacterial ribosomal protein s15 with diverse mrna regulatory structures.	rna-protein interactions are critical in many biological processes, yet how such interactions affect the evolution of both partners is still unknown. rna and protein structures are impacted very differently by mechanisms of genomic change. while most protein families are identifiable at the nucleotide level across large phylogenetic distances, rna families display far less nucleotide similarity and are often only shared by closely related bacterial species. ribosomal protein s15 has two rna bind ...	2015	26675164
mechanisms of ribosome stalling by secm at multiple elongation steps.	regulation of translating ribosomes is a major component of gene expression control network. in escherichia coli, ribosome stalling by the c-terminal arrest sequence of secm regulates the seca-dependent secretion pathway. previous studies reported many residues of secm peptide and ribosome exit tunnel are critical for stalling. however, the underlying molecular mechanism is still not clear at the atomic level. here, we present two cryo-em structures of the secm-stalled ribosomes at 3.3-3.7 å res ...	2015	26670735
structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue.	purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ...	2015	26673726
structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue.	purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ...	2015	26673726
initiation factor 2 stabilizes the ribosome in a semirotated conformation.	intersubunit rotation and movement of the l1 stalk, a mobile domain of the large ribosomal subunit, have been shown to accompany the elongation cycle of translation. the initiation phase of protein synthesis is crucial for translational control of gene expression; however, in contrast to elongation, little is known about the conformational rearrangements of the ribosome during initiation. bacterial initiation factors (ifs) 1, 2, and 3 mediate the binding of initiator trna and mrna to the small r ...	2015	26668356
synergistic effect of atp for ruva-ruvb-holliday junction dna complex formation.	the escherichia coli ruvb hexameric ring motor proteins, together with ruvas, promote branch migration of holliday junction dna. zero mode waveguides (zmws) constitute of nanosized holes and enable the visualization of a single fluorescent molecule under micromolar order of the molecules, which is applicable to characterize the formation of ruva-ruvb-holliday junction dna complex. in this study, we used zmws and counted the number of ruvbs binding to ruva-holliday junction dna complex. our data ...	2015	26658024
microbial rhodopsins: wide distribution, rich diversity and great potential.	one of the major topics in biophysics and physicobiology is to understand and utilize biological functions using various advanced techniques. taking advantage of the photoreactivity of the seven-transmembrane rhodopsin protein family has been actively investigated by a variety of methods. rhodopsins serve as models for membrane-embedded proteins, for photoactive proteins and as a fundamental tool for optogenetics, a new technology to control biological activity with light. in this review, we sum ...	2015	27493861
structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle.	the bacterial sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. intermediates in the sox pathway are covalently attached to the heterodimeric carrier protein soxyz through conjugation to a cysteine on a protein swinging arm. we have investigated how the carrier protein shuttles intermediates between the enzymes of the sox pathway using the interaction between soxyz and the enzyme soxb as our model. the carrier protein and enzyme interact only w ...	2015	26655737
deciphering the dynamics of non-covalent interactions affecting thermal stability of a protein: molecular dynamics study on point mutant of thermus thermophilus isopropylmalate dehydrogenase.	thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. in this study dynamic changes in the non-covalent interac ...	2015	26657745
atp regulation in bioproduction.	adenosine-5'-triphosphate (atp) is consumed as a biological energy source by many intracellular reactions. thus, the intracellular atp supply is required to maintain cellular homeostasis. the dependence on the intracellular atp supply is a critical factor in bioproduction by cell factories. recent studies have shown that changing the atp supply is critical for improving product yields. in this review, we summarize the recent challenges faced by researchers engaged in the development of engineere ...	2015	26655598
nmr structure and function of helicoverpa armigera sterol carrier protein-2, an important insecticidal target from the cotton bollworm.	the cotton bollworm, helicoverpa armigera, has developed strong resistance to many insecticides. sterol carrier protein-2 (scp-2) is an important non-specific lipid transfer protein in insects and appears to be a potential new target. in order to elucidate the structure and function of helicoverpa armigera scp-2 (hascp-2), nmr spectroscopy, docking simulations, mutagenesis and bioassays were performed. hascp-2 composed of five α-helices and four stranded β-sheets. the folds of α-helices and β-sh ...	2015	26655641
evolutionary limitation and opportunities for developing trna synthetase inhibitors with 5-binding-mode classification.	aminoacyl-trna synthetases (aarss) are enzymes that catalyze the transfer of amino acids to their cognate trnas as building blocks for translation. each of the aars families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. in addition, aarss in higher species have evolved important non-translational functions. these translational and non-translational functions of aars are attractive for developing antibacterial, antifungal, and antiparasitic agents ...	2015	26670257
consistency analysis of genome-scale models of bacterial metabolism: a metamodel approach.	genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. with the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. the results showed that a large number of reactions (~22%) are blocked in all the models where they are present. to unravel the nature of such inconsistencies a metamodel was construed by joining the 130 mo ...	2015	26629901
non-specific blocking of mir-17-5p guide strand in triple negative breast cancer cells by amplifying passenger strand activity.	conventional wisdom holds that only one of the two strands in a micro ribonucleic acid (mirna) precursor duplex is selected as the active mirna guide strand. the complementary mirna passenger strand, however, is thought to be inactive. high levels of the oncogenic mirna (oncomir) guide strand called mir-17-5p is overexpressed in triple negative breast cancer (tnbc) and can inhibit ribosomal translation of tumor suppressor gene mrnas, such as programmed cell death 4 (pdcd4) or phosphatase and ten ...	2015	26629823
engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.	lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ...	2015	26621798
engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.	lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ...	2015	26621798
clinical metagenomic identification of balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.	primary amoebic meningoencephalitis (pam) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes.	2015	26620704
activities of the peptidyl transferase center of ribosomes lacking protein l27.	the ribosome is the molecular machine responsible for protein synthesis in all living organisms. its catalytic core, the peptidyl transferase center (ptc), is built of rrna, although several proteins reach close to the inner rrna shell. in the escherichia coli ribosome, the flexible n-terminal tail of the ribosomal protein l27 contacts the a- and p-site trna. based on computer simulations of the ptc and on previous biochemical evidence, the n-terminal α-amino group of l27 was suggested to take p ...	2015	26475831
an s6:s18 complex inhibits translation of e. coli rpsf.	more than half of the ribosomal protein operons in escherichia coli are regulated by structures within the mrna transcripts that interact with specific ribosomal proteins to inhibit further protein expression. this regulation is accomplished using a variety of mechanisms and the rna structures responsible for regulation are often not conserved across bacterial phyla. a widely conserved mrna structure preceding the ribosomal protein operon containing rpsf and rpsr (encoding s6 and s18) was recent ...	2015	26447183
concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii.	we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ...	2015	26619013
concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii.	we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ...	2015	26619013