Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| shaping the mitochondrion: mitochondrial biogenesis, dynamics and dysfunction. conference on mitochondrial assembly and dynamics in health and disease. | 2009 | 19949411 | |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| communication between r481 and cu(b) in cytochrome bo(3) ubiquinol oxidase from escherichia coli. | the r481 residue of cytochrome bo(3) ubiquinol oxidase from e. coli is highly conserved in the heme-copper oxidase superfamily. it has been postulated to serve as part of a proton loading site that regulates proton translocation across the protein matrix of the enzyme. along these lines, proton pumping efficiency has been demonstrated to be abolished in many r481 mutants. however, r481q in bo(3) from e. coli has been shown to be fully functional, implying that the positive charge of the arginine ... | 2009 | 19928831 |
| solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175. | 2010 | 19927321 | |
| solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175. | 2010 | 19927321 | |
| the ligand-free state of the tpp riboswitch: a partially folded rna structure. | riboswitches are elements of mrna that regulate gene expression by undergoing structural changes upon binding of small ligands. although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. the ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the rna, with conformational hetero ... | 2009 | 19925806 |
| the ligand-free state of the tpp riboswitch: a partially folded rna structure. | riboswitches are elements of mrna that regulate gene expression by undergoing structural changes upon binding of small ligands. although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. the ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the rna, with conformational hetero ... | 2009 | 19925806 |
| expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase. | an archaeal-type phosphoenolpyruvate carboxylase (pepca) from clostridium perfringens has been expressed in escherichia coli in a soluble form with an amino-terminal his tag. the recombinant protein is enzymatically active and two crystal forms have been obtained. complete diffraction data extending to 3.13 angstrom resolution have been measured from a crystal soaked in kau(cn)(2), using radiation at a wavelength just above the au l(iii) edge. the asymmetric unit contains two tetramers of pepca. | 2009 | 19923749 |
| structure of an n-terminally truncated nudix hydrolase dr2204 from deinococcus radiodurans. | nudix pyrophosphatases are a well represented protein family in the deinococcus radiodurans genome. these hydrolases, which are known to be enzymatically active towards nucleoside diphosphate derivatives, play a role in cleansing the cell pool of potentially deleterious damage products. here, the structure of dr2204, the only adp-ribose pyrophosphatase in the d. radiodurans genome that is known to be active towards flavin adenosine dinucleotide (fad), is presented at 2.0 angstrom resolution. | 2009 | 19923723 |
| structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. | nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ... | 2010 | 19923209 |
| structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. | nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ... | 2010 | 19923209 |
| solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase. | due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ... | 2010 | 19922819 |
| solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase. | due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ... | 2010 | 19922819 |
| h135a controls the redox activity of the sco copper center. kinetic and spectroscopic studies of the his135ala variant of bacillus subtilis sco. | sco-like proteins contain copper bound by two cysteines and a histidine residue. although their function is still incompletely understood, there is a clear involvement with the assembly of cytochrome oxidases that contain the cu(a) center in subunit 2, possibly mediating the transfer of copper into the cu(a) binuclear site. we are investigating the reaction chemistry of bsco, the homologue from bacillus subtilis. our studies have revealed that bsco behaves more like a redox protein than a metall ... | 2009 | 19921776 |
| molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria. | the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ... | 2010 | 19917666 |
| molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria. | the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ... | 2010 | 19917666 |
| analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo. | small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ... | 2010 | 19917641 |
| analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo. | small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ... | 2010 | 19917641 |
| unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis. | heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ... | 2010 | 19917297 |
| unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis. | heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ... | 2010 | 19917297 |
| the conserved lysine69 residue plays a catalytic role in mycobacterium tuberculosis shikimate dehydrogenase. | the shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. m. tuberculosis aroe-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. structural and functional studies indicate that lysine69 may be involved in catalysis and/or substrate binding in m. tuberculosis shikimate dehydrogenase. investigation of the kinetic pro ... | 2009 | 19917104 |
| the linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility. | crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. for the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. this cluster play ... | 2008 | 19915655 |
| characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100. | burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ... | 2010 | 19915006 |
| characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100. | burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ... | 2010 | 19915006 |
| crystal and solution structures of a prokaryotic m16b peptidase: an open and shut case. | the m16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. the m16a and m16c subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. the eukaryotic m16b subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. here, we report the solu ... | 2009 | 19913481 |
| two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition. | in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ... | 2010 | 19906721 |
| two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition. | in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ... | 2010 | 19906721 |
| cryptochromes--a potential magnetoreceptor: what do we know and what do we want to know? | cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addresse ... | 2009 | 19906675 |
| cryptochromes--a potential magnetoreceptor: what do we know and what do we want to know? | cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addresse ... | 2009 | 19906675 |
| trnas: cellular barcodes for amino acids. | the role of trna in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mrna codon. over the same period, it has also become increasingly clear that the ribosome is not the only destination to which trnas deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoac ... | 2010 | 19903480 |
| function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase pa5185 from pseudomonas aeruginosa pao1. | the crystal structure of pa5185, a putative thioesterase from pseudomonas aeruginosa strain pao1, was solved using multi-wavelength anomalous diffraction to 2.4 a. analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. the crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative pa5185 substrate (coa or its derivative). using new crystallization conditions containing thi ... | 2008 | 19898606 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| molecular evolution of multisubunit rna polymerases: structural analysis. | comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ... | 2010 | 19895816 |
| molecular evolution of multisubunit rna polymerases: structural analysis. | comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ... | 2010 | 19895816 |
| direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a. | the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ... | 2010 | 19892705 |
| direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a. | the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ... | 2010 | 19892705 |
| macromolecular micromovements: how rna polymerase translocates. | multi-subunit dna-dependent rna polymerases synthesize rna molecules thousands of nucleotides long. the reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the dna template, or threading of the dna and the nascent rna molecule through the enzyme. reiteration of the nucleotide addition/translocation cycle without dissociation from the dna and rna requires both isomorphic and metamorphic confo ... | 2009 | 19889534 |
| atp-induced conformational changes in hsp70: molecular dynamics and experimental validation of an in silico predicted conformation. | the 70 kda heat shock proteins (hsp70s) play important roles in preventing the misfolding of proteins and repairing damage under stress by coupling atp binding and hydrolysis to protein substrate release and binding, respectively. atp binding is believed to induce closing of the hsp70 nucleotide binding domain (nbd) around the nucleotide. we report here a combined computational-experimental study of this open-closed transition. all-atom molecular dynamics simulations were performed for isolated ... | 2009 | 19883127 |
| isolation and characterization of tirandamycins from a marine-derived streptomyces sp. | the novel dienoyl tetramic acids tirandamycin c (1) and tirandamycin d (2) with activity against vancomycin-resistant enterococcus faecalis were isolated from the marine environmental isolate streptomyces sp. 307-9, which also produces the previously identified compounds tirandamycins a (3) and b (4). spectroscopic analysis of 1 and 2 indicated structural similarity to 3 and 4, with differences only in the pattern of pendant oxygenation on the bicyclic ketal system. the isolation of these putati ... | 2009 | 19883065 |
| the role of upf0157 in the folding of m. tuberculosis dephosphocoenzyme a kinase and the regulation of the latter by ctp. | targeting the biosynthetic pathway of coenzyme a (coa) for drug development will compromise multiple cellular functions of the tubercular pathogen simultaneously. structural divergence in the organization of the penultimate and final enzymes of coa biosynthesis in the host and pathogen and the differences in their regulation mark out the final enzyme, dephosphocoenzyme a kinase (coae) as a potential drug target. | 2009 | 19876400 |
| proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. | deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ... | 2010 | 19875382 |
| proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. | deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ... | 2010 | 19875382 |
| crystal structure of the aspartyl-trna synthetase from entamoeba histolytica. | the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ... | 2010 | 19874856 |
| crystal structure of the aspartyl-trna synthetase from entamoeba histolytica. | the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ... | 2010 | 19874856 |
| kinetics of stop codon recognition by release factor 1. | recognition of stop codons by class i release factors is a fundamental step in the termination phase of protein synthesis. since premature termination is costly to the cell, release factors have to efficiently discriminate between stop and sense codons. to understand the mechanism of discrimination between stop and sense codons, we developed a new, pre-steady state kinetic assay to monitor the interaction of rf1 with the ribosome. our results show that rf1 associates with similar association rat ... | 2009 | 19874047 |
| structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. | escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ... | 2010 | 19864691 |
| structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. | escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ... | 2010 | 19864691 |
| pharmacological targeting of the hsp70 chaperone. | the molecular chaperone, heat shock protein 70 (hsp70), acts at multiple steps in a protein's life cycle, including during the processes of folding, trafficking, remodeling and degradation. to accomplish these various tasks, the activity of hsp70 is shaped by a host of co-chaperones, which bind to the core chaperone and influence its functions. genetic studies have strongly linked hsp70 and its co-chaperones to numerous diseases, including cancer, neurodegeneration and microbial pathogenesis, ye ... | 2009 | 19860737 |
| spermine synthase. | spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ... | 2010 | 19859664 |
| spermine synthase. | spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ... | 2010 | 19859664 |