Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| protein-precursor trna contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease p. | bacterial ribonuclease p (rnase p) catalyzes the cleavage of 5' leader sequences from precursor trnas (pre-trnas). previously, all known substrate nucleotide specificities in this system are derived from rna-rna interactions with the rnase p rna subunit. here, we demonstrate that pre-trna binding affinities for bacillus subtilis and escherichia coli rnase p are enhanced by sequence-specific contacts between the fourth pre-trna nucleotide on the 5' side of the cleavage site (n(-4)) and the rnase ... | 2010 | 19932118 |
| protein-precursor trna contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease p. | bacterial ribonuclease p (rnase p) catalyzes the cleavage of 5' leader sequences from precursor trnas (pre-trnas). previously, all known substrate nucleotide specificities in this system are derived from rna-rna interactions with the rnase p rna subunit. here, we demonstrate that pre-trna binding affinities for bacillus subtilis and escherichia coli rnase p are enhanced by sequence-specific contacts between the fourth pre-trna nucleotide on the 5' side of the cleavage site (n(-4)) and the rnase ... | 2010 | 19932118 |
| n7-methylguanine at position 46 (m7g46) in trna from thermus thermophilus is required for cell viability at high temperatures through a trna modification network. | n(7)-methylguanine at position 46 (m(7)g46) in trna is produced by trna (m(7)g46) methyltransferase (trmb). to clarify the role of this modification, we made a trmb gene disruptant (deltatrmb) of thermus thermophilus, an extreme thermophilic eubacterium. the absence of trmb activity in cell extract from the deltatrmb strain and the lack of the m(7)g46 modification in trna(phe) were confirmed by enzyme assay, nucleoside analysis and rna sequencing. when the deltatrmb strain was cultured at high t ... | 2010 | 19934251 |
| solution structures and backbone dynamics of the ribosomal protein s6 and its permutant p(54-55). | the ribosomal protein s6 from thermus thermophilus has served as a model system for the study of protein folding, especially for understanding the effects of circular permutations of secondary structure elements. this study presents the structure of a permutant protein, the 96-residue p(54-55), and the structure of its 101-residue parent protein s6(wt) in solution. the data also characterizes the effects of circular permutation on the backbone dynamics of s6. consistent with crystallographic dat ... | 2010 | 19937661 |
| catalytic mechanism of human alpha-galactosidase. | the enzyme alpha-galactosidase (alpha-gal, also known as alpha-gal a; e.c. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. defects in human alpha-gal lead to the development of fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-gal is an active target of clinical research: there are currently two treatment options for fabry disease, recombinant enzyme replacement therapy (approved in ... | 2010 | 19940122 |
| catalytic mechanism of human alpha-galactosidase. | the enzyme alpha-galactosidase (alpha-gal, also known as alpha-gal a; e.c. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. defects in human alpha-gal lead to the development of fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-gal is an active target of clinical research: there are currently two treatment options for fabry disease, recombinant enzyme replacement therapy (approved in ... | 2010 | 19940122 |
| trna-dependent pre-transfer editing by prokaryotic leucyl-trna synthetase. | to prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-trna synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. in this work we studied the different editing pathways of class ia leucyl-trna synthetase (leurs). different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound an2690 that targets the post-transfer editing site of leurs. t ... | 2010 | 19940155 |
| trna-dependent pre-transfer editing by prokaryotic leucyl-trna synthetase. | to prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-trna synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. in this work we studied the different editing pathways of class ia leucyl-trna synthetase (leurs). different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound an2690 that targets the post-transfer editing site of leurs. t ... | 2010 | 19940155 |
| peptide-based antibodies against glutathione-binding domains suppress superoxide production mediated by mitochondrial complex i. | complex i (nqr) is a critical site of superoxide (o2-*) production and the major host of redox protein thiols in mitochondria. in response to oxidative stress, nqr-derived protein thiols at the 51- and 75-kda subunits are known to be reversibly s-glutathionylated. although several glutathionylated domains from nqr 51 and 75 kda have been identified, their roles in the regulatory functions remain to be explored. to gain further insights into protein s-glutathionylation of complex i, we used two p ... | 2010 | 19940158 |
| peptide-based antibodies against glutathione-binding domains suppress superoxide production mediated by mitochondrial complex i. | complex i (nqr) is a critical site of superoxide (o2-*) production and the major host of redox protein thiols in mitochondria. in response to oxidative stress, nqr-derived protein thiols at the 51- and 75-kda subunits are known to be reversibly s-glutathionylated. although several glutathionylated domains from nqr 51 and 75 kda have been identified, their roles in the regulatory functions remain to be explored. to gain further insights into protein s-glutathionylation of complex i, we used two p ... | 2010 | 19940158 |
| coupling atp utilization to protein remodeling by clpb, a hexameric aaa+ protein. | clpb and hsp104 are members of the aaa+ (atpases associated with various cellular activities) family of proteins and are molecular machines involved in thermotolerance. they are hexameric proteins containing 12 atp binding sites with two sites per protomer. clpb and hsp104 possess some innate protein remodeling activities; however, they require the collaboration of the dnak/hsp70 chaperone system to disaggregate and reactivate insoluble aggregated proteins. we investigated the mechanism by which ... | 2009 | 19940245 |
| the balance between pre- and post-transfer editing in trna synthetases. | the fidelity of trna aminoacylation is dependent in part on amino acid editing mechanisms. a hydrolytic activity that clears mischarged trnas typically resides in an active site on the trna synthetase that is distinct from its synthetic aminoacylation active site. a second pre-transfer editing pathway that hydrolyzes the trna synthetase aminoacyl adenylate intermediate can also be activated. pre- and post-transfer editing activities can co-exist within a single trna synthetase resulting in a red ... | 2010 | 19941860 |
| crystal structure of pyrococcus horikoshii tryptophanyl-trna synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-trna synthetase. | the ancient and ubiquitous aminoacyl-trna synthetases constitute a valuable model system for studying early evolutionary events. so far, the evolutionary relationship of tryptophanyl- and tyrosyl-trna synthetase (trprs and tyrrs) remains controversial. as trprs and tyrrs share low sequence homology but high structural similarity, a structure-based method would be advantageous for phylogenetic analysis of the enzymes. here, we present the first crystal structure of an archaeal trprs, the structur ... | 2010 | 19942682 |
| crystal structure of pyrococcus horikoshii tryptophanyl-trna synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-trna synthetase. | the ancient and ubiquitous aminoacyl-trna synthetases constitute a valuable model system for studying early evolutionary events. so far, the evolutionary relationship of tryptophanyl- and tyrosyl-trna synthetase (trprs and tyrrs) remains controversial. as trprs and tyrrs share low sequence homology but high structural similarity, a structure-based method would be advantageous for phylogenetic analysis of the enzymes. here, we present the first crystal structure of an archaeal trprs, the structur ... | 2010 | 19942682 |
| stereochemical mechanisms of trna methyltransferases. | methylation of trna on the four canonical bases adds structural complexity to the molecule, and improves decoding specificity and efficiency. while many trna methylases are known, detailed insight into the catalytic mechanism is only available in a few cases. of interest among all trna methylases is the structural basis for nucleotide selection, by which the specificity is limited to a single site, or broadened to multiple sites. general themes in catalysis include the basis for rate acceleratio ... | 2010 | 19944101 |
| cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. | aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ... | 2009 | 19946135 |
| aminoglycoside activity observed on single pre-translocation ribosome complexes. | aminoglycoside-class antibiotics bind directly to ribosomal rna, imparting pleiotropic effects on ribosome function. despite in-depth structural investigations of aminoglycoside-rna oligonucleotide and aminoglycoside-ribosome interactions, mechanisms explaining the unique ribosome inhibition profiles of chemically similar aminoglycosides remain elusive. here, using single-molecule fluorescence resonance energy transfer (smfret) methods, we show that high-affinity aminoglycoside binding to the co ... | 2009 | 19946275 |
| aminoglycoside activity observed on single pre-translocation ribosome complexes. | aminoglycoside-class antibiotics bind directly to ribosomal rna, imparting pleiotropic effects on ribosome function. despite in-depth structural investigations of aminoglycoside-rna oligonucleotide and aminoglycoside-ribosome interactions, mechanisms explaining the unique ribosome inhibition profiles of chemically similar aminoglycosides remain elusive. here, using single-molecule fluorescence resonance energy transfer (smfret) methods, we show that high-affinity aminoglycoside binding to the co ... | 2009 | 19946275 |
| the effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' nuclease assay. | real-time polymerase chain reaction (pcr) is the current method of choice for detection and quantification of nucleic acids, especially for molecular diagnostics. complementarity between primers and template is often crucial for pcr applications, as mismatches can severely reduce priming efficiency. however, little quantitative data on the effect of these mismatches is available. we quantitatively investigated the effects of primer-template mismatches within the 3'-end primer region on real-time ... | 2010 | 19948821 |
| shaping the mitochondrion: mitochondrial biogenesis, dynamics and dysfunction. conference on mitochondrial assembly and dynamics in health and disease. | 2009 | 19949411 | |
| copper trafficking in biology: an nmr approach. | copper ions are essential for living organisms because they are involved in several fundamental biological processes. biomolecules interacting with copper ions have to be characterized as such, when bound to the metal ion, and when they interact with other biomolecules or substrates. the characterization is both structural and dynamic. in this context, nmr is a preferred tool of investigation because it allows shedding light on what happens in solution. here, the nmr contribution to the copper t ... | 2009 | 19949444 |
| dynamics of the base of ribosomal a-site finger revealed by molecular dynamics simulations and cryo-em. | helix 38 (h38) of the large ribosomal subunit, with a length of 110 a, reaches the small subunit through intersubunit bridge b1a. previous cryo-em studies revealed that the tip of h38 moves by more than 10 a from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible h38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. we investigate a region including the elbow-shaped kink-turn (kt-38) i ... | 2010 | 19952067 |
| dynamics of the base of ribosomal a-site finger revealed by molecular dynamics simulations and cryo-em. | helix 38 (h38) of the large ribosomal subunit, with a length of 110 a, reaches the small subunit through intersubunit bridge b1a. previous cryo-em studies revealed that the tip of h38 moves by more than 10 a from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible h38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. we investigate a region including the elbow-shaped kink-turn (kt-38) i ... | 2010 | 19952067 |
| posttranslational control of transcription factor fixk2, a key regulator for the bradyrhizobium japonicum-soybean symbiosis. | rhizobial fixk-like proteins play essential roles in activating genes for endosymbiotic life in legume root nodules, such as genes for micro-oxic respiration. in the facultative soybean symbiont, bradyrhizobium japonicum, the fixk(2) protein is the key player in a complex regulatory network. the fixk(2) gene itself is activated by the 2-component regulatory system fixlj in response to a moderate decrease of the oxygen tension, and the fixk(2) protein distributes and amplifies this response to th ... | 2009 | 19955406 |
| the crystal structure of apo-ftsh reveals domain movements necessary for substrate unfolding and translocation. | the hexameric membrane-spanning atp-dependent metalloprotease ftsh is universally conserved in eubacteria, mitochondria, and chloroplasts, where it fulfills key functions in quality control and signaling. as a member of the self-compartmentalizing atpases associated with various cellular activities (aaa+ proteases), ftsh converts the chemical energy stored in atp via conformational rearrangements into a mechanical force that is used for substrate unfolding and translocation into the proteolytic ... | 2009 | 19955424 |
| tissue inhibitor of metalloproteinase 1 expression associated with gene demethylation confers anoikis resistance in early phases of melanocyte malignant transformation. | although anoikis resistance has been considered a hallmark of malignant phenotype, the causal relation between neoplastic transformation and anchorage-independent growth remains undefined. we developed an experimental model of murine melanocyte malignant transformation, where a melanocyte lineage (melan-a) was submitted to sequential cycles of anchorage blockade, resulting in progressive morphologic alterations, and malignant transformation. throughout this process, cells corresponding to premal ... | 2009 | 19956395 |
| synergistic cooperation between two clpb isoforms in aggregate reactivation. | bacterial aaa+ atpase clpb cooperates with dnak during reactivation of aggregated proteins. the clpb-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric clpb. two isoforms of clpb are produced in vivo: the full-length clpb95 and clpb80, which does not contain the substrate-interacting n-terminal domain. the biological role of the truncated isoform clpb80 is unknown. we found that resolubilization of aggregated proteins in escherichia coli afte ... | 2010 | 19961856 |
| synergistic cooperation between two clpb isoforms in aggregate reactivation. | bacterial aaa+ atpase clpb cooperates with dnak during reactivation of aggregated proteins. the clpb-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric clpb. two isoforms of clpb are produced in vivo: the full-length clpb95 and clpb80, which does not contain the substrate-interacting n-terminal domain. the biological role of the truncated isoform clpb80 is unknown. we found that resolubilization of aggregated proteins in escherichia coli afte ... | 2010 | 19961856 |
| the effect of spermine on the initiation of mitochondrial protein synthesis. | polyamines are important in both prokaryotic and eukaryotic translational systems. spermine is a quaternary aliphatic amine that is cationic under physiological conditions. in this paper, we demonstrate that spermine stimulates fmet-trna binding to mammalian mitochondrial 55s ribosomes. the stimulatory effect of spermine is independent of the identity of the mrna. the degree of stimulation of spermine is the same at all concentrations of mitochondrial initiation factor 2 (if2(mt)) and mitochondr ... | 2010 | 19962967 |
| the effect of spermine on the initiation of mitochondrial protein synthesis. | polyamines are important in both prokaryotic and eukaryotic translational systems. spermine is a quaternary aliphatic amine that is cationic under physiological conditions. in this paper, we demonstrate that spermine stimulates fmet-trna binding to mammalian mitochondrial 55s ribosomes. the stimulatory effect of spermine is independent of the identity of the mrna. the degree of stimulation of spermine is the same at all concentrations of mitochondrial initiation factor 2 (if2(mt)) and mitochondr ... | 2010 | 19962967 |
| lcca, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by haloferax volcanii. | laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. while laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. here, we report the purification and characterization of a laccase (lcca) from the halophilic archaeon haloferax volcanii. lcca was secreted at high levels into the culture supernatant of a recombinant h. volcanii strain, with peak activity (170 +/- ... | 2010 | 19966030 |
| lcca, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by haloferax volcanii. | laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. while laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. here, we report the purification and characterization of a laccase (lcca) from the halophilic archaeon haloferax volcanii. lcca was secreted at high levels into the culture supernatant of a recombinant h. volcanii strain, with peak activity (170 +/- ... | 2010 | 19966030 |
| the structure of the proline utilization a proline dehydrogenase domain inactivated by n-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction. | proline utilization a (puta) from escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. previous studies have shown that the binding of proline in the proline dehydrogenase (prodh) active site and subsequent reduction of the fad trigger global conformational changes that enhance puta-membrane affinity. these events cause puta to switch from its r ... | 2010 | 19994913 |
| expression of reck and matrix metalloproteinase-2 in ameloblastoma. | ameloblastoma is a frequent odontogenic benign tumor characterized by local invasiveness, high risk of recurrence and occasional metastasis and malignant transformation. matrix metalloproteinase-2 (mmp-2) promotes tumor invasion and progression by destroying the extracellular matrix (ecm) and basement membrane. for this proteolytic activity, the endogenous inhibitor is reversion-inducing cysteine rich protein with kazal motifs (reck). the aim of this study was to characterize the relationship be ... | 2009 | 19995435 |
| mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from thermus thermophilus. | homocitrate synthase (hcs) catalyzes aldol-type condensation of acetyl coenzyme a (acetyl-coa) and alpha-ketoglutarate (alpha-kg) to synthesize homocitrate (hc), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. as known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, hcs is regulated via feedback inhibition by the end product, lysine. here, we determined the crystal structures of hcs from thermus thermophilus ... | 2010 | 19996101 |
| functional significance of eif5a and its hypusine modification in eukaryotes. | the unusual basic amino acid, hypusine [n(epsilon)-(4-amino-2-hydroxybutyl)-lysine], is a modified lysine with the addition of the 4-aminobutyl moiety from the polyamine spermidine. this naturally occurring amino acid is a product of a unique posttranslational modification that occurs in only one cellular protein, eukaryotic translation initiation factor 5a (eif5a, eif-5a). hypusine is synthesized exclusively in this protein by two sequential enzymatic steps involving deoxyhypusine synthase (dhs ... | 2010 | 19997760 |
| functional significance of eif5a and its hypusine modification in eukaryotes. | the unusual basic amino acid, hypusine [n(epsilon)-(4-amino-2-hydroxybutyl)-lysine], is a modified lysine with the addition of the 4-aminobutyl moiety from the polyamine spermidine. this naturally occurring amino acid is a product of a unique posttranslational modification that occurs in only one cellular protein, eukaryotic translation initiation factor 5a (eif5a, eif-5a). hypusine is synthesized exclusively in this protein by two sequential enzymatic steps involving deoxyhypusine synthase (dhs ... | 2010 | 19997760 |
| studies on the mechanism of p-hydroxyphenylacetate 3-hydroxylase from pseudomonas aeruginosa: a system composed of a small flavin reductase and a large flavin-dependent oxygenase. | there are two known types of microbial two-component flavin-dependent monooxygenases that catalyze oxygenation of p-hydroxyphenylacetate (hpa), and they are distinguished by having structurally distinct reductases and oxygenases. this paper presents a detailed analysis of the properties of the enzyme from pseudomonas aeruginosa, an example of one group, and compares its properties to those published for the acinetobacter baumannii enzyme, an example of the alternative group. the reductase and ox ... | 2010 | 20000468 |
| the structural basis for mrna recognition and cleavage by the ribosome-dependent endonuclease rele. | translational control is widely used to adjust gene expression levels. during the stringent response in bacteria, mrna is degraded on the ribosome by the ribosome-dependent endonuclease, rele. the molecular basis for recognition of the ribosome and mrna by rele and the mechanism of cleavage are unknown. here, we present crystal structures of e. coli rele in isolation (2.5 a) and bound to programmed thermus thermophilus 70s ribosomes before (3.3 a) and after (3.6 a) cleavage. rele occupies the a ... | 2009 | 20005802 |
| 5-methylcytosine in rna: detection, enzymatic formation and biological functions. | the nucleobase modification 5-methylcytosine (m(5)c) is widespread both in dna and different cellular rnas. the functions and enzymatic mechanisms of dna m(5)c-methylation were extensively studied during the last decades. however, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in rna still remain to be elucidated. the recent development of a bisulfite sequencing approach for efficient m(5)c localization in various rna molecules puts ribo-m(5 ... | 2009 | 20007150 |
| 5-methylcytosine in rna: detection, enzymatic formation and biological functions. | the nucleobase modification 5-methylcytosine (m(5)c) is widespread both in dna and different cellular rnas. the functions and enzymatic mechanisms of dna m(5)c-methylation were extensively studied during the last decades. however, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in rna still remain to be elucidated. the recent development of a bisulfite sequencing approach for efficient m(5)c localization in various rna molecules puts ribo-m(5 ... | 2009 | 20007150 |
| estimating dna coverage and abundance in metagenomes using a gamma approximation. | shotgun sequencing generates large numbers of short dna reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. these reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). the feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative ... | 2009 | 20008478 |
| estimating dna coverage and abundance in metagenomes using a gamma approximation. | shotgun sequencing generates large numbers of short dna reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. these reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). the feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative ... | 2009 | 20008478 |
| high-throughput haplotype determination over long distances by haplotype fusion pcr and ligation haplotyping. | when combined with haplotype fusion pcr (hf-pcr), ligation haplotyping is a robust, high-throughput method for empirical determination of haplotypes, which can be applied to assaying both sequence and structural variation over long distances. unlike alternative approaches to haplotype determination, such as allele-specific pcr and long pcr, hf-pcr and ligation haplotyping do not suffer from mispriming or template-switching errors. in this method, hf-pcr is used to juxtapose dna sequences from si ... | 2009 | 20010928 |
| measurement and interpretation of 15n-1h residual dipolar couplings in larger proteins. | a decade ago, dr. l.e. kay and co-workers described an ingenious hnco-based triple-resonance experiment from which several protein backbone rdcs can be measured simultaneously (yang et al. (1999) [1]). they implemented a j-scaling technique in the (15)n dimension of the 3d experiment to obtain the nh rdcs. we have used this idea to carry out j-scaling in a 2d (15)n-(1)h-trosy experiment and have found it to be an excellent method to obtain nh rdcs for larger proteins upto 70 kda, far superior to ... | 2010 | 20018538 |
| measurement and interpretation of 15n-1h residual dipolar couplings in larger proteins. | a decade ago, dr. l.e. kay and co-workers described an ingenious hnco-based triple-resonance experiment from which several protein backbone rdcs can be measured simultaneously (yang et al. (1999) [1]). they implemented a j-scaling technique in the (15)n dimension of the 3d experiment to obtain the nh rdcs. we have used this idea to carry out j-scaling in a 2d (15)n-(1)h-trosy experiment and have found it to be an excellent method to obtain nh rdcs for larger proteins upto 70 kda, far superior to ... | 2010 | 20018538 |
| modifications of protein environment of the [2fe-2s] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex. | the rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the rieske iron-sulfur protein (isp) at the q(o)-site. structures of the isp from rhodobacter sphaeroides show that serine 154 and tyrosine 156 form h-bonds to s-1 of the [2fe-2s] cluster and to the sulfur atom of the cysteine liganding fe-1 of the cluster, respectively. these are responsible in part for the high potential (e(m)(,7) approximately 300 mv) and low pk(a) (7.6) of the isp, w ... | 2010 | 20023300 |
| modifications of protein environment of the [2fe-2s] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex. | the rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the rieske iron-sulfur protein (isp) at the q(o)-site. structures of the isp from rhodobacter sphaeroides show that serine 154 and tyrosine 156 form h-bonds to s-1 of the [2fe-2s] cluster and to the sulfur atom of the cysteine liganding fe-1 of the cluster, respectively. these are responsible in part for the high potential (e(m)(,7) approximately 300 mv) and low pk(a) (7.6) of the isp, w ... | 2010 | 20023300 |
| amidoligases with atp-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. | recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. preliminary studies also indicated that conjugation systems for other peptide tags on proteins, such as pupylation, have evolutionary links to cofactor/amino acid biosynthesis pathways. following up on these observations, we systematically investigated the non-ribosomal amidoligases of the atp-grasp, glutamine synthetase-like and acetyltransferase folds by classifying the kno ... | 2009 | 20023723 |
| mapping of the signal peptide-binding domain of escherichia coli seca using förster resonance energy transfer. | identification of the signal peptide-binding domain within seca atpase is an important goal for understanding the molecular basis of seca preprotein recognition as well as elucidating the chemo-mechanical cycle of this nanomotor during protein translocation. in this study, forster resonance energy transfer methodology was employed to map the location of the seca signal peptide-binding domain using a collection of functional monocysteine seca mutants and alkaline phosphatase signal peptides label ... | 2010 | 20025247 |
| elongation in translation as a dynamic interaction among the ribosome, trna, and elongation factors ef-g and ef-tu. | the ribosome is a complex macromolecular machine that translates the message encoded in the messenger rna and synthesizes polypeptides by linking the individual amino acids carried by the cognate transfer rnas (trnas). the protein elongation cycle, during which the trnas traverse the ribosome in a coordinated manner along a path of more than 100 a, is facilitated by large-scale rearrangements of the ribosome. these rearrangements go hand in hand with conformational changes of trna as well as elo ... | 2009 | 20025795 |
| dissecting the role of critical residues and substrate preference of a fatty acyl-coa synthetase (fadd13) of mycobacterium tuberculosis. | newly emerging multi-drug resistant strains of mycobacterium tuberculosis (m.tb) severely limit the treatment options for tuberculosis (tb); hence, new antitubercular drugs are urgently needed. the myma operon is essential for the virulence and intracellular survival of m.tb and thus represents an attractive target for the development of new antitubercular drugs. this study is focused on the structure-function relationship of fatty acyl-coa synthetase (fadd13, rv3089) belonging to the myma opero ... | 2009 | 20027301 |
| amyloidogenic sequences in native protein structures. | numerous short peptides have been shown to form beta-sheet amyloid aggregates in vitro. proteins that contain such sequences are likely to be problematic for a cell, due to their potential to aggregate into toxic structures. we investigated the structures of 30 proteins containing 45 sequences known to form amyloid, to see how the proteins cope with the presence of these potentially toxic sequences, studying secondary structure, hydrogen-bonding, solvent accessible surface area and hydrophobicit ... | 2009 | 20027621 |
| amyloidogenic sequences in native protein structures. | numerous short peptides have been shown to form beta-sheet amyloid aggregates in vitro. proteins that contain such sequences are likely to be problematic for a cell, due to their potential to aggregate into toxic structures. we investigated the structures of 30 proteins containing 45 sequences known to form amyloid, to see how the proteins cope with the presence of these potentially toxic sequences, studying secondary structure, hydrogen-bonding, solvent accessible surface area and hydrophobicit ... | 2009 | 20027621 |
| the pseudomonas aeruginosa magnesium transporter mgte inhibits transcription of the type iii secretion system. | pseudomonas aeruginosa is an opportunistic pathogen that causes life-long pneumonia in individuals with cystic fibrosis (cf). these long-term infections are maintained by bacterial biofilm formation in the cf lung. we have recently developed a model of p. aeruginosa biofilm formation on cultured cf airway epithelial cells. using this model, we discovered that mutation of a putative magnesium transporter gene, called mgte, led to increased cytotoxicity of p. aeruginosa toward epithelial cells. th ... | 2010 | 20028803 |
| the pseudomonas aeruginosa magnesium transporter mgte inhibits transcription of the type iii secretion system. | pseudomonas aeruginosa is an opportunistic pathogen that causes life-long pneumonia in individuals with cystic fibrosis (cf). these long-term infections are maintained by bacterial biofilm formation in the cf lung. we have recently developed a model of p. aeruginosa biofilm formation on cultured cf airway epithelial cells. using this model, we discovered that mutation of a putative magnesium transporter gene, called mgte, led to increased cytotoxicity of p. aeruginosa toward epithelial cells. th ... | 2010 | 20028803 |
| reductive coupling of nitrogen monoxide (*no) facilitated by heme/copper complexes. | the interactions of nitrogen monoxide (*no; nitric oxide) with transition metal centers continue to be of great interest, in part due to their importance in biochemical processes. here, we describe *no((g)) reductive coupling chemistry of possible relevance to that process (i.e., nitric oxide reductase (nor) biochemistry), which occurs at the heme/cu active site of cytochrome c oxidases (ccos). in this report, heme/cu/*no((g)) activity is studied using 1:1 ratios of heme and copper complex compo ... | 2010 | 20030370 |
| the oxidative dna glycosylases of mycobacterium tuberculosis exhibit different substrate preferences from their escherichia coli counterparts. | the dna glycosylases that remove oxidized dna bases fall into two general families: the fpg/nei family and the nth superfamily. based on protein sequence alignments, we identified four putative fpg/nei family members, as well as a putative nth protein in mycobacterium tuberculosis h37rv. all four fpg/nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. the mtunth protein was also overexpressed in soluble form. the substrate specificities of the purif ... | 2010 | 20031487 |
| the oxidative dna glycosylases of mycobacterium tuberculosis exhibit different substrate preferences from their escherichia coli counterparts. | the dna glycosylases that remove oxidized dna bases fall into two general families: the fpg/nei family and the nth superfamily. based on protein sequence alignments, we identified four putative fpg/nei family members, as well as a putative nth protein in mycobacterium tuberculosis h37rv. all four fpg/nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. the mtunth protein was also overexpressed in soluble form. the substrate specificities of the purif ... | 2010 | 20031487 |
| polymorphisms associated with resistance and cross-resistance to aminoglycosides and capreomycin in mycobacterium tuberculosis isolates from south korean patients with drug-resistant tuberculosis. | the aminoglycosides streptomycin, amikacin, and kanamycin and the cyclic polypeptide capreomycin are all widely used in second-line therapy for patients who develop multidrug-resistant tuberculosis. we have characterized a set of 106 clinical isolates of mycobacterium tuberculosis using phenotypic drug susceptibility testing (dst) to determine the extent of resistance to each agent and cross-resistance between agents. these results were compared with polymorphisms in the dna sequences of ribosom ... | 2010 | 20032248 |
| polymorphisms associated with resistance and cross-resistance to aminoglycosides and capreomycin in mycobacterium tuberculosis isolates from south korean patients with drug-resistant tuberculosis. | the aminoglycosides streptomycin, amikacin, and kanamycin and the cyclic polypeptide capreomycin are all widely used in second-line therapy for patients who develop multidrug-resistant tuberculosis. we have characterized a set of 106 clinical isolates of mycobacterium tuberculosis using phenotypic drug susceptibility testing (dst) to determine the extent of resistance to each agent and cross-resistance between agents. these results were compared with polymorphisms in the dna sequences of ribosom ... | 2010 | 20032248 |
| structural motifs of the bacterial ribosomal proteins s20, s18 and s16 that contact rrna present in the eukaryotic ribosomal proteins s25, s26 and s27a, respectively. | the majority of constitutive proteins in the bacterial 30s ribosomal subunit have orthologues in eukarya and archaea. the eukaryotic counterparts for the remainder (s6, s16, s18 and s20) have not been identified. we assumed that amino acid residues in the ribosomal proteins that contact rrna are to be constrained in evolution and that the most highly conserved of them are those residues that are involved in forming the secondary protein structure. we aligned the sequences of the bacterial riboso ... | 2010 | 20034956 |
| accommodation of tmrna-smpb into stalled ribosomes: a cryo-em study. | in eubacteria, translation of defective messenger rnas (mrnas) produces truncated polypeptides that stall on the ribosome. a quality control mechanism referred to as trans-translation is performed by transfer-messenger rna (tmrna), a specialized rna acting as both a trna and an mrna, associated with small protein b (smpb). so far, a clear view of the structural movements of both the protein and rna necessary to perform accommodation is still lacking. by using a construct containing the trna-like ... | 2010 | 20038631 |
| the adenosine wedge: a new structural motif in ribosomal rna. | here, we present a new recurrent rna arrangement, the so-called adenosine wedge (a-wedge), which is found in three places of the ribosomal rna in both ribosomal subunits. the arrangement has a hierarchical structure, consisting of elements previously described as recurrent motifs, namely, the along-groove packing motif, the a-minor and the hook-turn. within the a-wedge, these elements are involved in different types of cause-effect relationships, providing together for the particular tertiary st ... | 2010 | 20038632 |
| helix insertion into bilayers and the evolution of membrane proteins. | polytopic alpha-helical membrane proteins cannot spontaneously insert into lipid bilayers without assistance from polytopic alpha-helical membrane proteins that already reside in the membrane. this raises the question of how these proteins evolved. our current knowledge of the insertion of alpha-helices into natural and model membranes is reviewed with the goal of gaining insight into the evolution of membrane proteins. topics include: translocon-dependent membrane protein insertion, antibiotic ... | 2009 | 20039094 |
| helix insertion into bilayers and the evolution of membrane proteins. | polytopic alpha-helical membrane proteins cannot spontaneously insert into lipid bilayers without assistance from polytopic alpha-helical membrane proteins that already reside in the membrane. this raises the question of how these proteins evolved. our current knowledge of the insertion of alpha-helices into natural and model membranes is reviewed with the goal of gaining insight into the evolution of membrane proteins. topics include: translocon-dependent membrane protein insertion, antibiotic ... | 2009 | 20039094 |
| identification and biochemical characterization of molybdenum cofactor-binding proteins from arabidopsis thaliana. | the molybdenum cofactor (moco) forms part of the catalytic center in all eukaryotic molybdenum enzymes and is synthesized in a highly conserved pathway. among eukaryotes, very little is known about the processes taking place subsequent to moco biosynthesis, i.e. moco transfer, allocation, and insertion into molybdenum enzymes. in the model plant arabidopsis thaliana, we identified a novel protein family consisting of nine members that after recombinant expression are able to bind moco with k(d) ... | 2009 | 20040598 |
| identification and biochemical characterization of molybdenum cofactor-binding proteins from arabidopsis thaliana. | the molybdenum cofactor (moco) forms part of the catalytic center in all eukaryotic molybdenum enzymes and is synthesized in a highly conserved pathway. among eukaryotes, very little is known about the processes taking place subsequent to moco biosynthesis, i.e. moco transfer, allocation, and insertion into molybdenum enzymes. in the model plant arabidopsis thaliana, we identified a novel protein family consisting of nine members that after recombinant expression are able to bind moco with k(d) ... | 2009 | 20040598 |
| discovery of 3-formyl-tyrosine metabolites from pseudoalteromonas tunicata through heterologous expression. | genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (nrps) or polyketide synthase (pks) domains. recently, other condensation enzymes, such as the atp-grasp ligases, have been recognized as important players in natural product biosynthesis. in this study, sequence based searching for homologues of ddaf, the atp-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously ... | 2010 | 20041686 |
| discovery of 3-formyl-tyrosine metabolites from pseudoalteromonas tunicata through heterologous expression. | genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (nrps) or polyketide synthase (pks) domains. recently, other condensation enzymes, such as the atp-grasp ligases, have been recognized as important players in natural product biosynthesis. in this study, sequence based searching for homologues of ddaf, the atp-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously ... | 2010 | 20041686 |
| filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates. | chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ... | 2010 | 20042599 |
| filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates. | chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ... | 2010 | 20042599 |
| the chlamydial functional homolog of ksga confers kasugamycin sensitivity to chlamydia trachomatis and impacts bacterial fitness. | rrna adenine dimethyltransferases, represented by the escherichia coli ksga protein, are highly conserved phylogenetically and are generally not essential for growth. they are responsible for the post-transcriptional transfer of two methyl groups to two universally conserved adenosines located near the 3'end of the small subunit rrna and participate in ribosome maturation. all sequenced genomes of chlamydia reveal a ksga homolog in each species, including c. trachomatis. yet absence of a s-adeno ... | 2009 | 20043826 |
| thermodynamic characterization of naturally occurring rna tetraloops. | although tetraloops are one of the most frequently occurring secondary structure motifs in rna, less than one-third of the 30 most frequently occurring rna tetraloops have been thermodynamically characterized. therefore, 24 stem-loop sequences containing common tetraloops were optically melted, and the thermodynamic parameters deltah degrees , deltas degrees , deltag degrees (37,) and t(m) for each stem-loop were determined. these new experimental values, on average, are 0.7 kcal/mol different f ... | 2010 | 20047989 |
| assessing the quality of whole genome alignments in bacteria. | comparing genomes is an essential preliminary step to solve many problems in biology. matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. here, we describe two families of assessment measures whose purpose is to evaluate bacteria-oriented comparison tools. the first measure is based o ... | 2009 | 20049164 |
| structural insights into rna interference. | virtually all animals and plants utilize small rna molecules to control protein expression during different developmental stages and in response to viral infection. structural and mechanistic studies have begun to illuminate three fundamental aspects of these pathways: small rna biogenesis, formation of rna-induced silencing complexes (riscs), and targeting of complementary mrnas. here we review exciting recent progress in understanding how regulatory rnas are produced and how they trigger speci ... | 2010 | 20053548 |
| flexible recognition of the trna g18 methylation target site by trmh methyltransferase through first binding and induced fit processes. | transfer rna (gm18) methyltransferase (trmh) catalyzes methyl transfer from s-adenosyl-l-methionine to a conserved g18 in trna. we investigated the recognition mechanism of thermus thermophilus trmh for its guanosine target. thirteen yeast trna(phe) mutant transcripts were prepared in which the modification site and/or other nucleotides in the d-loop were substituted by dg, inosine, or other nucleotides. we then conducted methyl transfer kinetic studies, gel shift assays, and inhibition experime ... | 2010 | 20053984 |
| structure of sure protein from aquifex aeolicus vf5 at 1.5 a resolution. | sure is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. the structure of the sure protein from the hyperthermophile aquifex aeolicus has been solved at 1.5 a resolution using molecular replacement with one dimer in the asymmetric unit and refined to an r factor of 15.6%. the crystal packing reveals that two dimers assemble to form a tetram ... | 2009 | 20054112 |
| structure of putative 4-amino-4-deoxychorismate lyase from thermus thermophilus hb8. | the pyridoxal 5'-phosphate-dependent enzyme 4-amino-4-deoxychorismate lyase converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate in one of the crucial steps in the folate-biosynthesis pathway. the primary structure of the hypothetical protein ttha0621 from thermus thermophilus hb8 suggests that ttha0621 is a putative 4-amino-4-deoxychorismate lyase. here, the crystal structure of ttha0621 is reported at 1.93 a resolution. the asymmetric unit contained four ncs molecules related by ... | 2009 | 20054118 |
| multifrequency epr studies of manganese catalases provide a complete description of proteinaceous nitrogen coordination. | pulse electron paramagnetic resonance (epr) spectroscopy is employed at two very different excitation frequencies, 9.77 and 30.67 ghz, in the study of the nitrogen coordination environment of the mn(iii)mn(iv) state of the dimanganese-containing catalases from lactobacillus plantarum and thermus thermophilus. consistent with previous studies, the lower-frequency results reveal one unique histidine nitrogen-mn cluster interaction. for the first time, a second, more strongly hyperfine-coupled (14) ... | 2010 | 20055466 |
| structure and ligand binding properties of the epoxidase component of styrene monooxygenase . | styrene monooxygenase (smo) is a two-component flavoprotein monooxygenase that transforms styrene to styrene oxide in the first step of the styrene catabolic and detoxification pathway of pseudomonas putida s12. the crystal structure of the n-terminally histidine-tagged epoxidase component of this system, nsmoa, determined to 2.3 a resolution, indicates the enzyme exists as a homodimer in which each monomer forms two distinct domains. the overall architecture is most similar to that of p-hydroxy ... | 2010 | 20055497 |
| crystallization and preliminary x-ray crystallographic analysis of dna gyrase gyrb subunit from xanthomonas oryzae pv. oryzae. | dna gyrase is a type ii topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial dna. in this study, the n-terminal fragment of the gyrb subunit of dna gyrase from xanthomonas oryzae pv. oryzae was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.10 a resolution using a synchrotron-radiation source. the crystal belonged to space group i4(1), with unit-cell param ... | 2010 | 20057069 |
| crystallization and preliminary x-ray crystallographic analysis of dna gyrase gyrb subunit from xanthomonas oryzae pv. oryzae. | dna gyrase is a type ii topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial dna. in this study, the n-terminal fragment of the gyrb subunit of dna gyrase from xanthomonas oryzae pv. oryzae was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.10 a resolution using a synchrotron-radiation source. the crystal belonged to space group i4(1), with unit-cell param ... | 2010 | 20057069 |
| crystallization and preliminary x-ray crystallographic analysis of thermus thermophilus transcription elongation complex bound to gfh1. | rna polymerase (rnap) elongates rna by iterative nucleotide-addition cycles (nac). a specific structural state (or states) of rnap may be the target of transcription elongation factors. gfh1, a thermus thermophilus gre-family protein, inhibits nac. to elucidate which rnap structural state gfh1 associates with, the t. thermophilus rnap elongation complex (ec) was cocrystallized with gfh1. of the 70 dna/rna scaffolds tested, two (for ec1 and ec2) were successfully crystallized. in the presence of ... | 2010 | 20057074 |
| role of copper ion in regulating ligand binding in a myoglobin-based cytochrome c oxidase model. | cytochrome c oxidase (cco), the terminal enzyme in the mitochondrial respiratory chain, catalyzes the four-electron reduction of dioxygen to water in a binuclear center comprised of a high-spin heme (heme a(3)) and a copper atom (cu(b)) coordinated by three histidine residues. as a minimum model for cco, a mutant of sperm whale myoglobin, named cu(b)mb, has been engineered, in which a copper atom is held in the distal heme pocket by the native e7 histidine and two nonnative histidine residues. i ... | 2010 | 20070118 |
| an active dimanganese(iii)-tyrosyl radical cofactor in escherichia coli class ib ribonucleotide reductase. | escherichia coli class ib ribonucleotide reductase (rnr) converts nucleoside 5'-diphosphates to deoxynucleoside 5'-diphosphates and is expressed under iron-limited and oxidative stress conditions. this rnr is composed of two homodimeric subunits: alpha2 (nrde), where nucleotide reduction occurs, and beta2 (nrdf), which contains an unidentified metallocofactor that initiates nucleotide reduction. nrde and nrdf are found in an operon with nrdi, which encodes an unusual flavodoxin proposed to be in ... | 2010 | 20070127 |
| predicting the pathway involved in post-translational modification of elongation factor p in a subset of bacterial species. | background: the bacterial elongation factor p (ef-p) is strictly conserved in bacteria and essential for protein synthesis. it is homologous to the eukaryotic translation initiation factor 5a (eif5a). a highly conserved eif5a lysine is modified into an unusual amino acid derived from spermidine, hypusine. hypusine is absolutely required for eif5a's role in translation in saccharomyces cerevisiae. the homologous lysine of ef-p is also modified to a spermidine derivative in escherichia coli. howev ... | 2010 | 20070887 |
| genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. | the mobility of restriction-modification (rm) gene complexes and their association with genome rearrangements is a subject of active investigation. here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect rm-linked genome rearrangements. rm genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. they were flanked by direct and inverted repeats at a significantly high frequen ... | 2010 | 20071371 |
| telomere-centromere-driven genomic instability contributes to karyotype evolution in a mouse model of melanoma. | aneuploidy and chromosomal instability (cin) are hallmarks of most solid tumors. these alterations may result from inaccurate chromosomal segregation during mitosis, which can occur through several mechanisms including defective telomere metabolism, centrosome amplification, dysfunctional centromeres, and/or defective spindle checkpoint control. in this work, we used an in vitro murine melanoma model that uses a cellular adhesion blockade as a transforming factor to characterize telomeric and ce ... | 2010 | 20072649 |
| the nd2 subunit is labeled by a photoaffinity analogue of asimicin, a potent complex i inhibitor. | nadh:ubiquinone oxidoreductase (complex i) is the entry enzyme of mitochondrial oxidative phosphorylation. to obtain the structural information on inhibitor/quinone binding sites, we synthesized [3h]benzophenone-asimicin ([3h]bpa), a photoaffinity analogue of asimicin, which belongs to the acetogenin family known as the most potent complex i inhibitor. we found that [3h]bpa was photo-crosslinked to nd2, nd1 and nd5 subunits, by the three dimensional separation (blue-native/doubled sds-page) of [ ... | 2010 | 20074573 |
| unique features of animal mitochondrial translation systems. the non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. | in animal mitochondria, several codons are non-universal and their meanings differ depending on the species. in addition, the trna structures that decipher codons are sometimes unusually truncated. these features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. these organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. it is plausible that these events brought about the ... | 2010 | 20075606 |
| structure of intact thermus thermophilus v-atpase by cryo-em reveals organization of the membrane-bound v(o) motor. | the eubacterium thermus thermophilus uses a macromolecular assembly closely related to eukaryotic v-atpase to produce its supply of atp. this simplified v-atpase offers several advantages over eukaryotic v-atpases for structural analysis and investigation of the mechanism of the enzyme. here we report the structure of the complex at approximately 16 a resolution as determined by single particle electron cryomicroscopy (cryo-em). the resolution of the map and our use of cryo-em, rather than negat ... | 2010 | 20080582 |
| temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold. | a widely held hypothesis regarding the thermostability of thermophilic proteins states asserts that, at any given temperature, thermophilic proteins are more rigid than their mesophilic counterparts. many experimental and computational studies have addressed this question with conflicting results. here, we compare two homologous enzymes, one mesophilic (escherichia coli fmn-dependent nitroreductase; ntr) and one thermophilic (thermus thermophilus nadh oxidase; nox), by multiple molecular dynamic ... | 2010 | 20083491 |
| properties of escherichia coli ef-tu mutants designed for fluorescence resonance energy transfer from trna molecules. | here we describe the design, preparation and characterization of 10 ef-tu mutants of potential utility for the study of escherichia coli elongation factor tu (ef-tu) interaction with trna by a fluorescence resonance energy transfer assay. each mutant contains a single cysteine residue at positions in ef-tu that are proximal to trna sites within the aminoacyl-trna.ef-tu.gtp ternary complex that have previously been labeled with fluorophores. these positions fall in the 323-326 and 344-348 regions ... | 2010 | 20083494 |
| the path to next generation biofuels: successes and challenges in the era of synthetic biology. | volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for con ... | 2010 | 20089184 |
| new, closely related haloarchaeal viral elements with different nucleic acid types. | during the search for haloarchaeal viruses, we isolated and characterized a new pleomorphic lipid-containing virus, haloarcula hispanica pleomorphic virus 1 (hhpv-1), that infects the halophilic archaeon haloarcula hispanica. the virus contains a circular double-stranded dna genome of 8,082 bp in size. the organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the halovirus hrpv-1, a pleomorphic single-stranded dna virus tha ... | 2010 | 20089654 |
| structural basis for l-lysine feedback inhibition of homocitrate synthase. | the alpha-aminoadipate pathway of lysine biosynthesis is modulated at the transcriptional and biochemical levels by feedback inhibition. the first enzyme in the alpha-aminoadipate pathway, homocitrate synthase (hcs), is the target of the feedback regulation and is strongly inhibited by l-lysine. here we report the structure of schizosaccharomyces pombe hcs (sphcs) in complex with l-lysine. the structure illustrates that the amino acid directly competes with the substrate 2-oxoglutarate for bindi ... | 2010 | 20089861 |
| a major role of the recfor pathway in dna double-strand-break repair through esdsa in deinococcus radiodurans. | in deinococcus radiodurans, the extreme resistance to dna-shattering treatments such as ionizing radiation or desiccation is correlated with its ability to reconstruct a functional genome from hundreds of chromosomal fragments. the rapid reconstitution of an intact genome is thought to occur through an extended synthesis-dependent strand annealing process (esdsa) followed by dna recombination. here, we investigated the role of key components of the recf pathway in esdsa in this organism naturall ... | 2010 | 20090937 |
| genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles. | enzymes belonging to acyl:coa synthetase (acs) superfamily activate wide variety of substrates and play major role in increasing the structural and functional diversity of various secondary metabolites in microbes and plants. however, due to the large sequence divergence within the superfamily, it is difficult to predict their substrate preference by annotation transfer from the closest homolog. therefore, a large number of acs sequences present in public databases lack any functional annotation ... | 2010 | 20105319 |
| the regulatory protein rraa modulates rna-binding and helicase activities of the e. coli rna degradosome. | the escherichia coli endoribonuclease rnase e is an essential enzyme having key roles in mrna turnover and the processing of several structured rna precursors, and it provides the scaffold to assemble the multienzyme rna degradosome. the activity of rnase e is inhibited by the protein rraa, which can interact with the ribonuclease's degradosome-scaffolding domain. here, we report that rraa can bind to the rna helicase component of the degradosome (rhlb) and the two rna-binding sites in the degra ... | 2010 | 20106955 |