Publications

TitleAbstractYear
Filter
PMID(sorted ascending)
Filter
recent progress in bacillus subtilis sporulation.the gram-positive bacterium bacillus subtilis can initiate the process of sporulation under conditions of nutrient limitation. here, we review some of the last 5 years of work in this area, with a particular focus on the decision to initiate sporulation, dna translocation, cell-cell communication, protein localization and spore morphogenesis. the progress we describe has implications not only just for the study of sporulation but also for other biological systems where homologs of sporulation-sp ...201222091839
High-resolution structure of shikimate dehydrogenase from Thermotoga maritima reveals a tightly closed conformation.Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Structural analysis of a SDH from Thermotoga maritima encoded by the Tm0346 gene was performed to facilitate further structural comparisons between the various shikimate dehydrogenases. The crystal structure of SDH from T. maritima was determined at 1.45 SDH from T. maritima sh ...201122095087
High-resolution structure of shikimate dehydrogenase from Thermotoga maritima reveals a tightly closed conformation.Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Structural analysis of a SDH from Thermotoga maritima encoded by the Tm0346 gene was performed to facilitate further structural comparisons between the various shikimate dehydrogenases. The crystal structure of SDH from T. maritima was determined at 1.45 SDH from T. maritima sh ...201122095087
estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry.for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ...201122101334
estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry.for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ...201122101334
expression, purification, crystallization and preliminary x-ray analysis of ecgp123, an extremely stable monomeric green fluorescent protein with reversible photoswitching properties.enhanced consensus green protein variant 123 (ecgp123) is an extremely thermostable green fluorescent protein (gfp) that exhibits useful negative reversible photoswitching properties. ecgp123 was derived by the application of both a consensus engineering approach and a recursive evolutionary process. diffraction-quality crystals of recombinant ecgp123 were obtained by the hanging-drop vapour-diffusion method using peg 3350 as the precipitant. the ecgp123 crystal diffracted x-rays to 2.10 å resol ...201122102044
crystallization and preliminary x-ray diffraction of the first periplasmic domain of secdf, a translocon-associated membrane protein, from thermus thermophilus.a membrane-integrated sec component, secdf, associates with the secyeg protein-conducting channel and facilitates protein secretion and membrane-protein integration. secdf contains 12 transmembrane helices and two periplasmic domains. the first periplasmic domain (p1) plays an important role in protein translocation. here, the overexpression, purification and crystallization of the p1 domain of thermus thermophilus secdf are reported. the crystals diffracted x-rays to 2.3 å resolution and belong ...201122102233
Crystallization and preliminary X-ray crystallographic analysis of putative tRNA-modification enzymes from Pyrococcus furiosus and Thermus thermophilus.Methyltransferases form a major class of tRNA-modifying enzymes that are needed for the proper functioning of tRNA. Here, the expression, purification and crystallization of two related putative tRNA methyltransferases from two kingdoms of life are reported. The protein encoded by the gene pf1002 from the archaeon Pyrococcus furiosus was crystallized in the monoclinic space group P2(1). A complete data set was collected to 2.2 Å resolution. The protein encoded by the gene ttc1157 from the eubact ...201122102250
Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs.The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ...201122105070
Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs.The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ...201122105070
crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces pombe.homoisocitrate dehydrogenase (hicdh) catalyzes the conversion of homoisocitrate to 2-oxoadipate, the third enzymatic step in the α-aminoadipate pathway by which lysine is synthesized in fungi and certain archaebacteria. this enzyme represents a potential target for anti-fungal drug design. here, we describe the first crystal structures of a fungal hicdh, including structures of an apoenzyme and a binary complex with a glycine tri-peptide. the structures illustrate the homology of hicdh with othe ...201122105743
crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces pombe.homoisocitrate dehydrogenase (hicdh) catalyzes the conversion of homoisocitrate to 2-oxoadipate, the third enzymatic step in the α-aminoadipate pathway by which lysine is synthesized in fungi and certain archaebacteria. this enzyme represents a potential target for anti-fungal drug design. here, we describe the first crystal structures of a fungal hicdh, including structures of an apoenzyme and a binary complex with a glycine tri-peptide. the structures illustrate the homology of hicdh with othe ...201122105743
terpene biosynthesis: modularity rules.terpenes are the largest class of small-molecule natural products on earth, and the most abundant by mass. here, we summarize recent developments in elucidating the structure and function of the proteins involved in their biosynthesis. there are six main building blocks or modules (α, β, γ, δ, ε, and ζ) that make up the structures of these enzymes: the αα and αδ head-to-tail trans-prenyl transferases that produce trans-isoprenoid diphosphates from c(5) precursors; the ε head-to-head prenyl trans ...201122105807
terpene biosynthesis: modularity rules.terpenes are the largest class of small-molecule natural products on earth, and the most abundant by mass. here, we summarize recent developments in elucidating the structure and function of the proteins involved in their biosynthesis. there are six main building blocks or modules (α, β, γ, δ, ε, and ζ) that make up the structures of these enzymes: the αα and αδ head-to-tail trans-prenyl transferases that produce trans-isoprenoid diphosphates from c(5) precursors; the ε head-to-head prenyl trans ...201122105807
francisella rna polymerase contains a heterodimer of non-identical alpha subunits.abstract: background: all sequenced genomes of representatives of the francisella genus contain two rpoa genes, which encode non-identical rna polymerase (rnap) subunits, alpha1 and alpha2. in all other bacteria studied to date, a dimer of identical alpha subunits initiates the assembly of the catalytically proficient rnap core (subunit composition (alpha)2/beta/beta'). based on an observation that both alpha1 and alpha2 are incorporated into francisella rnap, charity et al. (2007) previously s ...201122108176
crystal structure of the central axis df complex of the prokaryotic v-atpase.v-atpases function as atp-dependent ion pumps in various membrane systems of living organisms. atp hydrolysis causes rotation of the central rotor complex, which is composed of the central axis d subunit and a membrane c ring that are connected by f and d subunits. here we determined the crystal structure of the df complex of the prokaryotic v-atpase of enterococcus hirae at 2.0-å resolution. the structure of the d subunit comprised a long left-handed coiled coil with a unique short β-hairpin re ...201122114184
sequence of the hyperplastic genome of the naturally competent thermus scotoductus sa-01.many strains of thermus have been isolated from hot environments around the world. thermus scotoductus sa-01 was isolated from fissure water collected 3.2 km below surface in a south african gold mine. the isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. the genomes from two different thermus thermophilus strains have been com ...201122115438
Trimming down a protein structure to its bare foldons: spatial organisation of the cooperative unit.Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, save the edge strand ß2, which is consistently missing in the folding transition states: despite being part of the S6 four-stranded sheet, ß2 seems not to be part of the protein's cooperative unit. The question is then if ß2 can be removed from the S6 structure without compromising folding cooperativity or ...201122117065
Trimming down a protein structure to its bare foldons: spatial organisation of the cooperative unit.Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, save the edge strand ß2, which is consistently missing in the folding transition states: despite being part of the S6 four-stranded sheet, ß2 seems not to be part of the protein's cooperative unit. The question is then if ß2 can be removed from the S6 structure without compromising folding cooperativity or ...201122117065
Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized.In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ...201122122402
Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized.In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ...201122122402
Molecular basis of dihydrouridine formation on tRNA.Dihydrouridine (D) is a highly conserved modified base found in tRNAs from all domains of life. Dihydrouridine synthase (Dus) catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of Thermus thermophilus Dus (TthDus), which is responsible for D formation at positions 20 and 20a, in complex with tRNA and with a short fragment of tRNA (D-loop). Dus interacts extensively with the D-arm and recognizes ...201122123979
effects of pressure and temperature on the binding of reca protein to single-stranded dna.the binding and polymerization of reca protein to dna is required for recombination, which is an essential function of life. we study the pressure and temperature dependence of reca binding to single-stranded dna in the presence of adenosine 5'-[γ-thio]triphosphate (atp[γ-s]), in a temperature regulated high pressure cell using fluorescence anisotropy. measurements were possible at temperatures between 5-60 °c and pressures up to 300 mpa. experiments were performed on escherichia coli reca and r ...201122123983
genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere.prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet earth with human beings (among others). however, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. an understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. the vast majorit ...201122126996
directed molecular evolution to design advanced red fluorescent proteins.fluorescent proteins have become indispensable imaging tools for biomedical research. continuing progress in fluorescence imaging, however, requires probes with additional colors and properties optimized for emerging techniques. here we summarize strategies for development of red-shifted fluorescent proteins. we discuss possibilities for knowledge-based rational design based on the photochemistry of fluorescent proteins and the position of the chromophore in protein structure. we consider advanc ...201122127219
the pfam protein families database.pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. pfam is available via servers in the uk (http://pfam.sanger.ac.uk/), the usa (http://pfam.janelia.org/) and sweden (http://pfam.sbc.su.se/). here, we report on changes that have occurred since our 2010 nar paper (release 24.0). over the last 2 years, we have generated 1840 new families and increased coverage of the uniprot knowledgebase (uniprotkb) to ne ...201122127870
the pfam protein families database.pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. pfam is available via servers in the uk (http://pfam.sanger.ac.uk/), the usa (http://pfam.janelia.org/) and sweden (http://pfam.sbc.su.se/). here, we report on changes that have occurred since our 2010 nar paper (release 24.0). over the last 2 years, we have generated 1840 new families and increased coverage of the uniprot knowledgebase (uniprotkb) to ne ...201122127870
substrate specificity of bacterial prolyl-trna synthetase editing domain is controlled by a tunable hydrophobic pocket.aminoacyl-trna synthetases catalyze the covalent attachment of amino acids onto their cognate trnas. high fidelity in this reaction is crucial to the accurate decoding of genetic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-trnas. prolyl-trna synthetases (prors) mischarge trna(pro) with alanine or cysteine due to their smaller or similar sizes relative to cognate proline. mischarged ala-trna(pro) is hydrolyzed by an editing domain (ins) present in most ...201122128149
substrate specificity of bacterial prolyl-trna synthetase editing domain is controlled by a tunable hydrophobic pocket.aminoacyl-trna synthetases catalyze the covalent attachment of amino acids onto their cognate trnas. high fidelity in this reaction is crucial to the accurate decoding of genetic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-trnas. prolyl-trna synthetases (prors) mischarge trna(pro) with alanine or cysteine due to their smaller or similar sizes relative to cognate proline. mischarged ala-trna(pro) is hydrolyzed by an editing domain (ins) present in most ...201122128149
Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P).Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ...201122128152
Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P).Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ...201122128152
crystal structure of human β-galactosidase: the structural basis of gm1 gangliosidosis and morquio b diseases.gm1 gangliosidosis and morquio b are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. these diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-gal), which lead to accumulations of the β-gal substrates, gm1 ganglioside and keratan sulfate. β-gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. the present study shows the crystal ...201122128166
crystal structure of human β-galactosidase: the structural basis of gm1 gangliosidosis and morquio b diseases.gm1 gangliosidosis and morquio b are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. these diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-gal), which lead to accumulations of the β-gal substrates, gm1 ganglioside and keratan sulfate. β-gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. the present study shows the crystal ...201122128166
Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase.The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ...201122128181
Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase.The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ...201122128181
mmdb: 3d structures and macromolecular interactions.close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3d) structure by standard sequence similarity searches. potentially, a great deal can be learned about proteins or protein families of interest from considering 3d structure, and to this day 3d structure data may remain an underutilized resource. here we present enhancements in the molecular modeling database (mmdb) and its data presentation, specifically pertaining to biologically re ...201122135289
mmdb: 3d structures and macromolecular interactions.close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3d) structure by standard sequence similarity searches. potentially, a great deal can be learned about proteins or protein families of interest from considering 3d structure, and to this day 3d structure data may remain an underutilized resource. here we present enhancements in the molecular modeling database (mmdb) and its data presentation, specifically pertaining to biologically re ...201122135289
crystal structure of the bacteriophage t4 late-transcription coactivator gp33 with the β-subunit flap domain of escherichia coli rna polymerase.activated transcription of the bacteriophage t4 late genes, which is coupled to concurrent dna replication, is accomplished by an initiation complex containing the host rna polymerase associated with two phage-encoded proteins, gp55 (the basal promoter specificity factor) and gp33 (the coactivator), as well as the dna-mounted sliding-clamp processivity factor of the phage t4 replisome (gp45, the activator). we have determined the 3.0 å-resolution x-ray crystal structure of gp33 complexed with it ...201122135460
The rate-limiting step in O(2) reduction by cytochrome ba(3) from Thermus thermophilus.Cytochrome ba(3) (ba(3)) of Thermus thermophilus (T. thermophilus) is a member of the heme-copper oxidase family, which has a binuclear catalytic center comprised of a heme (heme a(3)) and a copper (Cu(B)). The heme-copper oxidases generally catalyze the four electron reduction of molecular oxygen in a sequence involving several intermediates. We have investigated the reaction of the fully reduced ba(3) with O(2) using stopped-flow techniques. Transient visible absorption spectra indicated that ...201122138627
Overexpression, crystallization and preliminary X-ray crystallographic analysis of shikimate dehydrogenase from Archaeoglobus fulgidus.Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Previous structural studies have shown that SDH exists in two conformations, an open and a closed form, and it is believed that the conformational state is crucial to understanding its catalytic mechanism. In order to facilitate further structural comparisons among SDHs, includ ...201122139165
crystallization and preliminary crystallographic analysis of a putative glucokinase/hexokinase from thermus thermophilus.glucokinase/hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate, which is the first step of glycolysis. the open reading frame ttha0299 of the extreme thermophile thermus thermophilus encodes a putative glucokinase/hexokinase which contains the consensus sequence for proteins from the repressors, open reading frames and sugar kinases family. in this study, the glucokinase/hexokinase from t. thermophilus was purified and crystallized using polyethylene glycol 8000 as a prec ...201122139166
thermostable multicopper oxidase from thermus thermophilus hb27: crystallization and preliminary x-ray diffraction analysis of apo and holo forms.a thermostable multicopper oxidase from thermus thermophilus hb27 (tth-mco) was successfully crystallized using the sitting-drop and hanging-drop vapour-diffusion methods. crystallization conditions and preliminary x-ray diffraction data to 1.5 å resolution obtained using synchrotron radiation at 100 k are reported. the crystals belonged to space group c222(1), with unit-cell parameters a = 93.6, b = 110.3, c = 96.3 å. a monomer in the asymmetric unit yielded a matthews coefficient (v(m)) of 2.6 ...201122139175
seleno-detergent mad phasing of leukotriene c4 synthase in complex with dodecyl-β-d-selenomaltoside.dodecyl-β-d-selenomaltoside (seddm) is a seleno-detergent with a β-glycosidic seleno-ether in place of the ether moiety in dodecyl-β-d-maltoside. seleno-detergents are candidates for heavy-atom agents in experimental phasing of membrane proteins in protein crystallography. crystals of a nuclear membrane-embedded enzyme, leukotriene c(4) synthase (ltc(4)s), in complex with seddm were prepared and a multiwavelength anomalous diffraction (mad) experiment was performed. the seddm in the ltc(4)s crys ...201122139193
proline utilization by bacillus subtilis: uptake and catabolism.l-proline can be used by bacillus subtilis as a sole source of carbon or nitrogen. we traced l-proline utilization genetically to the putbcp (ycgmno) locus. the putbcp gene cluster encodes a high-affinity proline transporter (putp) and two enzymes, the proline dehydrogenase putb and the δ(1)-pyrroline-5-carboxylate dehydrogenase putc, which jointly catabolize l-proline to l-glutamate. northern blotting, primer extension, and putb-trea reporter gene fusion analysis showed that the putbcp locus is ...201122139509
epr-endor characterization of (17o, 1h, 2h) water in manganese catalase and its relevance to the oxygen-evolving complex of photosystem ii.the synthesis of efficient water-oxidation catalysts demands insight into the only known, naturally occurring water-oxidation catalyst, the oxygen-evolving complex (oec) of photosystem ii (psii). understanding the water oxidation mechanism requires knowledge of where and when substrate water binds to the oec. mn catalase in its mn(iii)-mn(iv) state is a protein model of the oec's s(2) state. from (17)o-labeled water exchanged into the di-μ-oxo di-mn(iii,iv) coordination sphere of mn catalase, cw ...201222142421
structural and functional insights into the dna replication factor cdc45 reveal an evolutionary relationship to the dhh family of phosphoesterases.cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of dna replication, as well as the progression of the replication fork. with gins, cdc45 is an essential co-factor of the mcm2-7 replicative helicase complex. despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. intriguingly, whereas homologues of both gins and mcm proteins have been described in archaea, no counterpart for cdc45 is ...201122147708
structural and functional insights into the dna replication factor cdc45 reveal an evolutionary relationship to the dhh family of phosphoesterases.cdc45 is an essential protein conserved in all eukaryotes and is involved both in the initiation of dna replication, as well as the progression of the replication fork. with gins, cdc45 is an essential co-factor of the mcm2-7 replicative helicase complex. despite its importance, no detailed information is available on either the structure or the biochemistry of the protein. intriguingly, whereas homologues of both gins and mcm proteins have been described in archaea, no counterpart for cdc45 is ...201122147708
isolation and characterization of the prochlorococcus carboxysome reveal the presence of the novel shell protein csos1d.cyanobacteria, including members of the genus prochlorococcus, contain icosahedral protein microcompartments known as carboxysomes that encapsulate multiple copies of the co(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) in a thin protein shell that enhances the catalytic performance of the enzyme in part through the action of a shell-associated carbonic anhydrase. however, the exact mechanism by which compartmentation provides a catalytic advantage to the enzyme is n ...201122155772
covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.evidence for an unusual catalysis of protonation/deprotonation by a reduced flavin mononucleotide cofactor is presented for type-2 isopentenyl diphosphate isomerase (idi-2), which catalyzes isomerization of the two fundamental building blocks of isoprenoid biosynthesis, isopentenyl diphosphate and dimethylallyl diphosphate. the covalent adducts formed between irreversible mechanism-based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxiranyl-3-buten-1-yl diphosphate, and the flavin cofa ...201122158896
rational design of an evolutionary precursor of glutaminyl-trna synthetase.the specificity of most aminoacyl-trna synthetases for an amino acid and cognate trna pair evolved before the divergence of the three domains of life. glutaminyl-trna synthetase (glnrs) evolved later and is derived from the archaeal-type nondiscriminating glutamyl-trna synthetase (glurs), an enzyme with relaxed trna specificity capable of forming both glu-trna(glu) and glu-trna(gln). the archaea lack glnrs and use a specialized amidotransferase to convert glu-trna(gln) to gln-trna(gln) needed fo ...201122158897
Genomic and proteomic characterization of the large Myoviridae bacteriophage ?TMA of the extreme thermophile Thermus thermophilus.A lytic phage, designated as ?TMA, was isolated from a Japanese hot spring using Thermus thermophilus HB27 as an indicator strain. Electron microscopic examination showed that ?TMA had an icosahedral head and a contractile tail. The circular double-stranded DNA sequence of ?TMA was 151,483 bp in length, and its organization was essentially same as that of ?YS40 except that the ?TMA genome contained genes for a pair of transposase and resolvase, and a gene for a serine to asparagine substituted o ...201122164349
Activity and regulation of an archaeal DNA-alkyltransferase: a conserved protein involved in repair of DNA alkylation damage.Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA-alkyltransferases. These are proteins conserved in Eucarya, Bacteria and Archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA-alkyltransferases is inactive and in eukaryotes is rapidly directed to degradation. ...201122167184
Activity and regulation of an archaeal DNA-alkyltransferase: a conserved protein involved in repair of DNA alkylation damage.Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA-alkyltransferases. These are proteins conserved in Eucarya, Bacteria and Archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA-alkyltransferases is inactive and in eukaryotes is rapidly directed to degradation. ...201122167184
an inhibitory c-terminal region dictates the specificity of a-adding enzymes.for efficient aminoacylation, trnas carry the conserved 3'-terminal sequence c-c-a, which is synthesized by highly specific trna nucleotidyltransferases (cca-adding enzymes). in several prokaryotes, this function is accomplished by separate enzymes for cc- and a-addition. as a-adding enzymes carry an n-terminal catalytic core identical to that of cca-adding enzymes, it is unclear why their activity is restricted. here, it is shown that c-terminal deletion variants of a-adding enzymes acquire ful ...201122167803
structural comparison of trna m1a58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions.abstract: background: trna m1a58 methyltransferases (trmi) catalyze the transfer of a methyl group from s-adenosyl-l-methionine to nitrogen 1 of adenine 58 in the t-loop of trnas from all three domains of life. the m1a58 modification has been shown to be essential for cell growth in yeast and for adaptation to high temperatures in thermophilic organisms. these enzymes were shown to be active as tetramers. the crystal structures of five trmis from hyperthermophilic archaea and thermophilic or me ...201122168821
lipid recognition propensities of amino acids in membrane proteins from atomic resolution data.protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. however, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions explicitly.201122168953
mechanisms and inhibition of uracil methylating enzymes.uracil methylation is essential for survival of organisms and passage of information from generation to generation with high fidelity. two alternative uridyl methylation enzymes, flavin-dependent thymidylate synthase and folate/fad-dependent rna methyltransferase, have joined the long-known classical enzymes, thymidylate synthase and sam-dependent rna methyltransferase. these alternative enzymes differ significantly from their classical counterparts in structure, cofactor requirements and chemic ...201122172597
mechanisms and inhibition of uracil methylating enzymes.uracil methylation is essential for survival of organisms and passage of information from generation to generation with high fidelity. two alternative uridyl methylation enzymes, flavin-dependent thymidylate synthase and folate/fad-dependent rna methyltransferase, have joined the long-known classical enzymes, thymidylate synthase and sam-dependent rna methyltransferase. these alternative enzymes differ significantly from their classical counterparts in structure, cofactor requirements and chemic ...201122172597
Comparative analyses of transport proteins encoded within the genomes of Mycobacterium tuberculosis and Mycobacterium leprae.The co-emergence of multidrug resistant pathogenic bacterial strains and the HIV pandemic has made tuberculosis a leading public health threat. The causative agent is Mycobacterium tuberculosis (Mtu), a facultative intracellular parasite. Mycobacterium leprae (Mle), a related organism that causes leprosy, is an obligate intracellular parasite. Given that different transporters are required for bacterial growth and persistence under a variety of growth conditions, we conducted comparative analyse ...201122179038
Comparative analyses of transport proteins encoded within the genomes of Mycobacterium tuberculosis and Mycobacterium leprae.The co-emergence of multidrug resistant pathogenic bacterial strains and the HIV pandemic has made tuberculosis a leading public health threat. The causative agent is Mycobacterium tuberculosis (Mtu), a facultative intracellular parasite. Mycobacterium leprae (Mle), a related organism that causes leprosy, is an obligate intracellular parasite. Given that different transporters are required for bacterial growth and persistence under a variety of growth conditions, we conducted comparative analyse ...201122179038
dynamic dissociating homo-oligomers and the control of protein function.homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. this review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of th ...201122182754
dynamic dissociating homo-oligomers and the control of protein function.homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. this review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of th ...201122182754
adaptation to trna acceptor stem structure by flexible adjustment in the catalytic domain of class i trna synthetases.class i aminoacyl-trna synthetases (aarss) use a rossmann-fold domain to catalyze the synthesis of aminoacyl-trnas required for decoding genetic information. while the rossmann-fold domain is conserved in evolution, the acceptor stem near the aminoacylation site varies among trna substrates, raising the question of how the conserved protein fold adapts to rna sequence variations. of interest is the existence of an unpaired c-a mismatch at the 1-72 position unique to bacterial initiator trna(fmet ...201122184460
crystal structure of release factor rf3 trapped in the gtp state on a rotated conformation of the ribosome.the class ii release factor rf3 is a gtpase related to elongation factor ef-g, which catalyzes release of class i release factors rf1 and rf2 from the ribosome after termination of protein synthesis. the 3.3 å crystal structure of the rf3·gdpnp·ribosome complex provides a high-resolution description of interactions and structural rearrangements that occur when binding of this translational gtpase induces large-scale rotational movements in the ribosome. rf3 induces a 7° rotation of the body and ...201222187675
Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria.Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2?m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this clus ...201122189493
Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria.Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2?m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this clus ...201122189493
functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of haloferax volcanii.the genome sequence of haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, rna modifications, small non-coding rnas, and ubiquitin-like small archaeal modifier proteins. the full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. notably, hfx. volcanii is together with halobacterium salinarum the only prok ...201122190865
an exit cavity was crucial to the polymerase activity of the early ribosome.the emergence of an rna entity capable of synthesizing peptides was a key prebiotic development. it is hypothesized that a precursor of the modern ribosomal exit tunnel was associated with this rna entity (e.g., "protoribosome" or "bonding entity") from the earliest time and played an essential role. various compounds that can bind and activate amino acids, including extremely short rna chains carrying amino acids, and possibly di- or tripeptides, would have associated with the internal cavity o ...201222191510
structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface.halophiles are extremophilic microorganisms growing optimally at high salt concentrations. there are two strategies used by halophiles to maintain proper osmotic pressure in their cytoplasm: accumulation of molar concentrations of potassium and chloride with extensive adaptation of the intracellular macromolecules ("salt-in" strategy) or biosynthesis and/or accumulation of organic osmotic solutes ("osmolyte" strategy). our work was aimed at contributing to the understanding of the shared molecul ...201122192175
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
inhibition of mycobacterium tuberculosis rna polymerase by binding of a gre factor homolog to secondary channel.because of the essential nature, each step of transcription viz, initiation, elongation and termination is subjected to elaborate regulation. a number of transcription factors modulate the rates of transcription at these different steps in addition to several inhibitors which shut down the process. many modulators including small molecules and proteinaceous inhibitors bind rna polymerase (rnap) secondary channel to control transcription. we describe here the first small protein inhibitor of tran ...201122194445
cloning, expression, and homology modeling of groel protein from leptospira interrogans serovar autumnalis strain n2.leptospirosis is an infectious bacterial disease caused by leptospira species. in this study, we cloned and sequenced the gene encoding the immunodominant protein groel from l. interrogans serovar autumnalis strain n2, which was isolated from the urine of a patient during an outbreak of leptospirosis in chennai, india. this groel gene encodes a protein of 60 kda with a high degree of homology (99% similarity) to those of other leptospiral serovars. recombinant groel was overexpressed in escheric ...201122196358
non-heme manganese catalase--the 'other' catalase.non-heme manganese catalases are widely distributed over microbial life and represent an environmentally important alternative to heme-containing catalases in antioxidant defense. manganese catalases contain a binuclear manganese complex as their catalytic active site rather than a heme, and cycle between mn(2)(ii,ii) and mn(2)(iii,iii) states during turnover. x-ray crystallography has revealed the key structural elements of the binuclear manganese active site complex that can serve as the start ...201122198285
non-heme manganese catalase--the 'other' catalase.non-heme manganese catalases are widely distributed over microbial life and represent an environmentally important alternative to heme-containing catalases in antioxidant defense. manganese catalases contain a binuclear manganese complex as their catalytic active site rather than a heme, and cycle between mn(2)(ii,ii) and mn(2)(iii,iii) states during turnover. x-ray crystallography has revealed the key structural elements of the binuclear manganese active site complex that can serve as the start ...201122198285
kinetic studies of the reactions of o(2) and no with reduced thermus thermophilus ba(3) and bovine aa(3) using photolabile carriers.the reactions of molecular oxygen (o(2)) and nitric oxide (no) with reduced thermus thermophilus (tt) ba(3) and bovine heart aa(3) were investigated by time-resolved optical absorption spectroscopy to establish possible relationships between the structural diversity of these enzymes and their reaction dynamics. to determine whether the photodissociated carbon monoxide (co) in the co flow-flash experiment affects the ligand binding dynamics, we monitored the reactions in the absence and presence ...201122201543
substrate channeling in proline metabolism.proline metabolism is an important pathway that has relevance in several cellular functions such as redox balance, apoptosis, and cell survival. results from different groups have indicated that substrate channeling of proline metabolic intermediates may be a critical mechanism. one intermediate is pyrroline-5-carboxylate (p5c), which upon hydrolysis opens to glutamic semialdehyde (gsa). recent structural and kinetic evidence indicate substrate channeling of p5c/gsa occurs in the proline catabol ...201222201749
Unique structural features and sequence motifs of proline utilization A (PutA).Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related mon ...201222201760
architecture and conservation of the bacterial dna replication machinery, an underexploited drug target.new antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. we can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of n ...201222206257
reconstitution of respiratory oxidases in membrane nanodiscs for investigation of proton-coupled electron transfer.the function of membrane-bound transporters is commonly affected by the milieu of the hydrophobic, membrane-spanning part of the transmembrane protein. consequently, functional studies of these proteins often involve incorporation into a native-like bilayer where the lipid components of the membrane can be controlled. the classical approach is to reconstitute the purified protein into liposomes. even though the use of such liposomes is essential for studies of transmembrane transport processes i ...201122209982
reconstitution of respiratory oxidases in membrane nanodiscs for investigation of proton-coupled electron transfer.the function of membrane-bound transporters is commonly affected by the milieu of the hydrophobic, membrane-spanning part of the transmembrane protein. consequently, functional studies of these proteins often involve incorporation into a native-like bilayer where the lipid components of the membrane can be controlled. the classical approach is to reconstitute the purified protein into liposomes. even though the use of such liposomes is essential for studies of transmembrane transport processes i ...201122209982
transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor rex.redox-sensing repressor rex was previously implicated in the control of anaerobic respiration in response to the cellular nadh/nad(+) levels in gram-positive bacteria. we utilized the comparative genomics approach to infer candidate rex-binding dna motifs and assess the rex regulon content in 119 genomes from 11 taxonomic groups. both dna-binding and nad-sensing domains are broadly conserved in rex orthologs identified in the phyla firmicutes, thermotogales, actinobacteria, chloroflexi, deinococ ...201122210771
transcription initiation factor dksa has diverse effects on rna chain elongation.bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ...201122210857
transcription initiation factor dksa has diverse effects on rna chain elongation.bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ...201122210857
structure of the pilus assembly protein tadz from eubacterium rectale: implications for polar localization.the tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type iv pili. the pilus assembly protein tadz (called cpae in caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type iv pilus biogenesis systems. the crystal structure of tadz from eubacterium rectale (ertadz), in complex with atp and mg(2+) , was determined to 2.1 å resolution. ertadz contains an atypical atpase domain with a variant of a deviant walker-a motif that re ...201122211578
the fggy carbohydrate kinase family: insights into the evolution of functional specificities.function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. however, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. here, using the fggy carbohydrate kinase family as an example, we bu ...201122215998
construction and transformation of a thermotoga-e. coli shuttle vector.abstract: background: thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. they may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. a lack of genetic tools has hampered the investigation and application of these organisms. this study aims to develop a genetic transfer system for thermotoga spp.. results: methods for preparing and handling thermotoga solid cultures under aerobic condi ...201222225774
structural changes that occur upon photolysis of the fe(ii)(a3)-co complex in the cytochrome ba(3)-oxidase of thermus thermophilus: a combined x-ray crystallographic and infrared spectral study demonstrates co binding to cu(b).the purpose of the work was to provide a crystallographic demonstration of the venerable idea that co photolyzed from ferrous heme-a(3) moves to the nearby cuprous ion in the cytochrome c oxidases. crystal structures of co-bound cytochrome ba(3)-oxidase from thermus thermophilus, determined at ~2.8-3.2å resolution, reveal a fe-c distance of ~2.0å, a cu-o distance of 2.4å and a fe-c-o angle of ~126°. upon photodissociation at 100k, x-ray structures indicate loss of fe(a3)-co and appearance of cu( ...201122226917
physiology of resistant deinococcus geothermalis bacterium aerobically cultivated in low manganese medium.this dynamic proteome study describes the physiology of growth and survival of deinococcus geothermalis, in conditions simulating paper machine waters being aerobic, warm, and low in carbon and manganese. industrial environment of this species differ from its natural habitats, geothermal springs and deep ocean subsurfaces, by being highly exposed to oxygen. quantitative proteome analysis using two-dimensional gel electrophoresis and bioinformatic tools showed expression change for 165 proteins f ...201222228732
on the molecular mechanism of gc content variation among eubacterial genomes.as a key parameter of genome sequence variation, the gc content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this gc content variation and its relationship to other fundamental processes. previously, we classified eubacteria into dnae-based groups (the dimeric combination of dna polymerase iii alpha subunits), according to a hypothesis where gc content variation is essentially governed by genome replication and dna repai ...201222230424
structure of n-formylglycinamide ribonucleotide amidotransferase ii (purl) from thermus thermophilus hb8.the crystal structure of purl from thermus thermophilus hb8 (ttpurl; ttha1519) was determined in complex with an adenine nucleotide, po(4)(3-) and mg(2+) at 2.35 å resolution. ttpurl consists of 29 α-helices and 28 β-strands, and one loop is disordered. ttpurl consists of four domains, a1, a2, b1 and b2, and the structures of the a1-b1 and a2-b2 domains were almost identical to each other. although the sequence identity between ttpurl and purl from thermotoga maritima (tmpurl) is higher than tha ...201222232163
crystallization and preliminary neutron diffraction studies of adp-ribose pyrophosphatase-i from thermus thermophilus hb8.adp-ribose pyrophosphatase-i from thermus thermophilus hb8 (ttadprase-i) prevents the intracellular accumulation of adp-ribose by hydrolyzing it to amp and ribose 5'-phosphate. to understand the catalytic mechanism of ttadprase-i, it is necessary to investigate the role of glutamates and metal ions as well as the coordination of water molecules located at the active site. a macroseeding method was developed in order to obtain a large ttadprase-i crystal which was suitable for a neutron diffracti ...201122232170
a-site residues move independently from p-site residues in all-atom molecular dynamics simulations of the 70s bacterial ribosome.the ribosome is a large macromolecular machine, and correlated motion between residues is necessary for coordinating function across multiple protein and rna chains. we ran two all-atom, explicit solvent molecular dynamics simulations of the bacterial ribosome and calculated correlated motion between residue pairs by using mutual information. because of the short timescales of our simulation (ns), we expect that dynamics are largely local fluctuations around the crystal structure. we hypothesize ...201222235290
a novel phage-encoded transcription antiterminator acts by suppressing bacterial rna polymerase pausing.gp39, a small protein encoded by thermus thermophilus phage p23-45, specifically binds the host rna polymerase (rnap) and inhibits transcription initiation. here, we demonstrate that gp39 also acts as an antiterminator during transcription through intrinsic terminators. the antitermination activity of gp39 relies on its ability to suppress transcription pausing at poly(u) tracks. gp39 also accelerates transcription elongation by decreasing rnap pausing and backtracking but does not significantly ...201222238378
visual tracking of plant virus infection and movement using a reporter myb transcription factor that activates anthocyanin biosynthesis.insertion of reporter genes into plant virus genomes is a common experimental strategy to research many aspects of the viral infection dynamics. their numerous advantages make fluorescent proteins the markers of choice in most studies. however, the use of fluorescent proteins still has some limitations, such as the need of specialized material and facilities to detect the fluorescence. here, we demonstrate a visual reporter marker system to track virus infection and movement through the plant. t ...201222238422
classification of protein functional surfaces using structural characteristics.protein structure and function are closely related, especially in functional surfaces, which are local spatial regions that perform the biological functions. also, protein structures tend to evolve more slowly than amino acid sequences. we have therefore developed a method to classify proteins using the structures of functional surfaces; we call it protein surface classification (psc). psc may reflect functional relationships among proteins and may detect evolutionary relationships among highly ...201222238424
the antibiotic thermorubin inhibits protein synthesis by binding to inter-subunit bridge b2a of the ribosome.thermorubin is a small-molecule inhibitor of bacterial protein synthesis, but relatively little is known about the molecular mechanism by which it blocks translation. the structure of the complex between thermorubin and the 70s ribosome from thermus thermophilus reported here shows that thermorubin interacts with the ribosome in a way that is distinct from any other known class of ribosome inhibitor. though it is structurally similar to tetracycline, it binds to the ribosome at an entirely diffe ...201222240456
structural and biochemical characterization of hp0315 from helicobacter pylori as a vapd protein with an endoribonuclease activity.vapd-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3d structure of these proteins. recently, a relationship between the cas2 family of ribonucleases associated with the crispr system of microbial immunity and vapd was suggested. here, we show for the first time the structure of a member of the vapd family and present a relationship of vapd with cas2 family and toxin-antitoxin (ta) systems. the crystal structure o ...201222241770
key role of two ftsa terminal domains in its bidirectional polymerization.the effect of two different truncations involving either the 1c domain or the simultaneous absence of the s12-13 β-strands of the ftsa protein from streptococcus pneumoniae, located at opposite terminal sides in the molecular structure, suggests that they are essential for atp-dependent polymerization. these two truncated proteins are not able to polymerize themselves but can be incorporated to some extent into the ftsa+ polymers during the assembling process. consequently, they block the growth ...201222247552
the roles of rhodobacter sphaeroides copper chaperones pcu(a)c and sco (prrc) in the assembly of the copper centers of the aa(3)-type and the cbb(3)-type cytochrome c oxidases.the α proteobacter rhodobacter sphaeroides accumulates two cytochrome c oxidases (cco) in its cytoplasmic membrane during aerobic growth: a mitochondrial-like aa(3)-type cco containing a di-copper cu(a) center and mono-copper cu(b), plus a cbb(3)-type cco that contains cu(b) but lacks cu(a). three copper chaperones are located in the periplasm of r. sphaeroides, pcu(a)c, prrc (sco) and cox11. cox11 is required to assemble cu(b) of the aa(3)-type but not the cbb(3)-type cco. prrc is homologous to ...201222248670
Refresh
firstprev
...31323334353637383940...
nextlast
Displaying items 3301 - 3400 of 5451