Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| flexibility within the rotor and stators of the vacuolar h+-atpase. | the v-atpase is a membrane-bound protein complex which pumps protons across the membrane to generate a large proton motive force through the coupling of an atp-driven 3-stroke rotary motor (v1) to a multistroke proton pump (vo). this is done with near 100% efficiency, which is achieved in part by flexibility within the central rotor axle and stator connections, allowing the system to flex to minimise the free energy loss of conformational changes during catalysis. we have used electron microscop ... | 2013 | 24312643 |
| structure-function features of a mycoplasma glycolipid synthase derived from structural data integration, molecular simulations, and mutational analysis. | glycoglycerolipids are structural components of mycoplasma membranes with a fundamental role in membrane properties and stability. their biosynthesis is mediated by glycosyltransferases (gt) that catalyze the transfer of glycosyl units from a sugar nucleotide donor to diacylglycerol. the essential function of glycolipid synthases in mycoplasma viability, and the absence of glycoglycerolipids in animal host cells make these gt enzymes a target for drug discovery by designing specific inhibitors. ... | 2013 | 24312618 |
| in silico insights of l-glutamate: structural features in vacuum and in complex with its receptor. | structural properties of the glutamate in vacuum and in complex with its receptor were analyzed. the analysis was focused on global properties, attempting to characterize features such as overall flexibility and common trends in the conformation set. the glutamate, as other ligands in complex with the receptor, adopts a spatial conformation that corresponds to one of the possible molecular equilibrium states in physiological conditions. the glutamate forms an extended structure for all cases, bu ... | 2013 | 24307941 |
| a structured-based model for the decreased activity of ala222val and glu429ala methylenetetrahydrofolate reductase (mthfr) mutants. | the structure of human methylenetetrahydrofolate reductase (mthfr) is not known either by nmr or by x-ray methods. phosphorylation seems to play an important role in the functioning of this flavoprotein. mthfr catalyzes an irreversible reaction in homocysteine metabolism. phosphorylation decreases the activity of mthfr by enhancing the sensitivity of the enzyme to sadenosylmethione. two common polymorphisms in mthfr, ala222val and glu429ala, can result in a number of vascular diseases. effects o ... | 2013 | 24307772 |
| dna binding properties of human cdc45 suggest a function as molecular wedge for dna unwinding. | the cell division cycle protein 45 (cdc45) represents an essential replication factor that, together with the mcm2-7 complex and the four subunits of gins, forms the replicative dna helicase in eukaryotes. recombinant human cdc45 (hcdc45) was structurally characterized and its dna-binding properties were determined. synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle x-ray scattering and atomic force microscopy revealed that hcdc45 exists as an alpha-heli ... | 2013 | 24293646 |
| dna binding properties of human cdc45 suggest a function as molecular wedge for dna unwinding. | the cell division cycle protein 45 (cdc45) represents an essential replication factor that, together with the mcm2-7 complex and the four subunits of gins, forms the replicative dna helicase in eukaryotes. recombinant human cdc45 (hcdc45) was structurally characterized and its dna-binding properties were determined. synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle x-ray scattering and atomic force microscopy revealed that hcdc45 exists as an alpha-heli ... | 2013 | 24293646 |
| genetically encoded fluorescent indicator for imaging nad(+)/nadh ratio changes in different cellular compartments. | the ratio of nad(+)/nadh is a key indicator that reflects the overall redox state of the cells. until recently, there were no methods for real time nad(+)/nadh monitoring in living cells. genetically encoded fluorescent probes for nad(+)/nadh are fundamentally new approach for studying the nad(+)/nadh dynamics. | 2013 | 24286672 |
| genetically encoded fluorescent indicator for imaging nad(+)/nadh ratio changes in different cellular compartments. | the ratio of nad(+)/nadh is a key indicator that reflects the overall redox state of the cells. until recently, there were no methods for real time nad(+)/nadh monitoring in living cells. genetically encoded fluorescent probes for nad(+)/nadh are fundamentally new approach for studying the nad(+)/nadh dynamics. | 2013 | 24286672 |
| structural and physiological analyses of the alkanesulphonate-binding protein (ssua) of the citrus pathogen xanthomonas citri. | the uptake of sulphur-containing compounds plays a pivotal role in the physiology of bacteria that live in aerobic soils where organosulfur compounds such as sulphonates and sulphate esters represent more than 95% of the available sulphur. until now, no information has been available on the uptake of sulphonates by bacterial plant pathogens, particularly those of the xanthomonas genus, which encompasses several pathogenic species. in the present study, we characterised the alkanesulphonate uptak ... | 2013 | 24282519 |
| conserved distal loop residues in the hsp104 and clpb middle domain contact nucleotide-binding domain 2 and enable hsp70-dependent protein disaggregation. | the homologous hexameric aaa(+) proteins, hsp104 from yeast and clpb from bacteria, collaborate with hsp70 to dissolve disordered protein aggregates but employ distinct mechanisms of intersubunit collaboration. how hsp104 and clpb coordinate polypeptide handover with hsp70 is not understood. here, we define conserved distal loop residues between middle domain (md) helix 1 and 2 that are unexpectedly critical for hsp104 and clpb collaboration with hsp70. surprisingly, the hsp104 and clpb md dista ... | 2013 | 24280225 |
| conserved distal loop residues in the hsp104 and clpb middle domain contact nucleotide-binding domain 2 and enable hsp70-dependent protein disaggregation. | the homologous hexameric aaa(+) proteins, hsp104 from yeast and clpb from bacteria, collaborate with hsp70 to dissolve disordered protein aggregates but employ distinct mechanisms of intersubunit collaboration. how hsp104 and clpb coordinate polypeptide handover with hsp70 is not understood. here, we define conserved distal loop residues between middle domain (md) helix 1 and 2 that are unexpectedly critical for hsp104 and clpb collaboration with hsp70. surprisingly, the hsp104 and clpb md dista ... | 2013 | 24280225 |
| systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution. | we present a novel analysis of compositional order (co) based on the occurrence of frequent amino-acid triplets (fts) that appear much more than random in protein sequences. the method captures all types of proteomic compositional order including single amino-acid runs, tandem repeats, periodic structure of motifs and otherwise low complexity amino-acid regions. we introduce new order measures, distinguishing between 'regularity', 'periodicity' and 'vocabulary', to quantify these phenomena and t ... | 2013 | 24278003 |
| overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism. | the psychrophilic, hydrocarbonoclastic microorganism colwellia psychrerythraea is important in global nutrient cycling and bioremediation. in order to investigate how this organism can live so efficiently at low temperatures (~4°c), thermal denaturation studies of a small electron transfer protein from colwellia were performed. colwellia cytochrome c552 was overexpressed in escherichia coli, isolated, purified, and characterized by uv-visible absorption spectroscopy. the melting temperature (tm) ... | 2013 | 24275750 |
| overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism. | the psychrophilic, hydrocarbonoclastic microorganism colwellia psychrerythraea is important in global nutrient cycling and bioremediation. in order to investigate how this organism can live so efficiently at low temperatures (~4°c), thermal denaturation studies of a small electron transfer protein from colwellia were performed. colwellia cytochrome c552 was overexpressed in escherichia coli, isolated, purified, and characterized by uv-visible absorption spectroscopy. the melting temperature (tm) ... | 2013 | 24275750 |
| a cylindrical specimen holder for electron cryo-tomography. | the use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. this leads to the "missing wedge" problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but nev ... | 2014 | 24275523 |
| bacterial cell-envelope glycoconjugates. | prokaryotic glycosylation fulfills an important role in maintaining and protecting the structural integrity and function of the bacterial cell wall, as well as serving as a flexible adaption mechanism to evade environmental and host-induced pressure. the scope of bacterial and archaeal protein glycosylation has considerably expanded over the past decade(s), with numerous examples covering the glycosylation of flagella, pili, glycosylated enzymes, as well as surface-layer proteins. this article a ... | 2013 | 24274370 |
| structure of escherichia coli rna polymerase holoenzyme at last. | 2013 | 24272941 | |
| novel highly thermostable endolysin from thermus scotoductus mat2119 bacteriophage ph2119 with amino acid sequence similarity to eukaryotic peptidoglycan recognition proteins. | in this study, we present the discovery and characterization of a highly thermostable endolysin from bacteriophage ph2119 infecting thermus strain mat2119 isolated from geothermal areas in iceland. nucleotide sequence analysis of the 16s rrna gene affiliated the strain with the species thermus scotoductus. bioinformatics analysis has allowed identification in the genome of phage 2119 of an open reading frame (468 bp in length) coding for a 155-amino-acid basic protein with an mr of 17,555. ph211 ... | 2014 | 24271162 |
| dynamic dna underpins chromosome dynamics. | a recent article by meyer and co-workers provides a detailed description of the dynamics of base-step conformational transitions and of the first steps to the basepair opening. these results underpin the essential role that dna dynamics place in the dna structural transitions that accompany the active processes of transcription, replication, and recombination in bacterial and eukaryotic chromatin. | 2013 | 24268134 |
| biological diversity in the patent system. | biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. to address this problem we text mined 11 million patent documents for 6 million latin species names from the global names index (gni) established by the global biodiversity information facility (gbif) and encyclopedia of life (eol). we identified 76,274 full latin species names from 23,882 genera in 767,955 patent documents. 2 ... | 2013 | 24265714 |
| density functional study for the bridged dinuclear center based on a high-resolution x-ray crystal structure of ba3 cytochrome c oxidase from thermus thermophilus. | strong electron density for a peroxide type dioxygen species bridging the fea3 and cub dinuclear center (dnc) was observed in the high-resolution (1.8 å) x-ray crystal structures (pdb entries 3s8g and 3s8f) of ba3 cytochrome c oxidase (cco) from thermus thermophilus. the crystals represent the as-isolated x-ray photoreduced cco structures. the bridging peroxide was proposed to arise from the recombination of two radiation-produced ho(•) radicals formed either very near to or even in the space be ... | 2013 | 24262070 |
| two homologous ef-g proteins from pseudomonas aeruginosa exhibit distinct functions. | genes encoding two proteins corresponding to elongation factor g (ef-g) were cloned from pseudomonas aeruginosa. the proteins encoded by these genes are both members of the efg i subfamily. the gene encoding one of the forms of ef-g is located in the str operon and the resulting protein is referred to as ef-g1a while the gene encoding the other form of ef-g is located in another part of the genome and the resulting protein is referred to as ef-g1b. these proteins were expressed and purified to 9 ... | 2013 | 24260360 |
| structure of the proteus vulgaris higb-(higa)2-higb toxin-antitoxin complex. | bacterial toxin-antitoxin (ta) systems regulate key cellular processes to promote cell survival during periods of stress. during steady-state cell growth, antitoxins typically interact with their cognate toxins to inhibit activity presumably by preventing substrate recognition. we solved two x-ray crystal structures of the proteus vulgaris tetrameric higb-(higa)2-higb ta complex and found that, unlike most other ta systems, the antitoxin higa makes minimal interactions with toxin higb. higb adop ... | 2013 | 24257752 |
| structure of the proteus vulgaris higb-(higa)2-higb toxin-antitoxin complex. | bacterial toxin-antitoxin (ta) systems regulate key cellular processes to promote cell survival during periods of stress. during steady-state cell growth, antitoxins typically interact with their cognate toxins to inhibit activity presumably by preventing substrate recognition. we solved two x-ray crystal structures of the proteus vulgaris tetrameric higb-(higa)2-higb ta complex and found that, unlike most other ta systems, the antitoxin higa makes minimal interactions with toxin higb. higb adop ... | 2013 | 24257752 |
| crystal structure of the γ-hydroxymuconic semialdehyde dehydrogenase from pseudomonas sp. strainwbc-3, a key enzyme involved in para-nitrophenol degradation. | para-nitrophenol (pnp) is a highly toxic compound with threats to mammalian health. the pnpe-encoded γ-hydroxymuconic semialdehyde dehydrogenase catalyzes the reduction of γ-hydroxymuconic semialdehyde to maleylacetate in pseudomonas sp. strain wbc-3, playing a key role in the catabolism of pnp to krebs cycle intermediates. however, the catalyzing mechanism by pnpe has not been well understood. | 2013 | 24252642 |
| architecture and gene repertoire of the flexible genome of the extreme acidophile acidithiobacillus caldus. | acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the acidithiobacillales. as such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. in this study, we explore the genomic diversity of a. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. | 2013 | 24250794 |
| molecular basis of adp inhibition of vacuolar (v)-type atpase/synthase. | reduction of atp hydrolysis activity of vacuolar-type atpase/synthase (v0v1) as a result of adp inhibition occurs as part of the normal mechanism of v0v1 of thermus thermophilus but not v0v1 of enterococcus hirae or eukaryotes. to investigate the molecular basis for this difference, domain-swapped chimeric v1 consisting of both t. thermophilus and e. hirae enzymes were generated, and their function was analyzed. the data showed that the interaction between the nucleotide binding and c-terminal d ... | 2013 | 24247239 |
| molecular basis of adp inhibition of vacuolar (v)-type atpase/synthase. | reduction of atp hydrolysis activity of vacuolar-type atpase/synthase (v0v1) as a result of adp inhibition occurs as part of the normal mechanism of v0v1 of thermus thermophilus but not v0v1 of enterococcus hirae or eukaryotes. to investigate the molecular basis for this difference, domain-swapped chimeric v1 consisting of both t. thermophilus and e. hirae enzymes were generated, and their function was analyzed. the data showed that the interaction between the nucleotide binding and c-terminal d ... | 2013 | 24247239 |
| comparative xylose metabolism among the ascomycetes c. albicans, s. stipitis and s. cerevisiae. | the ascomycetes candida albicans, saccharomyces cerevisiae and scheffersomyces stipitis metabolize the pentose sugar xylose very differently. s. cerevisiae fails to grow on xylose, while c. albicans can grow, and s. stipitis can both grow and ferment xylose to ethanol. however, all three species contain highly similar genes that encode potential xylose reductases and xylitol dehydrogenases required to convert xylose to xylulose, and xylulose supports the growth of all three fungi. we have create ... | 2013 | 24236198 |
| analysis of the mechanism of nucleosome survival during transcription. | maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. our previous data identified a key intermediate (a small intranucleosomal dna loop, ø-loop) that is likely required for nucleosome survival during transcription by rna polymerase ii (pol ii) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. to evaluate these predictions, we analysed transcription through ... | 2013 | 24234452 |
| analysis of the mechanism of nucleosome survival during transcription. | maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. our previous data identified a key intermediate (a small intranucleosomal dna loop, ø-loop) that is likely required for nucleosome survival during transcription by rna polymerase ii (pol ii) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. to evaluate these predictions, we analysed transcription through ... | 2013 | 24234452 |
| protein biosynthesis in mitochondria. | translation, that is biosynthesis of polypeptides in accordance with information encoded in the genome, is one of the most important processes in the living cell, and it has been in the spotlight of international research for many years. the mechanisms of protein biosynthesis in bacteria and in the eukaryotic cytoplasm are now understood in great detail. however, significantly less is known about translation in eukaryotic mitochondria, which is characterized by a number of unusual features. in t ... | 2013 | 24228873 |
| in planta mutagenesis of src homology 3 domain-like fold of ndhs, a ferredoxin-binding subunit of the chloroplast nadh dehydrogenase-like complex in arabidopsis: a conserved arg-193 plays a critical role in ferredoxin binding. | chloroplast nadh dehydrogenase-like (ndh) complex mediates cyclic electron transport around photosystem i and chlororespiration in angiosperms. the src homology 3 domain (sh3)-like fold protein ndhs/crr31 is an ndh subunit that is necessary for high affinity binding of ferredoxin, indicating that chloroplast ndh functions as a ferredoxin:plastoquinone oxidoreductase. however, the mechanism of the interaction between ndhs and ferredoxin is unclear. in this study, we analyzed their interaction in ... | 2013 | 24225949 |
| structure and assembly of an inner membrane platform for initiation of type iv pilus biogenesis. | type iv pili are long fibers that are assembled by polymerization of a major pilin protein in the periplasm of a wide range of bacteria and archaea. they play crucial roles in pathogenesis, dna transformation, and motility, and are capable of rapid retraction, generating powerful motor forces. piln and pilo are integral inner membrane proteins that are essential for type iv pilus formation. here, we show that piln and pilo from thermus thermophilus can be isolated as a complex with pilm, a cytop ... | 2013 | 24218553 |
| type iv pilus biogenesis, twitching motility, and dna uptake in thermus thermophilus: discrete roles of antagonistic atpases pilf, pilt1, and pilt2. | natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species. thermus thermophilus hb27 has emerged as the leading model organism for studies of dna transporters in thermophilic bacteria. recently, we identified a zinc-binding polymerization nucleoside triphosphatase (ntpase), pilf, which is essential for the transport of dna through the outer membrane. here, we present genetic evidence that ... | 2014 | 24212586 |
| directed polymerase evolution. | polymerases evolved in nature to synthesize dna and rna, and they underlie the storage and flow of genetic information in all cells. the availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. to circumvent these limit ... | 2013 | 24211837 |
| directed polymerase evolution. | polymerases evolved in nature to synthesize dna and rna, and they underlie the storage and flow of genetic information in all cells. the availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. to circumvent these limit ... | 2013 | 24211837 |
| correlation between supercoiling and conformational motions of the bacterial flagellar filament. | the bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. we investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales. thermal fluctuations ... | 2013 | 24209861 |
| mechanisms of copper homeostasis in bacteria. | copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. however, free copper is a potential hazard because of its high chemical reactivity. consequently, organisms exert a tight control on cu(+) transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a ... | 2013 | 24205499 |
| aminoacylation of plasmodium falciparum trna(asn) and insights in the synthesis of asparagine repeats. | genome sequencing revealed an extreme at-rich genome and a profusion of asparagine repeats associated with low complexity regions (lcrs) in proteins of the malarial parasite plasmodium falciparum. despite their abundance, the function of these lcrs remains unclear. because they occur in almost all families of plasmodial proteins, the occurrence of lcrs cannot be associated with any specific metabolic pathway; yet their accumulation must have given selective advantages to the parasite. translatio ... | 2013 | 24196969 |
| niche specialization of novel thaumarchaeota to oxic and hypoxic acidic geothermal springs of yellowstone national park. | novel lineages of the phylum thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. the primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °c), acidic (ph~3) iron oxide and sulfur sediment environments of yellowstone national park (ynp). metabolic reconstruction ... | 2013 | 24196321 |
| niche specialization of novel thaumarchaeota to oxic and hypoxic acidic geothermal springs of yellowstone national park. | novel lineages of the phylum thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. the primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °c), acidic (ph~3) iron oxide and sulfur sediment environments of yellowstone national park (ynp). metabolic reconstruction ... | 2013 | 24196321 |
| purification, crystallization and preliminary crystallographic analysis of katb, a manganese catalase from anabaena pcc 7120. | catalases are enzymes that play an important role in the detoxification of hydrogen peroxide (h2o2) in aerobic organisms. among catalases, haem-containing catalases are ubiquitously distributed and their enzymatic mechanism is very well understood. on the other hand, manganese catalases that contain a bimanganese core in the active site have been less well characterized and their mode of action is not fully understood. the genome of anabaena pcc 7120 does not show the presence of a haem catalase ... | 2013 | 24192374 |
| cloning, expression, purification, crystallization and preliminary crystallographic analysis of the putative nlpc/p60 endopeptidase, ttha0266, from thermus thermophilus hb8. | autolysins belong to a protein family involved in peptidoglycan degradation and remodelling. within this family, nlpc/p60 endopeptidases are involved in the hydrolysis of the peptide arm of peptidoglycan. in this work, the putative nlpc/p60 endopeptidase ttha0266 from thermus thermophilus hb8 was overexpressed, purified and crystallized. the crystals diffracted to 2.4 å resolution and belonged to the hexagonal space group p6(1), with unit-cell parameters a = b = 71.19, c = 198.68 å, γ = 120°. se ... | 2013 | 24192372 |
| cloning, overexpression, purification and crystallization of malate dehydrogenase from thermus thermophilus. | malate dehydrogenase (mdh) has been used as a conjugate for enzyme immunoassay of a wide variety of compounds, such as drugs of abuse, drugs used in repetitive therapeutic application and hormones. in consideration of the various biotechnological applications of mdh, investigations of mdh from thermus thermophilus were carried out to further understand the properties of this enzyme. the dna fragment containing the open reading frame of mdh was amplified from the genomic dna of t. thermophilus an ... | 2013 | 24192361 |
| 12-fold symmetry of the putative portal protein from the thermus thermophilus bacteriophage g20c determined by x-ray analysis. | in tailed bacteriophages and several animal viruses, the portal protein forms the gateway through which viral dna is translocated into the head structure during viral particle assembly. in the mature virion the portal protein exists as a dodecamer, while recombinant portal proteins from several phages, including spp1 and cnph82, have been shown to form 13-subunit assemblies. a putative portal protein from the thermostable bacteriophage g20c has been cloned, overexpressed and purified. crystals o ... | 2013 | 24192358 |
| crystallization and preliminary x-ray study of alanine dehydrogenase from bacillus pseudofirmus of4. | alanine dehydrogenase (of4ald) from the alkaliphilic bacillus pseudofirmus of4 was expressed and purified with a his6 tag in a form suitable for x-ray crystallographic analysis. crystals were grown by the hanging-drop vapour-diffusion method at 289 k using a solution consisting of 0.1 m tris-hcl ph 8.0, 0.2 m liso4, 22%(w/v) peg 3350. x-ray diffraction data were collected to 2.8 å resolution. the crystal belonged to the triclinic space group p1, with unit-cell parameters a = 88.04, b = 105.59, c ... | 2013 | 24192355 |
| crystallization and preliminary x-ray diffraction studies of staphylococcus aureus homoserine dehydrogenase. | staphylococcus aureus is a gram-positive nosocomial pathogen. the prevalence of multidrug-resistant s. aureus strains in both hospital and community settings makes it imperative to characterize new drug targets to combat s. aureus infections. in this context, enzymes involved in cell-wall maintenance and essential amino-acid biosynthesis are significant drug targets. homoserine dehydrogenase (hsd) is an oxidoreductase that is involved in the reversible conversion of l-aspartate semialdehyde to l ... | 2013 | 24192352 |
| comparative analysis of barophily-related amino acid content in protein domains of pyrococcus abyssi and pyrococcus furiosus. | amino acid substitution patterns between the nonbarophilic pyrococcus furiosus and its barophilic relative p. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environme ... | 2013 | 24187517 |
| outside-in assembly pathway of the type iv pilus system in myxococcus xanthus. | type iv pili (t4p) are ubiquitous bacterial cell surface structures that undergo cycles of extension, adhesion, and retraction. t4p function depends on a highly conserved envelope-spanning macromolecular machinery consisting of 10 proteins that localizes polarly in myxococcus xanthus. using this localization, we investigated the entire t4p machinery assembly pathway by systematically profiling the stability of all and the localization of eight of these proteins in the absence of other t4p machin ... | 2014 | 24187092 |
| ultradeep pyrosequencing and molecular modeling identify key structural features of hepatitis b virus rnase h, a putative target for antiviral intervention. | last-generation nucleoside/nucleotide analogues are potent against hepatitis b virus (hbv) and have a high barrier to resistance. however, delayed responses have been observed in patients previously exposed to other drugs of the same class, long-term resistance is possible, and cure of infection cannot be achieved with these therapies, emphasizing the need for alternative therapeutic approaches. the hbv rnase h represents an interesting target because its enzyme activity is essential to the hbv ... | 2014 | 24173223 |
| biophysical characterization of a recombinant aminopeptidase ii from the thermophilic bacterium bacillus stearothermophilus. | in the present study, the biophysical properties of his6-tagged bacillus stearothermophilus aminopeptidase ii (his6-tagged bsampii) are characterized in detail by gel-filtration, analytical ultracentrifugation, and various spectroscopic techniques. using size-exclusion chromatography and analytical ultracentrifugation, we demonstrate that his6-tagged bsampii exists predominantly as a dimer in solution. the enzyme is active and stable at phs ranging from 6.5 to 8.5. far-uv circular dichroism anal ... | 2013 | 24165863 |
| biophysical characterization of a recombinant aminopeptidase ii from the thermophilic bacterium bacillus stearothermophilus. | in the present study, the biophysical properties of his6-tagged bacillus stearothermophilus aminopeptidase ii (his6-tagged bsampii) are characterized in detail by gel-filtration, analytical ultracentrifugation, and various spectroscopic techniques. using size-exclusion chromatography and analytical ultracentrifugation, we demonstrate that his6-tagged bsampii exists predominantly as a dimer in solution. the enzyme is active and stable at phs ranging from 6.5 to 8.5. far-uv circular dichroism anal ... | 2013 | 24165863 |
| translational regulation of yersinia enterocolitica mrna encoding a type iii secretion substrate. | yersinia enterocolitica type iii secretion machines transport yopq and other yop effectors into host immune cells. yopd and its chaperone lcrh are essential components of the yersinia type iii pathway, enabling effector translocation into host cells. yopd, lcrh, and yscm1 also regulate yop expression post-transcriptionally in response to environmental signals; however, the molecular mechanisms for this regulation and yop secretion are unknown. we show here that yopd associates with 30 s ribosoma ... | 2013 | 24158443 |
| metagenomic approach for the isolation of a thermostable β-galactosidase with high tolerance of galactose and glucose from soil samples of turpan basin. | β-galactosidases can be used to produce low-lactose milk and dairy products for lactose intolerant people. although commercial β-galactosidases have outstanding lactose hydrolysis ability, their thermostability is low, and reaction products have strong inhibition to these enzymes. in addition, the β-galactosidases possessing simultaneously high thermostability and tolerance of galactose and glucose are still seldom reported until now. therefore, identification of novel β-galactosidases with high ... | 2013 | 24156692 |
| iodotyrosine deiodinase: a unique flavoprotein present in organisms of diverse phyla. | iodide is required for thyroid hormone synthesis in mammals and other vertebrates. the role of both iodide and iodinated tyrosine derivatives is currently unknown in lower organisms, yet the presence of a key enzyme in iodide conservation, iodotyrosine deiodinase (iyd), is suggested by genomic data from a wide range of multicellular organisms as well as some bacteria. a representative set of these genes has now been expressed, and the resulting enzymes all catalyze reductive deiodination of diio ... | 2014 | 24153409 |
| structure of the secy channel during initiation of protein translocation. | many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic secy or eukaryotic sec61 complexes, and are translocated across the membrane during their synthesis. crystal structures of the inactive channel show that the secy subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. the closed channel has an empty ... | 2013 | 24153188 |
| structure of the secy channel during initiation of protein translocation. | many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic secy or eukaryotic sec61 complexes, and are translocated across the membrane during their synthesis. crystal structures of the inactive channel show that the secy subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. the closed channel has an empty ... | 2013 | 24153188 |
| the central role of protein s12 in organizing the structure of the decoding site of the ribosome. | the ribosome decodes mrna by monitoring the geometry of codon-anticodon base-pairing using a set of universally conserved 16s rrna nucleotides within the conformationally dynamic decoding site. by applying single-molecule fret and x-ray crystallography, we have determined that conditional-lethal, streptomycin-dependence mutations in ribosomal protein s12 interfere with trna selection by allowing conformational distortions of the decoding site that impair gtpase activation of ef-tu during the trn ... | 2013 | 24152548 |
| a comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly. | assembly of the ribosome from its protein and rna constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. since the early 1960's, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear.we utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembl ... | 2013 | 24152303 |
| evolution of crispr rna recognition and processing by cas6 endonucleases. | in many bacteria and archaea, small rnas derived from clustered regularly interspaced short palindromic repeats (crisprs) associate with crispr-associated (cas) proteins to target foreign dna for destruction. in type i and iii crispr/cas systems, the cas6 family of endoribonucleases generates functional crispr-derived rnas by site-specific cleavage of repeat sequences in precursor transcripts. crispr repeats differ widely in both sequence and structure, with varying propensity to form hairpin fo ... | 2013 | 24150936 |
| evolution of crispr rna recognition and processing by cas6 endonucleases. | in many bacteria and archaea, small rnas derived from clustered regularly interspaced short palindromic repeats (crisprs) associate with crispr-associated (cas) proteins to target foreign dna for destruction. in type i and iii crispr/cas systems, the cas6 family of endoribonucleases generates functional crispr-derived rnas by site-specific cleavage of repeat sequences in precursor transcripts. crispr repeats differ widely in both sequence and structure, with varying propensity to form hairpin fo ... | 2013 | 24150936 |
| type i pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines. | pyridoxal 5'-phosphate (plp)-dependent enzymes of fold type i, the most studied structural class of the plp-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. these enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (pks) and nonribosomal peptides (nrps). the aim of this work is to provide a proteome-wide view of the distribution and characteristics of type i domains covalently ... | 2013 | 24148833 |
| identification and characterization of a novel trehalose synthase gene derived from saline-alkali soil metagenomes. | a novel trehalose synthase (tres) gene was identified from a metagenomic library of saline-alkali soil by a simple activity-based screening system. sequence analysis revealed that tres encodes a protein of 552 amino acids, with a deduced molecular weight of 63.3 kda. after being overexpressed in escherichia coli and purified, the enzymatic properties of tres were investigated. the recombinant tres displayed its optimal activity at ph 9.0 and 45 °c, and the addition of most common metal ions (1 o ... | 2013 | 24146994 |
| clostridium difficile glutamate dehydrogenase is a secreted enzyme that confers resistance to h2o2. | clostridium difficile produces an nad-specific glutamate dehydrogenase (gdh), which converts l-glutamate into α-ketoglutarate through an irreversible reaction. the enzyme gdh is detected in the stool samples of patients with c. difficile-associated disease and serves as one of the diagnostic tools to detect c. difficile infection (cdi). we demonstrate here that supernatant fluids of c. difficile cultures contain gdh. to understand the role of gdh in the physiology of c. difficile, an isogenic in ... | 2014 | 24145018 |
| transferable denitrification capability of thermus thermophilus. | laboratory-adapted strains of thermus spp. have been shown to require oxygen for growth, including the model strains t. thermophilus hb27 and hb8. in contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. the use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. in this process, nit ... | 2014 | 24141123 |
| temperature dependence of the dna double helix at the nanoscale: structure, elasticity, and fluctuations. | biological organisms exist over a broad temperature range of -15°c to +120°c, where many molecular processes involving dna depend on the nanoscale properties of the double helix. here, we present results of extensive molecular dynamics simulations of dna oligomers at different temperatures. we show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of t ... | 2013 | 24138866 |
| a novel type of n-acetylglutamate synthase is involved in the first step of arginine biosynthesis in corynebacterium glutamicum. | arginine biosynthesis in corynebacterium glutamicum consists of eight enzymatic steps, starting with acetylation of glutamate, catalysed by n-acetylglutamate synthase (nags). there are different kinds of known nagss, for example, "classical" arga, bifunctional argj, argo, and s-nags. however, since c. glutamicum possesses a monofunctional argj, which catalyses only the fifth step of the arginine biosynthesis pathway, glutamate must be acetylated by an as of yet unknown nags gene. | 2013 | 24138314 |
| visualization of the joining of ribosomal subunits reveals the presence of 80s ribosomes in the nucleus. | in eukaryotes the 40s and 60s ribosomal subunits are assembled in the nucleolus, but there appear to be mechanisms preventing mrna binding, 80s formation, and initiation of translation in the nucleus. to visualize association between ribosomal subunits, we tagged pairs of drosophila ribosomal proteins (rps) located in different subunits with mutually complementing halves of fluorescent proteins. pairs of tagged rps expected to interact, or be adjacent in the 80s structure, showed strong fluoresc ... | 2013 | 24129492 |
| staphylococcus epidermidis csm1 is a 3'-5' exonuclease. | clustered regularly interspaced short palindromic repeats (crispr) offer an adaptive immune system that protects bacteria and archaea from nucleic acid invaders through an rna-mediated nucleic acid cleavage mechanism. our knowledge of nucleic acid cleavage mechanisms is limited to three examples of widely different ribonucleoprotein particles that target either dna or rna. staphylococcus epidermidis belongs to the type iii-a crispr system and has been shown to interfere with invading dna in vivo ... | 2013 | 24121684 |
| staphylococcus epidermidis csm1 is a 3'-5' exonuclease. | clustered regularly interspaced short palindromic repeats (crispr) offer an adaptive immune system that protects bacteria and archaea from nucleic acid invaders through an rna-mediated nucleic acid cleavage mechanism. our knowledge of nucleic acid cleavage mechanisms is limited to three examples of widely different ribonucleoprotein particles that target either dna or rna. staphylococcus epidermidis belongs to the type iii-a crispr system and has been shown to interfere with invading dna in vivo ... | 2013 | 24121684 |
| conformational and thermodynamic hallmarks of dna operator site specificity in the copper sensitive operon repressor from streptomyces lividans. | metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. the copper sensitive operon repressor (csor) family is widely distributed in bacteria and controls the expression of copper efflux systems. csor operator sites consist of g-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. here, we use a structurally characterized csor from streptomyces li ... | 2013 | 24121681 |
| conformational and thermodynamic hallmarks of dna operator site specificity in the copper sensitive operon repressor from streptomyces lividans. | metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. the copper sensitive operon repressor (csor) family is widely distributed in bacteria and controls the expression of copper efflux systems. csor operator sites consist of g-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. here, we use a structurally characterized csor from streptomyces li ... | 2013 | 24121681 |
| structure of the homodimeric glycine decarboxylase p-protein from synechocystis sp. pcc 6803 suggests a mechanism for redox regulation. | glycine decarboxylase, or p-protein, is a pyridoxal 5'-phosphate (plp)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. p-protein from the cyanobacterium synechocystis sp. pcc 6803 is an α2 homodimer with high homology to eukaryotic p-proteins. the crystal structure of the apoenzyme shows the c terminus locked in a closed conformation by a disulfide bond between cys(972) i ... | 2013 | 24121504 |
| structure and activity of the rna-targeting type iii-b crispr-cas complex of thermus thermophilus. | the crispr-cas system is a prokaryotic host defense system against genetic elements. the type iii-b crispr-cas system of the bacterium thermus thermophilus, the ttcmr complex, is composed of six different protein subunits (cmr1-6) and one crrna with a stoichiometry of cmr112131445361:crrna1. the ttcmr complex copurifies with crrna species of 40 and 46 nt, originating from a distinct subset of crispr loci and spacers. the ttcmr complex cleaves the target rna at multiple sites with 6 nt intervals ... | 2013 | 24119403 |
| minimal mechanistic model of sirna-dependent target rna slicing by recombinant human argonaute 2 protein. | argonaute (ago) proteins are the key component of the rna-induced silencing complex and mediate rna interference (rnai) in association with small rnas. although overall the mechanism of rnai is well understood, many molecular details of this complex process are not. here we report about in-depth steady-state and, in particular, pre-steady-state characterization of sirna binding, target rna recognition, sequence-specific cleavage and product release by recombinant human ago 2 (hago2). in combinin ... | 2013 | 24101500 |
| crystallization and preliminary crystallographic analysis of ganb, a gh42 intracellular β-galactosidase from geobacillus stearothermophilus. | geobacillus stearothermophilus t-6 is a gram-positive thermophilic soil bacterium that contains a multi-enzyme system for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. the bacterium uses a number of endo-acting extracellular enzymes that break down the high-molecular-weight polysaccharides into decorated oligosaccharides. these oligosaccharides enter the cell and are further hydrolyzed into sugar monomers by a set of intracellular glycoside hydrolase ... | 2013 | 24100561 |
| functional role of methylation of g518 of the 16s rrna 530 loop by gidb in mycobacterium tuberculosis. | posttranscriptional modifications of bacterial rrna serve a variety of purposes, from stabilizing ribosome structure to preserving its functional integrity. here, we investigated the functional role of one rrna modification in particular-the methylation of guanosine at position 518 (g518) of the 16s rrna in mycobacterium tuberculosis. based on previously reported evidence that g518 is located 5 å; from proline 44 of ribosomal protein s12, which interacts directly with the mrna wobble position of ... | 2013 | 24100503 |
| intra- and intermolecular regulatory interactions in upf1, the rna helicase central to nonsense-mediated mrna decay in yeast. | rna helicases are involved in almost every aspect of rna metabolism, yet very little is known about the regulation of this class of enzymes. in saccharomyces cerevisiae, the stability and translational fidelity of nonsense-containing mrnas are controlled by the group i rna helicase upf1 and the proteins it interacts with, upf2 and upf3. combining the yeast two-hybrid system with genetic analysis, we show here that the cysteine- and histidine-rich (ch) domain and the rna helicase domain of yeast ... | 2013 | 24100012 |
| construction of an in vitro bypassed pyruvate decarboxylation pathway using thermostable enzyme modules and its application to n-acetylglutamate production. | metabolic engineering has emerged as a practical alternative to conventional chemical conversion particularly in biocommodity production processes. however, this approach is often hampered by as yet unidentified inherent mechanisms of natural metabolism. one of the possible solutions for the elimination of the negative effects of natural regulatory mechanisms on artificially engineered metabolic pathway is to construct an in vitro pathway using a limited number of enzymes. employment of thermost ... | 2013 | 24099461 |
| thermal adaptation of conformational dynamics in ribonuclease h. | the relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. the study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conformational dynamics. in particular, ribonuclease hi (rnase h), an 18 kd globular protein that hydrolyzes the rna strand of rna:dna hybrid substrates, has been extensively studied by ... | 2013 | 24098095 |
| archaeal ubiquitin-like samp3 is isopeptide-linked to proteins via a ubaa-dependent mechanism. | samp1 and samp2 are ubiquitin-like proteins that function as protein modifiers and are required for the production of sulfur-containing biomolecules in the archaeon haloferax volcanii. here we report a novel small archaeal modifier protein (named samp3) with a β-grasp fold and c-terminal diglycine motif characteristic of ubiquitin that is functional in protein conjugation in hfx. volcanii. samp3 conjugates were dependent on the ubiquitin-activating e1 enzyme homolog of archaea (ubaa) for synthes ... | 2013 | 24097257 |
| archaeal ubiquitin-like samp3 is isopeptide-linked to proteins via a ubaa-dependent mechanism. | samp1 and samp2 are ubiquitin-like proteins that function as protein modifiers and are required for the production of sulfur-containing biomolecules in the archaeon haloferax volcanii. here we report a novel small archaeal modifier protein (named samp3) with a β-grasp fold and c-terminal diglycine motif characteristic of ubiquitin that is functional in protein conjugation in hfx. volcanii. samp3 conjugates were dependent on the ubiquitin-activating e1 enzyme homolog of archaea (ubaa) for synthes ... | 2013 | 24097257 |
| crystal structure of human seryl-trna synthetase and ser-sa complex reveals a molecular lever specific to higher eukaryotes. | seryl-trna synthetase (serrs), an essential enzyme for translation, also regulates vascular development. this "gain-of-function" has been linked to the une-s domain added to vertebrate serrs during evolution. however, the significance of two insertions also specific to higher eukaryotic serrs remains elusive. here, we determined the crystal structure of human serrs in complex with ser-sa, an aminoacylation reaction intermediate analog, at 2.9 å resolution. despite a 70 å distance, binding of ser ... | 2013 | 24095058 |
| the role of the mitochondrial ribosome in human disease: searching for mutations in 12s mitochondrial rrna with high disruptive potential. | mutations of mitochondrial dna are linked to many human diseases. despite the identification of a large number of variants in the mitochondrially encoded rrna (mt-rrna) genes, the evidence supporting their pathogenicity is, at best, circumstantial. establishing the pathogenicity of these variations is of major diagnostic importance. here, we aim to estimate the disruptive effect of mt-rrna variations on the function of the mitochondrial ribosome. in the absence of direct biochemical methods to s ... | 2013 | 24092330 |
| the role of the mitochondrial ribosome in human disease: searching for mutations in 12s mitochondrial rrna with high disruptive potential. | mutations of mitochondrial dna are linked to many human diseases. despite the identification of a large number of variants in the mitochondrially encoded rrna (mt-rrna) genes, the evidence supporting their pathogenicity is, at best, circumstantial. establishing the pathogenicity of these variations is of major diagnostic importance. here, we aim to estimate the disruptive effect of mt-rrna variations on the function of the mitochondrial ribosome. in the absence of direct biochemical methods to s ... | 2013 | 24092330 |
| ndufaf7 methylates arginine 85 in the ndufs2 subunit of human complex i. | complex i (nadh ubiquinone oxidoreductase) in mammalian mitochondria is an l-shaped assembly of 44 subunits. one arm is embedded in the inner membrane with the other protruding ∼100 å into the matrix of the organelle. the extrinsic arm contains binding sites for nadh and the primary electron acceptor fmn, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking fmn to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction b ... | 2013 | 24089531 |
| basic properties of rotary dynamics of the molecular motor enterococcus hirae v1-atpase. | v-atpases are rotary molecular motors that generally function as proton pumps. we recently solved the crystal structures of the v1 moiety of enterococcus hirae v-atpase (ehv1) and proposed a model for its rotation mechanism. here, we characterized the rotary dynamics of ehv1 using single-molecule analysis employing a load-free probe. ehv1 rotated in a counterclockwise direction, exhibiting two distinct rotational states, namely clear and unclear, suggesting unstable interactions between the roto ... | 2013 | 24089518 |
| interplay between the trigger loop and the f loop during rna polymerase catalysis. | the trigger loop (tl) in the rna polymerase (rnap) active center plays key roles in the reactions of nucleotide addition and rna cleavage catalyzed by rnap. the adjacent f loop (fl) was proposed to contribute to rnap catalysis by modulating structural changes in the tl. here, we investigate the interplay between these two elements during transcription by bacterial rnap. thermodynamic analysis of catalysis by rnap variants with mutations in the tl and fl suggests that the tl is the key element re ... | 2013 | 24089145 |
| interplay between the trigger loop and the f loop during rna polymerase catalysis. | the trigger loop (tl) in the rna polymerase (rnap) active center plays key roles in the reactions of nucleotide addition and rna cleavage catalyzed by rnap. the adjacent f loop (fl) was proposed to contribute to rnap catalysis by modulating structural changes in the tl. here, we investigate the interplay between these two elements during transcription by bacterial rnap. thermodynamic analysis of catalysis by rnap variants with mutations in the tl and fl suggests that the tl is the key element re ... | 2013 | 24089145 |
| the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation. | full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ... | 2013 | 24084083 |
| the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation. | full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ... | 2013 | 24084083 |
| menaquinone biosynthesis: formation of aminofutalosine requires a unique radical sam enzyme. | menaquinone (mk, vitamin k2) is a lipid-soluble molecule that participates in the bacterial electron transport chain. in mammalian cells, mk functions as an essential vitamin for the activation of various proteins involved in blood clotting and bone metabolism. recently, a new pathway for the biosynthesis of this cofactor was discovered in streptomyces coelicolor a3(2) in which chorismate is converted to aminofutalosine in a reaction catalyzed by mqna and an unidentified enzyme. here, we reconst ... | 2013 | 24083939 |
| protein folding on the ribosome studied using nmr spectroscopy. | nmr spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. in recent years nmr methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. des ... | 2013 | 24083462 |
| fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome. | determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. ... | 2013 | 24081579 |
| fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome. | determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. ... | 2013 | 24081579 |
| mechanisms of eukaryotic transcription. | a report on the cold spring harbor laboratory mechanisms of eukaryotic transcription meeting, cold spring harbor, new york, usa, august 27–31, 2013. | 2013 | 24079829 |
| archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in sulfolobus acidocaldarius. | in this study, the in vitro and in vivo functions of the only two identified protein phosphatases, saci-ptp and saci-pp2a, in the crenarchaeal model organism sulfolobus acidocaldarius were investigated. biochemical characterization revealed that saci-ptp is a dual-specific phosphatase (against pser/pthr and ptyr), whereas saci-pp2a exhibited specific pser/pthr activity and inhibition by okadaic acid. deletion of saci_pp2a resulted in pronounced alterations in growth, cell shape and cell size, wh ... | 2013 | 24078887 |
| subunit positioning and stator filament stiffness in regulation and power transmission in the v1 motor of the manduca sexta v-atpase. | the vacuolar h(+)-atpase (v-atpase) is an atp-driven proton pump essential to the function of eukaryotic cells. its cytoplasmic v1 domain is an atpase, normally coupled to membrane-bound proton pump vo via a rotary mechanism. how these asymmetric motors are coupled remains poorly understood. low energy status can trigger release of v1 from the membrane and curtail atp hydrolysis. to investigate the molecular basis for these processes, we have carried out cryo-electron microscopy three-dimensiona ... | 2014 | 24075871 |
| structural, biochemical and genetic characterization of dissimilatory atp sulfurylase from allochromatium vinosum. | atp sulfurylase (atps) catalyzes a key reaction in the global sulfur cycle by reversibly converting inorganic sulfate (so4 (2-)) with atp to adenosine 5'-phosphosulfate (aps) and pyrophosphate (ppi). in this work we report on the sat encoded dissimilatory atp sulfurylase from the sulfur-oxidizing purple sulfur bacterium allochromatium vinosum. in this organism, the sat gene is located in one operon and co-transcribed with the aprmba genes for membrane-bound aps reductase. like aps reductase, sat ... | 2013 | 24073218 |