Publications

universal pathway for posttransfer editing reactions: insights from the crystal structure of ttphers with puromycin.	at the amino acid binding and recognition step, phenylalanyl-trna synthetase (phers) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. resampling of tyr-trna(phe) to phers increasing the number of correctly charged trna molecules has recently been revealed. thus, the very same editing site of phers promotes hydrolysis of misacylated trna species, associated both with cis- and trans-editing pathways. here we report the crystal structure o ...	2015	25775602
substrate, product, and cofactor: the extraordinarily flexible relationship between the cde superfamily and heme.	pfam clan 0032, also known as the cde superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most im ...	2015	25778630
the ingenious structure of central rotor apparatus in vov1; key for both complex disassembly and energy coupling between v1 and vo.	vacuolar type rotary h+-atpases (vov1) couple atp synthesis/hydrolysis by v1 with proton translocation by vo via rotation of a central rotor apparatus composed of the v1-df rotor shaft, a socket-like vo-c (eukaryotic vo-d) and the hydrophobic rotor ring. reconstitution experiments using subcomplexes revealed a weak binding affinity of v1-df to vo-c despite the fact that torque needs to be transmitted between v1-df and vo-c for the tight energy coupling between v1 and vo. mutation of a short heli ...	2015	25756791
a prime/boost strategy using dna/fowlpox recombinants expressing the genetically attenuated e6 protein as a putative vaccine against hpv-16-associated cancers.	considering the high number of new cases of cervical cancer each year that are caused by human papilloma viruses (hpvs), the development of an effective vaccine for prevention and therapy of hpv-associated cancers, and in particular against the high-risk hpv-16 genotype, remains a priority. vaccines expressing the e6 and e7 proteins that are detectable in all hpv-positive pre-cancerous and cancer cells might support the treatment of hpv-related lesions and clear already established tumors.	2015	25763880
phylogenetic analysis of vitamin b12-related metabolism in mycobacterium tuberculosis.	comparison of genome sequences from clinical isolates of mycobacterium tuberculosis with phylogenetically-related pathogens mycobacterium marinum, mycobacterium kansasii, and mycobacterium leprae reveals diversity amongst genes associated with vitamin b12-related metabolism. diversity is generated by gene deletion events, differential acquisition of genes by horizontal transfer, and single nucleotide polymorphisms (snps) with predicted impact on protein function and transcriptional regulation. d ...	2015	25988174
evolution of the metazoan mitochondrial replicase.	the large number of complete mitochondrial dna (mtdna) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. by investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtdna polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by ex ...	2015	25740821
structure of the vacuolar h+-atpase rotary motor reveals new mechanistic insights.	vacuolar h(+)-atpases are multisubunit complexes that operate with rotary mechanics and are essential for membrane proton transport throughout eukaryotes. here we report a ∼ 1 nm resolution reconstruction of a v-atpase in a different conformational state from that previously reported for a lower-resolution yeast model. the stator network of the v-atpase (and by implication that of other rotary atpases) does not change conformation in different catalytic states, and hence must be relatively rigid ...	2015	25661654
supramolecular protein assembly supports immobilization of a cytochrome p450 monooxygenase system as water-insoluble gel.	diverse applications of the versatile bacterial cytochrome p450 enzymes (p450s) are hampered by their requirement for the auxiliary proteins, ferredoxin reductases and ferredoxins, that transfer electrons to p450s. notably, this limits the use of p450s as immobilized enzymes for industrial purposes. herein, we demonstrate the immobilization of a bacterial p450 and its redox protein partners by supramolecular complex formation using a self-assembled heterotrimeric protein. employment of homodimer ...	2015	25733255
heterotrimeric nadh-oxidizing methylenetetrahydrofolate reductase from the acetogenic bacterium acetobacterium woodii.	the methylenetetrahydrofolate reductase (mthfr) of acetogenic bacteria catalyzes the reduction of methylene-thf, which is highly exergonic with nadh as the reductant. therefore, the enzyme was suggested to be involved in energy conservation by reducing ferredoxin via electron bifurcation, followed by na(+) translocation by the rnf complex. the enzyme was purified from acetobacterium woodii and shown to have an unprecedented subunit composition containing the three subunits rnfc2, metf, and metv. ...	2015	25733614
role of nad⁺-dependent malate dehydrogenase in the metabolism of methylomicrobium alcaliphilum 20z and methylosinus trichosporium ob3b.	we have expressed the l-malate dehydrogenase (mdh) genes from aerobic methanotrophs methylomicrobium alcaliphilum 20z and methylosinus trichosporium ob3b as his-tagged proteins in escherichia coli. the substrate specificities, enzymatic kinetics and oligomeric states of the mdhs have been characterized. both mdhs were nad⁺-specific and thermostable enzymes not affected by metal ions or various organic metabolites. the mdh from m. alcaliphilum 20z was a homodimeric (2 × 35 kda) enzyme displaying ...	2015	27682078
trna biology in mitochondria.	mitochondria are the powerhouses of eukaryotic cells. they are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. these organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. among them, mitochondria use many specific pathways to obtain complete and functional sets of trnas as required for translatio ...	2015	25734984
bactobolin a binds to a site on the 70s ribosome distinct from previously seen antibiotics.	the ribosome is the target of a large number of antibiotics. here, we report a 3.4-å-resolution crystal structure of bactobolin a bound to 70s ribosome-trna complex. the antibiotic binds at a previously unseen site in the 50s subunit and displaces trna bound at the p-site. it thus likely has a similar mechanism of action as blasticidin s despite binding to a different site. the structure also rationalizes previously identified resistance mutations.	2015	25562208
unraveling the mechanistic features of rna polymerase ii termination by the 5'-3' exoribonuclease rat1.	within a complex with rai1, the 5'-3' exoribonuclease rat1 promotes termination of rna polymerase ii (rnapii) on protein-coding genes, but its underlying molecular mechanism is still poorly understood. using in vitro transcription termination assays, we have found that rnapii is prone to more effective termination by rat1/rai1 when its catalytic site is disrupted due to ntp misincorporation, implying that paused rnapii, which is often found in vivo near termination sites, could adopt a similar c ...	2015	25722373
structural basis for recognition of g-1-containing trna by histidyl-trna synthetase.	aminoacyl-trna synthetases (aarss) play a crucial role in protein translation by linking trnas with cognate amino acids. among all the trnas, only trna(his) bears a guanine base at position -1 (g-1), and it serves as a major recognition element for histidyl-trna synthetase (hisrs). despite strong interests in the histidylation mechanism, the trna recognition and aminoacylation details are not fully understood. we herein present the 2.55 å crystal structure of hisrs complexed with trna(his), whic ...	2015	25722375
an intermolecular binding mechanism involving multiple lysm domains mediates carbohydrate recognition by an endopeptidase.	lysm domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing n-acetylglucosamine (glcnac) moieties, such as chitin and peptidoglycan. in bacteria, the functional significance of the involvement of multiple lysm domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. here, a structural study of the thermus thermophilus nlpc/p60 endopeptidase cont ...	2015	25760608
identification of two structural elements important for ribosome-dependent gtpase activity of elongation factor 4 (ef4/lepa).	the bacterial translational gtpase ef4/lepa is structurally similar to the canonical elongation factor ef-g. while sharing core structural features with other translational gtpases, the function of ef4 remains unknown. recent structural data locates the unique c-terminal domain (ctd) of ef4 in proximity to the ribosomal peptidyl transferase center (ptc). to investigate the functional role of ef4's ctd we have constructed three c-terminal truncation variants. these variants are fully functional w ...	2015	25712150
analysis of the cooperative atpase cycle of the aaa+ chaperone clpb from thermus thermophilus by using ordered heterohexamers with an alternating subunit arrangement.	the clpb/hsp104 chaperone solubilizes and reactivates protein aggregates in cooperation with dnak/hsp70 and its cofactors. the clpb/hsp104 protomer has two aaa+ modules, aaa-1 and aaa-2, and forms a homohexamer. in the hexamer, these modules form a two-tiered ring in which each tier consists of homotypic aaa+ modules. by atp binding and its hydrolysis at these aaa+ modules, clpb/hsp104 exerts the mechanical power required for protein disaggregation. although atpase cycle of this chaperone has be ...	2015	25713084
hemq: an iron-coproporphyrin oxidative decarboxylase for protoheme synthesis in firmicutes and actinobacteria.	genes for chlorite dismutase-like proteins are found widely among heme-synthesizing bacteria and some archaea. it is now known that among the firmicutes and actinobacteria these proteins do not possess chlorite dismutase activity but instead are essential for heme synthesis. these proteins, named hemq, are iron-coproporphyrin (coproheme) decarboxylases that catalyze the oxidative decarboxylation of coproheme iii into protoheme ix. as purified, hemqs do not contain bound heme, but readily bind ex ...	2015	25711532
aida: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.	most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available.	2015	25701568
structure of escherichia coli dgtp triphosphohydrolase: a hexameric enzyme with dna effector molecules.	the escherichia coli dgt gene encodes a dgtp triphosphohydrolase whose detailed role still remains to be determined. deletion of dgt creates a mutator phenotype, indicating that the dgtpase has a fidelity role, possibly by affecting the cellular dntp pool. in the present study, we have investigated the structure of the dgt protein at 3.1-å resolution. one of the obtained structures revealed a protein hexamer that contained two molecules of single-stranded dna. the presence of dna caused signific ...	2015	25694425
2-thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in rna and dna duplexes.	2-thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. in particular, the 5-substituted-2-thiouridines (s2us) present in trna play an important role in tuning the translation process through codon-anticodon interactions. the enhanced thermodynamic stability of s2u-containing rna duplexes and the preferred s2u-a versus s2u-g base pairing are appreciated characteristics of s2u-modified molecular probes. recently, we have demonstrated that 2-thiouri ...	2015	25690900
rna polymerase-induced remodelling of nusa produces a pause enhancement complex.	pausing during transcription elongation is a fundamental activity in all kingdoms of life. in bacteria, the essential protein nusa modulates transcriptional pausing, but its mechanism of action has remained enigmatic. by combining structural and functional studies we show that a helical rearrangement induced in nusa upon interaction with rna polymerase is the key to its modulatory function. this conformational change leads to an allosteric re-positioning of conserved basic residues that could en ...	2015	25690895
synergistic effects of atp and rna binding to human dead-box protein ddx1.	rna helicases of the dead-box protein family form the largest group of helicases. the human dead-box protein 1 (ddx1) plays an important role in trna and mrna processing, is involved in tumor progression and is also hijacked by several virus families such as hiv-1 for replication and nuclear export. although important in many cellular processes, the mechanism of ddx1's enzymatic function is unknown. we have performed equilibrium titrations and transient kinetics to determine affinities for nucle ...	2015	25690890
identification of a second gtp-bound magnesium ion in archaeal initiation factor 2.	eukaryotic and archaeal translation initiation processes involve a heterotrimeric gtpase e/aif2 crucial for accuracy of start codon selection. in eukaryotes, the gtpase activity of eif2 is assisted by a gtpase-activating protein (gap), eif5. in archaea, orthologs of eif5 are not found and aif2 gtpase activity is thought to be non-assisted. however, no in vitro gtpase activity of the archaeal factor has been reported to date. here, we show that aif2 significantly hydrolyses gtp in vitro. within a ...	2015	25690901
arginine-rhamnosylation as new strategy to activate translation elongation factor p.	ribosome stalling at polyproline stretches is common and fundamental. in bacteria, translation elongation factor p (ef-p) rescues such stalled ribosomes, but only when it is post-translationally activated. in escherichia coli, activation of ef-p is achieved by (r)-β-lysinylation and hydroxylation of a conserved lysine. here we have unveiled a markedly different modification strategy in which a conserved arginine of ef-p is rhamnosylated by a glycosyltransferase (earp) using dtdp-l-rhamnose as a ...	2015	25686373
a prokaryotic twist on argonaute function.	argonaute proteins can be found in all three domains of life. in eukaryotic organisms, argonaute is, as the functional core of the rna-silencing machinery, critically involved in the regulation of gene expression. despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic argonaute proteins, the biological function of bacterial and archaeal argonautes has remained elusive. this review discusses new findings in the field that shed light on the structure and fun ...	2015	25692904
eukaryotic lyr proteins interact with mitochondrial protein complexes.	in eukaryotic cells, mitochondria host ancient essential bioenergetic and biosynthetic pathways. lyr (leucine/tyrosine/arginine) motif proteins (lyrms) of the complex1_lyr-like superfamily interact with protein complexes of bacterial origin. many lyr proteins function as extra subunits (lyrm3 and lyrm6) or novel assembly factors (lyrm7, lyrm8, acn9 and fmc1) of the oxidative phosphorylation (oxphos) core complexes. structural insights into complex i accessory subunits lyrm6 and lyrm3 have been p ...	2015	25686363
novel flp pilus biogenesis-dependent natural transformation.	natural transformation has been described in bacterial species spread through nearly all major taxonomic groups. however, the current understanding of the structural components and the regulation of competence development is derived from only a few model organisms. although natural transformation was discovered in members of the actinobacteria (high gc gram-positive bacteria) more than four decades ago, the structural components or the regulation of the competence system have not been studied in ...	2015	25713572
the bypass of zipa by overexpression of ftsn requires a previously unknown conserved ftsn motif essential for ftsa-ftsn interaction supporting a model in which ftsa monomers recruit late cell division proteins to the z ring.	assembly of the divisome in escherichia coli occurs in two temporally distinct steps. first, ftsz filaments attached to the membrane through interaction with ftsa and zipa coalesce into a z ring at midcell. then, additional proteins are recruited to the z ring in a hierarchical manner to form a complete divisome, activated by the arrival of ftsn. recently, we proposed that the interaction of ftsa with itself competes with its ability to recruit downstream division proteins (both require the ic d ...	2015	25496259
activity of select dehydrogenases with sepharose-immobilized n(6)-carboxymethyl-nad.	n(6)-carboxymethyl-nad (n(6)-cm-nad) can be used to immobilize nad onto a substrate containing terminal primary amines. we previously immobilized n(6)-cm-nad onto sepharose beads and showed that thermotoga maritima glycerol dehydrogenase could use the immobilized cofactor with cofactor recycling. we now show that saccharomyces cerevisiae alcohol dehydrogenase, rabbit muscle l-lactate dehydrogenase (type xi), bovine liver l-glutamic dehydrogenase (type iii), leuconostoc mesenteroides glucose-6-ph ...	2015	25611453
structural basis for transcription reactivation by rapa.	rna polymerase (rnap) loses activity during transcription as it stalls at various inactive states due to erratic translocation. reactivation of these stalled rnaps is essential for efficient rna synthesis. here we report a 4.7-å resolution crystal structure of the escherichia coli rnap core enzyme in complex with atpase rapa that is involved in reactivating stalled rnaps. the structure reveals that rapa binds at the rna exit channel of the rnap and makes the channel unable to accommodate the for ...	2015	25646438
distinct pathways of rna polymerase regulation by a phage-encoded factor.	transcription antitermination is a common strategy of gene expression regulation, but only a few transcription antitermination factors have been studied in detail. here, we dissect the transcription antitermination mechanism of xanthomonas oryzae virus xp10 protein p7, which binds host rna polymerase (rnap) and regulates both transcription initiation and termination. we show that p7 suppresses intrinsic termination by decreasing rnap pausing and increasing the transcription complex stability, in ...	2015	25646468
diversity in (p)ppgpp metabolism and effectors.	bacteria produce guanosine tetraphosphate and pentaphosphate, collectively named (p)ppgpp, in response to a variety of environmental stimuli. these two remarkable molecules regulate many cellular processes, including the central dogma processes and metabolism, to ensure survival and adaptation. work in escherichia coli laid the foundation for understanding the molecular details of (p)ppgpp and its cellular functions. as recent studies expand to other species, it is apparent that there exists con ...	2015	25636134
mutations in ribosomal proteins, rpl4 and rack1, suppress the phenotype of a thermospermine-deficient mutant of arabidopsis thaliana.	thermospermine acts in negative regulation of xylem differentiation and its deficient mutant of arabidopsis thaliana, acaulis5 (acl5), shows excessive xylem formation and severe dwarfism. studies of two dominant suppressors of acl5, sac51-d and sac52-d, have revealed that sac51 and sac52 encode a transcription factor and a ribosomal protein l10 (rpl10), respectively, and these mutations enhance translation of the sac51 mrna, which contains conserved upstream open reading frames in the 5' leader. ...	2015	25625317
advancing the development of glycated protein biosensing technology: next-generation sensing molecules.	research advances in biochemical molecules have led to the development of convenient and reproducible biosensing molecules for glycated proteins, such as those based on the enzymes fructosyl amino acid oxidase (faox) or fructosyl peptide oxidase (fpox). recently, more attractive biosensing molecules with potential applications in next-generation biosensing of glycated proteins have been aggressively reported. we review 2 such molecules, fructosamine 6-kinase (fn6k) and fructosyl amino acid-bindi ...	2015	25627465
role of δ1-pyrroline-5-carboxylate dehydrogenase supports mitochondrial metabolism and host-cell invasion of trypanosoma cruzi.	proline is crucial for energizing critical events throughout the life cycle of trypanosoma cruzi, the etiological agent of chagas disease. the proline breakdown pathway consists of two oxidation steps, both of which produce reducing equivalents as follows: the conversion of proline to δ(1)-pyrroline-5-carboxylate (p5c), and the subsequent conversion of p5c to glutamate. we have identified and characterized the δ(1)-pyrroline-5-carboxylate dehydrogenase from t. cruzi (tcp5cdh) and report here on ...	2015	25623067
engineering the genome of thermus thermophilus using a counterselectable marker.	thermus thermophilus is an extremely thermophilic bacterium that is widely used as a model thermophile, in large part due to its amenability to genetic manipulation. here we describe a system for the introduction of genomic point mutations or deletions using a counterselectable marker consisting of a conditionally lethal mutant allele of phes encoding the phenylalanyl-trna synthetase α-subunit. mutant phes with an a294g amino acid substitution renders cells sensitive to the phenylalanine analog ...	2015	25605305
structural insights into mis-regulation of protein kinase a in human tumors.	the extensively studied camp-dependent protein kinase a (pka) is involved in the regulation of critical cell processes, including metabolism, gene expression, and cell proliferation; consequentially, mis-regulation of pka signaling is implicated in tumorigenesis. recent genomic studies have identified recurrent mutations in the catalytic subunit of pka in tumors associated with cushing's syndrome, a kidney disorder leading to excessive cortisol production, and also in tumors associated with fibr ...	2015	25605907
redox state of flavin adenine dinucleotide drives substrate binding and product release in escherichia coli succinate dehydrogenase.	the complex ii family of enzymes, comprising respiratory succinate dehydrogenases and fumarate reductases, catalyzes reversible interconversion of succinate and fumarate. in contrast to the covalent flavin adenine dinucleotide (fad) cofactor assembled in these enzymes, soluble fumarate reductases (e.g., those from shewanella frigidimarina) that assemble a noncovalent fad cannot catalyze succinate oxidation but retain the ability to reduce fumarate. in this study, an sdha-h45a variant that elimin ...	2015	25569225
substrate trna recognition mechanism of eubacterial trna (m1a58) methyltransferase (trmi).	trmi generates n(1)-methyladenosine at position 58 (m(1)a58) in trna. the thermus thermophilus trna(phe) transcript was methylated efficiently by t. thermophilus trmi, whereas the yeast trna(phe) transcript was poorly methylated. fourteen chimeric trna transcripts derived from these two trnas revealed that trmi recognized the combination of aminoacyl stem, variable region, and t-loop. this was confirmed by 10 deletion trna variants: trmi methylated transcripts containing the aminoacyl stem, vari ...	2015	25593312
conformational changes of elongation factor g on the ribosome during trna translocation.	the universally conserved gtpase elongation factor g (ef-g) catalyzes the translocation of trna and mrna on the ribosome after peptide bond formation. despite numerous studies suggesting that ef-g undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of ef-g in complex with the ribosome. here, we report four atomic-resolution crystal structures of ef-g bound to the ribosome programmed in the pre- and posttra ...	2015	25594181
hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides.	the degradation mechanisms of natural and artificial hydrazides have been elucidated. here we screened and isolated bacteria that utilize the acylhydrazide 4-hydroxybenzoic acid 1-phenylethylidene hydrazide (hbph) from soils. physiological and phylogenetic studies identified one bacterium as microbacterium sp. strain hm58-2, from which we purified intracellular hydrazidase, cloned its gene, and prepared recombinant hydrazidase using an escherichia coli expression system. the microbacterium sp. h ...	2015	25583978
structural biology. division of labor in transhydrogenase by alternating proton translocation and hydride transfer.	nadph/nadp(+) (the reduced form of nadp(+)/nicotinamide adenine dinucleotide phosphate) homeostasis is critical for countering oxidative stress in cells. nicotinamide nucleotide transhydrogenase (th), a membrane enzyme present in both bacteria and mitochondria, couples the proton motive force to the generation of nadph. we present the 2.8 å crystal structure of the transmembrane proton channel domain of th from thermus thermophilus and the 6.9 å crystal structure of the entire enzyme (holo-th). ...	2015	25574024
identification of fah domain-containing protein 1 (fahd1) as oxaloacetate decarboxylase.	fumarylacetoacetate hydrolase (fah) domain-containing proteins occur in both prokaryotes and eukaryotes, where they carry out diverse enzymatic reactions, probably related to structural differences in their respective fah domains; however, the precise relationship between structure of the fah domain and the associated enzyme function remains elusive. in mammals, three fah domain-containing proteins, fahd1, fahd2a, and fahd2b, are known; however, their enzymatic function, if any, remains to be de ...	2015	25575590
enzyme dynamics from nmr spectroscopy.	conspectus: biological activities of enzymes, including regulation or coordination of mechanistic stages preceding or following the chemical step, may depend upon kinetic or equilibrium changes in protein conformations. exchange of more open or flexible conformational states with more closed or constrained states can influence inhibition, allosteric regulation, substrate recognition, formation of the michaelis complex, side reactions, and product release. nmr spectroscopy has long been applied t ...	2015	25574774
specific and non-specific interactions of parb with dna: implications for chromosome segregation.	the segregation of many bacterial chromosomes is dependent on the interactions of parb proteins with centromere-like dna sequences called pars that are located close to the origin of replication. in this work, we have investigated the binding of bacillus subtilis parb to dna in vitro using a variety of biochemical and biophysical techniques. we observe tight and specific binding of a parb homodimer to the pars sequence. binding of parb to non-specific dna is more complex and displays apparent po ...	2015	25572315
association between intrinsic disorder and serine/threonine phosphorylation in mycobacterium tuberculosis.	serine/threonine phosphorylation is an important mechanism that is involved in the regulation of protein function. in eukaryotes, phosphorylation occurs predominantly in intrinsically disordered regions of proteins. though serine/threonine phosphorylation and protein disorder are much less prevalent in prokaryotes, some bacteria have high levels of serine/threonine phosphorylation and disorder, including the medically important m. tuberculosis. here i show that serine/threonine phosphorylation s ...	2015	25648268
nucleoid occlusion protein noc recruits dna to the bacterial cell membrane.	to proliferate efficiently, cells must co-ordinate division with chromosome segregation. in bacillus subtilis, the nucleoid occlusion protein noc binds to specific dna sequences (nbss) scattered around the chromosome and helps to protect genomic integrity by coupling the initiation of division to the progression of chromosome replication and segregation. however, how it inhibits division has remained unclear. here, we demonstrate that noc associates with the cell membrane via an n-terminal amphi ...	2015	25568309
cdc45 (cell division cycle protein 45) guards the gate of the eukaryote replisome helicase stabilizing leading strand engagement.	dna replication licensing is now understood to be the pathway that leads to the assembly of double hexamers of minichromosome maintenance (mcm2-7) at origin sites. cell division control protein 45 (cdc45) and gins proteins activate the latent mcm2-7 helicase by inducing allosteric changes through binding, forming a cdc45/mcm2-7/gins (cmg) complex that is competent to unwind duplex dna. the cmg has an active gate between subunits mcm2 and mcm5 that opens and closes in response to nucleotide bindi ...	2015	25561522
production of dioxygen in the dark: dismutases of oxyanions.	o₂-generating reactions are exceedingly rare in biology and difficult to mimic synthetically. perchlorate-respiring bacteria enzymatically detoxify chlorite (clo₂(-) ), the end product of the perchlorate (clo(4)(-) ) respiratory pathway, by rapidly converting it to dioxygen (o₂) and chloride (cl(-)). this reaction is catalyzed by a heme-containing protein, called chlorite dismutase (cld), which bears no structural or sequence relationships with known peroxidases or other heme proteins and is par ...	2015	25707466
high throughput screen identifies natural product inhibitor of phenylalanyl-trna synthetase from pseudomonas aeruginosa and streptococcus pneumoniae.	pseudomonas aeruginosa and streptococcus pneumoniae are causative agents in a wide range of infections. genes encoding proteins corresponding to phenylalanyl-trna synthetase (phers) were cloned from both bacteria. the two forms of phers were kinetically evaluated and the k(m)'s for p. aeruginosa phers with its three substrates, phenylalanine, atp and trna(phe) were determined to be 48, 200, and 1.2 µm, respectively, while the k(m)'s for s. pneumoniae phers with respect to phenylalanine, atp and ...	2015	25601215
crystallization and preliminary x-ray analysis of the nad+-reducing [nife] hydrogenase from hydrogenophilus thermoluteolus th-1.	nad+-reducing [nife] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of nad+ and nadh. here, the isolation, purification and crystallization of the nad+-reducing [nife] hydrogenase from hydrogenophilus thermoluteolus th-1 are reported. crystals of the nad+-reducing [nife] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. the crystal diffracted to 2. ...	2015	25615977
in pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.	despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. in this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are ...	2015	25615870
convergent evolution of aua decoding in bacteria and archaea.	deciphering aua codons is a difficult task for organisms, because aua and aug specify isoleucine (ile) and methionine (met), separately. each of the other purine-ending sense co-don sets (nnr) specifies a single amino acid in the universal genetic code. in bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (l or lysidine) and 2-agmatinylcytidine (agm(2)c or agmatidine), respectively, are found at the first letter of the anticodon of trna(ile) responsible for aua codons. these modifi ...	2014	25629511
convergent evolution of aua decoding in bacteria and archaea.	deciphering aua codons is a difficult task for organisms, because aua and aug specify isoleucine (ile) and methionine (met), separately. each of the other purine-ending sense co-don sets (nnr) specifies a single amino acid in the universal genetic code. in bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (l or lysidine) and 2-agmatinylcytidine (agm(2)c or agmatidine), respectively, are found at the first letter of the anticodon of trna(ile) responsible for aua codons. these modifi ...	2014	25629511
two-subunit enzymes involved in eukaryotic post-transcriptional trna modification.	trna modifications are crucial for efficient and accurate protein translation, with defects often linked to disease. there are 7 cytoplasmic trna modifications in the yeast saccharomyces cerevisiae that are formed by an enzyme consisting of a catalytic subunit and an auxiliary protein, 5 of which require only a single subunit in bacteria, and 2 of which are not found in bacteria. these enzymes include the deaminase tad2-tad3, and the methyltransferases trm6-trm61, trm8-trm82, trm7-trm732, and tr ...	2014	25625329
two-subunit enzymes involved in eukaryotic post-transcriptional trna modification.	trna modifications are crucial for efficient and accurate protein translation, with defects often linked to disease. there are 7 cytoplasmic trna modifications in the yeast saccharomyces cerevisiae that are formed by an enzyme consisting of a catalytic subunit and an auxiliary protein, 5 of which require only a single subunit in bacteria, and 2 of which are not found in bacteria. these enzymes include the deaminase tad2-tad3, and the methyltransferases trm6-trm61, trm8-trm82, trm7-trm732, and tr ...	2014	25625329
the identification and characterization of non-coding and coding rnas and their modified nucleosides by mass spectrometry.	the analysis of ribonucleic acids (rna) by mass spectrometry has been a valuable analytical approach for more than 25 years. in fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from rna isolated out of biological samples. this review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. applications of mass spectrometry in the identification, characterization and quantification of modified nucleo ...	2014	25616408
the identification and characterization of non-coding and coding rnas and their modified nucleosides by mass spectrometry.	the analysis of ribonucleic acids (rna) by mass spectrometry has been a valuable analytical approach for more than 25 years. in fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from rna isolated out of biological samples. this review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. applications of mass spectrometry in the identification, characterization and quantification of modified nucleo ...	2014	25616408
pseudomonas aeruginosa isolates from dental unit waterlines can be divided in two distinct groups, including one displaying phenotypes similar to isolates from cystic fibrosis patients.	pseudomonas aeruginosa displays broad genetic diversity, giving it an astonishing capacity to adapt to a variety of environments and to infect a wide range of hosts. while many p. aeruginosa isolates of various origins have been analyzed, isolates from cystic fibrosis (cf) patients have received the most attention. less is known about the genetic and phenotypic diversity of p. aeruginosa isolates that colonize other environments where flourishing biofilms can be found. in the present study, 29 p ...	2014	25653647
pseudomonas aeruginosa isolates from dental unit waterlines can be divided in two distinct groups, including one displaying phenotypes similar to isolates from cystic fibrosis patients.	pseudomonas aeruginosa displays broad genetic diversity, giving it an astonishing capacity to adapt to a variety of environments and to infect a wide range of hosts. while many p. aeruginosa isolates of various origins have been analyzed, isolates from cystic fibrosis (cf) patients have received the most attention. less is known about the genetic and phenotypic diversity of p. aeruginosa isolates that colonize other environments where flourishing biofilms can be found. in the present study, 29 p ...	2014	25653647
an mrps12 mutation modifies aminoglycoside sensitivity caused by 12s rrna mutations.	several homoplasmic pathologic mutations in mitochondrial dna, such as those causing leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. therefore, other elements must modify their pathogenicity. discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasm ...	2014	25642242
an mrps12 mutation modifies aminoglycoside sensitivity caused by 12s rrna mutations.	several homoplasmic pathologic mutations in mitochondrial dna, such as those causing leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. therefore, other elements must modify their pathogenicity. discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasm ...	2014	25642242
trigger loop folding determines transcription rate of escherichia coli's rna polymerase.	two components of the rna polymerase (rnap) catalytic center, the bridge helix and the trigger loop (tl), have been linked with changes in elongation rate and pausing. here, single molecule experiments with the wt and two tl-tip mutants of the escherichia coli enzyme reveal that tip mutations modulate rnap's pause-free velocity, identifying tl conformational changes as one of two rate-determining steps in elongation. consistent with this observation, we find a direct correlation between helix pr ...	2014	25552559
trigger loop folding determines transcription rate of escherichia coli's rna polymerase.	two components of the rna polymerase (rnap) catalytic center, the bridge helix and the trigger loop (tl), have been linked with changes in elongation rate and pausing. here, single molecule experiments with the wt and two tl-tip mutants of the escherichia coli enzyme reveal that tip mutations modulate rnap's pause-free velocity, identifying tl conformational changes as one of two rate-determining steps in elongation. consistent with this observation, we find a direct correlation between helix pr ...	2014	25552559
a structural determinant in the uracil dna glycosylase superfamily for the removal of uracil from adenine/uracil base pairs.	the uracil dna glycosylase superfamily consists of several distinct families. family 2 mismatch-specific uracil dna glycosylase (mug) from escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, t/u, g/u and c/u. family 1 uracil n-glycosylase (ung) from e. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the a/u base pair. here, we report the identification of an important structural determinant that un ...	2014	25550433
a structural determinant in the uracil dna glycosylase superfamily for the removal of uracil from adenine/uracil base pairs.	the uracil dna glycosylase superfamily consists of several distinct families. family 2 mismatch-specific uracil dna glycosylase (mug) from escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, t/u, g/u and c/u. family 1 uracil n-glycosylase (ung) from e. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the a/u base pair. here, we report the identification of an important structural determinant that un ...	2014	25550433
structure of the pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial trna-dependent asparagine biosynthesis.	many prokaryotes lack a trna synthetase to attach asparagine to its cognate trna(asn), and instead synthesize asparagine from trna(asn)-bound aspartate. this conversion involves two enzymes: a nondiscriminating aspartyl-trna synthetase (nd-asprs) that forms asp-trna(asn), and a heterotrimeric amidotransferase gatcab that amidates asp-trna(asn) to form asn-trna(asn) for use in protein synthesis. nd-asprs, gatcab, and trna(asn) may assemble in an ∼400-kda complex, known as the asn-transamidosome, ...	2014	25548166
structure of the pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial trna-dependent asparagine biosynthesis.	many prokaryotes lack a trna synthetase to attach asparagine to its cognate trna(asn), and instead synthesize asparagine from trna(asn)-bound aspartate. this conversion involves two enzymes: a nondiscriminating aspartyl-trna synthetase (nd-asprs) that forms asp-trna(asn), and a heterotrimeric amidotransferase gatcab that amidates asp-trna(asn) to form asn-trna(asn) for use in protein synthesis. nd-asprs, gatcab, and trna(asn) may assemble in an ∼400-kda complex, known as the asn-transamidosome, ...	2014	25548166
conformational preferences underlying reduced activity of a thermophilic ribonuclease h.	the conformational basis for reduced activity of the thermophilic ribonuclease hi enzyme from thermus thermophilus, compared to its mesophilic homolog from escherichia coli, is elucidated using a combination of nmr spectroscopy and molecular dynamics (md) simulations. explicit-solvent all-atom md simulations of the two wild-type proteins and an e. coli mutant in which a glycine residue is inserted after position 80 to mimic the t. thermophilus protein reproduce the differences in conformational ...	2014	25550198
conformational preferences underlying reduced activity of a thermophilic ribonuclease h.	the conformational basis for reduced activity of the thermophilic ribonuclease hi enzyme from thermus thermophilus, compared to its mesophilic homolog from escherichia coli, is elucidated using a combination of nmr spectroscopy and molecular dynamics (md) simulations. explicit-solvent all-atom md simulations of the two wild-type proteins and an e. coli mutant in which a glycine residue is inserted after position 80 to mimic the t. thermophilus protein reproduce the differences in conformational ...	2014	25550198
crystal structure of thermobifida fusca cse1 reveals target dna binding site.	the clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) defense system is the only adaptive and inheritable immunity found in prokaryotes. the immunity is achieved through a multistep process of adaptation, expression, and interference. in the type i-e system, interference is mediated by the crispr-associated complex for antiviral defense (cascade), which recognizes invading double-stranded dna (dsdna) through the protospacer adjacent motif (pam) by one of ...	2014	25420472
crystal structure of thermobifida fusca cse1 reveals target dna binding site.	the clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) defense system is the only adaptive and inheritable immunity found in prokaryotes. the immunity is achieved through a multistep process of adaptation, expression, and interference. in the type i-e system, interference is mediated by the crispr-associated complex for antiviral defense (cascade), which recognizes invading double-stranded dna (dsdna) through the protospacer adjacent motif (pam) by one of ...	2014	25420472
trnas as antibiotic targets.	transfer rnas (trnas) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. this review focuses on the role of trnas in bacterial antibiosis. we will discuss examples of antibiotics that target multiple stages in trna biology from trna biogenesis and modification, mature trnas, aminoacylation of trna as well as prevention of proper trna function by small molecules binding to the ribosome. finally, the r ...	2014	25547494
trnas as antibiotic targets.	transfer rnas (trnas) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. this review focuses on the role of trnas in bacterial antibiosis. we will discuss examples of antibiotics that target multiple stages in trna biology from trna biogenesis and modification, mature trnas, aminoacylation of trna as well as prevention of proper trna function by small molecules binding to the ribosome. finally, the r ...	2014	25547494
cmr4 is the slicer in the rna-targeting cmr crispr complex.	clustered regularly interspaced short palindromic repeat (crispr) loci and crispr-associated (cas) proteins form an adaptive immune system that protects prokaryotes against plasmids and viruses. the cmr complex, a type iii-b effector complex, uses the crispr rna (crrna) as a guide to target rna. here, we show that the cmr complex of pyrococcus furiosus cleaves rna at multiple sites that are 6 nt apart and are positioned relative to the 5'-end of the crrna. we identified cmr4 as the slicer and de ...	2014	25541196
cmr4 is the slicer in the rna-targeting cmr crispr complex.	clustered regularly interspaced short palindromic repeat (crispr) loci and crispr-associated (cas) proteins form an adaptive immune system that protects prokaryotes against plasmids and viruses. the cmr complex, a type iii-b effector complex, uses the crispr rna (crrna) as a guide to target rna. here, we show that the cmr complex of pyrococcus furiosus cleaves rna at multiple sites that are 6 nt apart and are positioned relative to the 5'-end of the crrna. we identified cmr4 as the slicer and de ...	2014	25541196
transfer rna methyltransferases from thermoplasma acidophilum, a thermoacidophilic archaeon.	we investigated trna methyltransferase activities in crude cell extracts from the thermoacidophilic archaeon thermoplasma acidophilum. we analyzed the modified nucleosides in native initiator and elongator trnamet, predicted the candidate genes for the trna methyltransferases on the basis of the trnamet and trnaleu sequences, and characterized trm5, trm1 and trm56 by purifying recombinant proteins. we found that the ta0997, ta0931, and ta0836 genes of t. acidophilum encode trm1, trm56 and trm5, ...	2014	25546389
transfer rna methyltransferases from thermoplasma acidophilum, a thermoacidophilic archaeon.	we investigated trna methyltransferase activities in crude cell extracts from the thermoacidophilic archaeon thermoplasma acidophilum. we analyzed the modified nucleosides in native initiator and elongator trnamet, predicted the candidate genes for the trna methyltransferases on the basis of the trnamet and trnaleu sequences, and characterized trm5, trm1 and trm56 by purifying recombinant proteins. we found that the ta0997, ta0931, and ta0836 genes of t. acidophilum encode trm1, trm56 and trm5, ...	2014	25546389
a novel cytosolic nadh:quinone oxidoreductase from methanothermobacter marburgensis.	methanothermobacter marburgensis is a strictly anaerobic, thermophilic methanogenic archaeon that uses methanogenesis to convert h2 and co2 to energy. m. marburgensis is one of the best-studied methanogens, and all genes required for methanogenic metabolism have been identified. nonetheless, the present study describes a gene (gene id 9704440) coding for a putative	2014	25372605
ttomp85, a β-barrel assembly protein, functions by barrel augmentation.	outer membrane proteins are vital for gram-negative bacteria and organisms that inherited organelles from them. proteins from the omp85/bama family conduct the insertion of membrane proteins into the outer membrane. we show that an eight-stranded outer membrane β-barrel protein, ttoa, is inserted and folded into liposomes by an omp85 homologue. furthermore, we recorded the channel conductance of this omp85 protein in black lipid membranes, alone and in the presence of peptides comprising the seq ...	2014	25537637
ttomp85, a β-barrel assembly protein, functions by barrel augmentation.	outer membrane proteins are vital for gram-negative bacteria and organisms that inherited organelles from them. proteins from the omp85/bama family conduct the insertion of membrane proteins into the outer membrane. we show that an eight-stranded outer membrane β-barrel protein, ttoa, is inserted and folded into liposomes by an omp85 homologue. furthermore, we recorded the channel conductance of this omp85 protein in black lipid membranes, alone and in the presence of peptides comprising the seq ...	2014	25537637
enhancing allosteric inhibition in thermus thermophilus phosphofructokinase.	the coupling between the binding of the substrate fru-6-p and the inhibitor phospho(enol)pyruvate (pep) in phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus is much weaker than that seen in a pfk from bacillus stearothermophilus. from the crystal structures of bacillus stearothermophilus pfk (bspfk) the residues at positions 59, 158, and 215 in bspfk are located on the path leading from the allosteric site to the nearest active site and are part of the intricate hydroge ...	2014	25531642
enhancing allosteric inhibition in thermus thermophilus phosphofructokinase.	the coupling between the binding of the substrate fru-6-p and the inhibitor phospho(enol)pyruvate (pep) in phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus is much weaker than that seen in a pfk from bacillus stearothermophilus. from the crystal structures of bacillus stearothermophilus pfk (bspfk) the residues at positions 59, 158, and 215 in bspfk are located on the path leading from the allosteric site to the nearest active site and are part of the intricate hydroge ...	2014	25531642
the bacterial flagellar protein export apparatus processively transports flagellar proteins even with extremely infrequent atp hydrolysis.	for self-assembly of the bacterial flagellum, a specific protein export apparatus utilizes atp and proton motive force (pmf) as the energy source to transport component proteins to the distal growing end. the export apparatus consists of a transmembrane pmf-driven export gate and a cytoplasmic atpase complex composed of flih, flii and flij. the flii(6)flij complex is structurally similar to the α(3)β(3)γ complex of f(o)f(1)-atpase. flij allows the gate to efficiently utilize pmf to drive flagell ...	2014	25531309
molecular details of a starch utilization pathway in the human gut symbiont eubacterium rectale.	eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. starch is one of the most abundant glycans in the human diet, and e. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. here we present the results of a quantitative proteomics study in which we identify two glycoside hydr ...	2014	25388295
molecular details of a starch utilization pathway in the human gut symbiont eubacterium rectale.	eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. starch is one of the most abundant glycans in the human diet, and e. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. here we present the results of a quantitative proteomics study in which we identify two glycoside hydr ...	2014	25388295
evolution of oligomeric state through allosteric pathways that mimic ligand binding.	evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. we showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. in this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the pyrr family of pyrimidine operon attenuators. in this family, a perfectly s ...	2014	25525255
metatranscriptomics of n2-fixing cyanobacteria in the amazon river plume.	biological n2 fixation is an important nitrogen source for surface ocean microbial communities. however, nearly all information on the diversity and gene expression of organisms responsible for oceanic n2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from ...	2014	25514535
metatranscriptomics of n2-fixing cyanobacteria in the amazon river plume.	biological n2 fixation is an important nitrogen source for surface ocean microbial communities. however, nearly all information on the diversity and gene expression of organisms responsible for oceanic n2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from ...	2014	25514535
structural basis for the interaction of protein s1 with the escherichia coli ribosome.	in gram-negative bacteria, the multi-domain protein s1 is essential for translation initiation, as it recruits the mrna and facilitates its localization in the decoding centre. in sharp contrast to its functional importance, s1 is still lacking from the high-resolution structures available for escherichia coli and thermus thermophilus ribosomes and thus the molecular mechanism governing the s1-ribosome interaction has still remained elusive. here, we present the structure of the n-terminal s1 do ...	2014	25510494
structural basis for the interaction of protein s1 with the escherichia coli ribosome.	in gram-negative bacteria, the multi-domain protein s1 is essential for translation initiation, as it recruits the mrna and facilitates its localization in the decoding centre. in sharp contrast to its functional importance, s1 is still lacking from the high-resolution structures available for escherichia coli and thermus thermophilus ribosomes and thus the molecular mechanism governing the s1-ribosome interaction has still remained elusive. here, we present the structure of the n-terminal s1 do ...	2014	25510494
crystal structure of subunits d and f in complex gives insight into energy transmission of the eukaryotic v-atpase from saccharomyces cerevisiae.	eukaryotic v1vo-atpases hydrolyze atp in the v1 domain coupled to ion pumping in vo. a unique mode of regulation of v-atpases is the reversible disassembly of v1 and vo, which reduces atpase activity and causes silencing of ion conduction. the subunits d and f are proposed to be key in these enzymatic processes. here, we describe the structures of two conformations of the subunit df assembly of saccharomyces cerevisiae (scdf) v-atpase at 3.1 å resolution. subunit d (scd) consists of a long pair ...	2014	25505269
crystal structure of subunits d and f in complex gives insight into energy transmission of the eukaryotic v-atpase from saccharomyces cerevisiae.	eukaryotic v1vo-atpases hydrolyze atp in the v1 domain coupled to ion pumping in vo. a unique mode of regulation of v-atpases is the reversible disassembly of v1 and vo, which reduces atpase activity and causes silencing of ion conduction. the subunits d and f are proposed to be key in these enzymatic processes. here, we describe the structures of two conformations of the subunit df assembly of saccharomyces cerevisiae (scdf) v-atpase at 3.1 å resolution. subunit d (scd) consists of a long pair ...	2014	25505269
thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from geobacillus kaustophilus hta426.	thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. in this study, we constructed an error-prone strain of the thermophile geobacillus kaustophilus hta426 and investigated thermoadaptation-directed enzyme evolution using the strain. a mutation frequency assay using the antibiotics rifampin and streptomycin revealed that g. kaustophilus had substantially higher mutability than escherichia coli and bacill ...	2014	25326311
thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from geobacillus kaustophilus hta426.	thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. in this study, we constructed an error-prone strain of the thermophile geobacillus kaustophilus hta426 and investigated thermoadaptation-directed enzyme evolution using the strain. a mutation frequency assay using the antibiotics rifampin and streptomycin revealed that g. kaustophilus had substantially higher mutability than escherichia coli and bacill ...	2014	25326311
a mechanistic model of cor15 protein function in plant freezing tolerance: integration of structural and functional characteristics.	plants as sessile organisms are strongly challenged by environmental stresses. many plants species are able to cold-acclimate, acquiring higher freezing tolerance upon exposure to low but non-freezing temperatures. among a plethora of adaptational processes, this involves the accumulation of cold regulated (cor) proteins that are assumed to stabilize and protect cellular structures during freezing. however, their molecular functions are largely unknown. we recently reported a comprehensive study ...	2014	25496049
on the validation of crystallographic symmetry and the quality of structures.	in 2008, zwart and colleagues observed that the fraction of the structures deposited in the pdb alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (ncs) was about 6%, and that this percentage was rising annually. a few years later, poon and colleagues found that 2% of all the crystal structures in the pdb belonged to higher symmetry space groups than those assigned to them. here, i report an analysis of the x-ray diffraction data deposited for this class of structures, wh ...	2014	25352397
on the validation of crystallographic symmetry and the quality of structures.	in 2008, zwart and colleagues observed that the fraction of the structures deposited in the pdb alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (ncs) was about 6%, and that this percentage was rising annually. a few years later, poon and colleagues found that 2% of all the crystal structures in the pdb belonged to higher symmetry space groups than those assigned to them. here, i report an analysis of the x-ray diffraction data deposited for this class of structures, wh ...	2014	25352397
first evidence for substrate channeling between proline catabolic enzymes: a validation of domain fusion analysis for predicting protein-protein interactions.	proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase (p5cdh) catalyze the four-electron oxidation of proline to glutamate via the intermediates p5c and l-glutamate-γ-semialdehyde (gsa). in gram-negative bacteria, prodh and p5cdh are fused together in the bifunctional enzyme proline utilization a (puta) whereas in other organisms prodh and p5cdh are expressed as separate monofunctional enzymes. substrate channeling has previously been shown for bifunctional putas, bu ...	2014	25492892