Publications

environment specific substitution tables for thermophilic proteins.	thermophilic organisms are able to live at high temperatures ranging from 50 to > 100 degrees c. their proteins must be sufficiently stable to function under these extreme conditions; however, the basis for thermostability remains elusive. subtle differences between thermophilic and mesophilic molecules can be found when sequences or structures from homologous proteins are compared, but often these differences are family-specific and few general rules have been derived. the availability of compl ...	2007	17430559
mechanism of chimera formation during the multiple displacement amplification reaction.	multiple displacement amplification (mda) is a method used for amplifying limiting dna sources. the high molecular weight amplified dna is ideal for dna library construction. while this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of mda to generate chimeric dna rearrangements in the amplified dna. determining the source of the dna rearrangements would be an important step towards reducing or eliminating them.	2007	17430586
a tale of two oxidation states: bacterial colonization of arsenic-rich environments.	microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ...	2007	17432936
hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker.	hsp70 chaperones assist in protein folding, disaggregation, and membrane translocation by binding to substrate proteins with an atp-regulated affinity that relies on allosteric coupling between atp-binding and substrate-binding domains. we have studied single- and two-domain versions of the e. coli hsp70, dnak, to explore the mechanism of interdomain communication. we show that the interdomain linker controls atpase activity by binding to a hydrophobic cleft between subdomains ia and iia. furthe ...	2007	17434124
structural basis for converting a general transcription factor into an operon-specific virulence regulator.	rfah, a paralog of the general transcription factor nusg, is recruited to elongating rna polymerase at specific regulatory sites. the x-ray structure of escherichia coli rfah reported here reveals two domains. the n-terminal domain displays high similarity to that of nusg. in contrast, the alpha-helical coiled-coil c domain, while retaining sequence similarity, is strikingly different from the beta barrel of nusg. to our knowledge, such an all-beta to all-alpha transition of the entire domain is ...	2007	17434131
comparison of fungal 80 s ribosomes by cryo-em reveals diversity in structure and conformation of rrna expansion segments.	compared to the prokaryotic 70 s ribosome, the eukaryotic 80 s ribosome contains additional ribosomal proteins and extra segments of rrna, referred to as rrna expansion segments (es). these eukaryotic-specific rrna es are mainly on the periphery of the 80 s ribosome, as revealed by cryo-electron microscopy (cryo-em) studies, but their precise function is not known. to address the question of whether the rrna es are structurally conserved among 80 s ribosomes of different fungi we performed cryo- ...	2007	17434183
high-throughput identification of inhibitors of human mitochondrial peptide deformylase.	the human mitochondrial peptide deformylase (hspdf) provides a potential new target for broadly acting antiproliferative agents. to identify novel nonpeptidomimetic and nonhydroxamic acid-based inhibitors of hspdf, the authors have developed a high-throughput screening (hts) strategy using a fluorescence polarization (fp)-based binding assay as the primary assay for screening chemical libraries, followed by an enzymatic-based assay to confirm hits, prior to characterization of their antiprolifer ...	2007	17435169
analysis of the assembly profiles for mitochondrial- and nuclear-dna-encoded subunits into complex i.	complex i of the respiratory chain is composed of at least 45 subunits that assemble together at the mitochondrial inner membrane. defects in human complex i result in energy generation disorders and are also implicated in parkinson's disease and altered apoptotic signaling. the assembly of this complex is poorly understood and is complicated by its large size and its regulation by two genomes, with seven subunits encoded by mitochondrial dna (mtdna) and the remainder encoded by nuclear genes. h ...	2007	17438127
site-specific s-glutathiolation of mitochondrial nadh ubiquinone reductase.	the generation of reactive oxygen species in mitochondria acts as a redox signal in triggering cellular events such as apoptosis, proliferation, and senescence. overproduction of superoxide (o2-) and o2--derived oxidants changes the redox status of the mitochondrial gsh pool. an electron transport protein, mitochondrial complex i, is the major host of reactive/regulatory protein thiols. an important response of protein thiols to oxidative stress is to reversibly form protein mixed disulfide vi ...	2007	17444656
structures of modified eef2 80s ribosome complexes reveal the role of gtp hydrolysis in translocation.	on the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mrna-trna complex is thought to be provided by gtp hydrolysis of an elongation factor (eef2 in eukaryotes, ef-g in bacteria). we have obtained cryo-em reconstructions of eukaryotic ribosomes complexed with adp-ribosylated eef2 (adpr-eef2), before and after gtp hydrolysis, providing a structural basis for analyzing the gtpase-coupled mechanism of translocation. using the adp-ribosyl group as ...	2007	17446867
enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in methanocaldococcus jannaschii.	the archaeon methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme b biosyntheses. in each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. the genome sequence of m. jannaschii encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. the genes are more similar to each other than to p ...	2007	17449626
the 51-63 base pair of trna confers specificity for binding by ef-tu.	elongation factor tu (ef-tu) exhibits significant specificity for the different elongator trna bodies in order to offset its variable affinity to the esterified amino acid. three x-ray cocrystal structures reveal that while most of the contacts with the protein involve the phosphodiester backbone of trna, a single hydrogen bond is observed between the glu390 and the amino group of a guanine in the 51-63 base pair in the t-stem of trna. here we show that the glu390ala mutation of thermus thermoph ...	2007	17449728
rnammer: consistent and rapid annotation of ribosomal rna genes.	the publication of a complete genome sequence is usually accompanied by annotations of its genes. in contrast to protein coding genes, genes for ribosomal rna (rrna) are often poorly or inconsistently annotated. this makes comparative studies based on rrna genes difficult. we have therefore created computational predictors for the major rrna species from all kingdoms of life and compiled them into a program called rnammer. the program uses hidden markov models trained on data from the 5s ribosom ...	2007	17452365
mechanism for the ttdnaa-tt-oric cooperative interaction at high temperature and duplex opening at an unusual at-rich region in thermoanaerobacter tengcongensis.	thermoanaerobacter tengcongensis is an anaerobic low-gc thermophilic bacterium. to further elucidate the replication initiation of chromosomal dna at high temperature, the interaction between the replication initiator (ttdnaa) and the putative origin (tt-oric) in this thermophile was investigated. we found that efficient binding of ttdnaa to tt-oric at high temperature requires (i) at least two neighboring dnaa boxes, (ii) the specific feature of the ttdnaa domain iv and (iii) the self-oligomeri ...	2007	17452366
loop anchor modification causes the population of an alternative native state in an sh3-like domain.	many stably folded proteins are proposed to contain long, unstructured loops. a series of hybrid proteins (ebe1-4) containing the folded scaffold of photosystem i accessory protein e (psae), an sh3-like protein, and the 40-residue heme-binding loop of cytochrome b(5) was created to inspect the dependence of thermodynamic and kinetic parameters on the residues at the interface of folded and flexible regions. compared to the simplest hybrid (ebe1), the chimeras differed by gly insertions (ebe2, eb ...	2007	17456740
the outer membrane secretin pilq from neisseria meningitidis binds dna.	neisseria meningitidis is naturally competent for transformation throughout its growth cycle. transformation in neisserial species is coupled to the expression of type iv pili, which are present on the cell surface as bundled filamentous appendages, and are assembled, extruded and retracted by the pilus biogenesis components. during the initial phase of the transformation process, binding and uptake of dna takes place with entry through a presumed outer-membrane channel into the periplasm. this ...	2007	17464074
evolutionary rates vary among rrna structural elements.	understanding patterns of rrna evolution is critical for a number of fields, including structure prediction and phylogeny. the standard model of rna evolution is that compensatory mutations in stems make up the bulk of the changes between homologous sequences, while unpaired regions are relatively homogeneous. we show that considerable heterogeneity exists in the relative rates of evolution of different secondary structure categories (stems, loops, bulges, etc.) within the rrna, and that in euka ...	2007	17468501
real-time footprinting of dna in the first kinetically significant intermediate in open complex formation by escherichia coli rna polymerase.	the architecture of cellular rna polymerases (rnaps) dictates that transcription can begin only after promoter dna bends into a deep channel and the start site nucleotide (+1) binds in the active site located on the channel floor. formation of this transcriptionally competent "open" complex (rp(o)) by escherichia coli rnap at the lambdap(r) promoter is greatly accelerated by dna upstream of base pair -47 (with respect to +1). here we report real-time hydroxyl radical (*oh) and potassium permanga ...	2007	17470797
posttranslational synthesis of hypusine: evolutionary progression and specificity of the hypusine modification.	a naturally occurring unusual amino acid, hypusine [n (epsilon)-(4-amino-2-hydroxybutyl)-lysine] is a component of a single cellular protein, eukaryotic translation initiation factor 5a (eif5a). it is a modified lysine with structural contribution from the polyamine spermidine. hypusine is formed in a novel posttranslational modification that involves two enzymes, deoxyhypusine synthase (dhs) and deoxyhypusine hydroxylase (dohh). eif5a and deoxyhypusine/hypusine modification are essential for gr ...	2007	17476569
post-transcriptional modification mapping in the clostridium acetobutylicum 16s rrna by mass spectrometry and reverse transcriptase assays.	post-transcriptional modifications in ribosomal rna are believed to fine-tune the rna functions. the present study describes the characterization of the post-transcriptional modifications in clostridium acetobutylicum 16s rrna, using high-pressure liquid chromatography (hplc) coupled to electrospray ionization mass spectrometry and reverse transcriptase assays. the combination of these techniques allowed the identification of eleven modified nucleosides, which were mapped onto the rrna sequence. ...	2007	17478509
structural elements defining elongation factor tu mediated suppression of codon ambiguity.	in most prokaryotes asn-trna(asn) and gln-trna(gln) are formed by amidation of aspartate and glutamate mischarged onto trna(asn) and trna(gln), respectively. coexistence in the organism of mischarged asp-trna(asn) and glu-trna(gln) and the homologous asn-trna(asn) and gln-trna(gln) does not, however, lead to erroneous incorporation of asp and glu into proteins, since ef-tu discriminates the misacylated trnas from the correctly charged ones. this property contrasts with the canonical function of ...	2007	17478519
fine-tuning of translation termination efficiency in saccharomyces cerevisiae involves two factors in close proximity to the exit tunnel of the ribosome.	in eukaryotes, release factors 1 and 3 (erf1 and erf3) are recruited to promote translation termination when a stop codon on the mrna enters at the ribosomal a-site. however, their overexpression increases termination efficiency only moderately, suggesting that other factors might be involved in the termination process. to determine such unknown components, we performed a genetic screen in saccharomyces cerevisiae that identified genes increasing termination efficiency when overexpressed. for th ...	2007	17483428
structural genomics and drug discovery.	structure determination has already proven useful for lead optimization and direct drug design. the number of high-resolution structures available in public databases today exceeds 30,000 and will definitely aid in structure-based drug design. structural genomics approaches covering whole genomes, topologically similar proteins or gene families are great assets for further progress in the development of new drugs. however, membrane proteins representing 70% of current drug targets are poorly cha ...	2007	17488474
structural basis for functional mimicry of long-variable-arm trna by transfer-messenger rna.	tmrna and small protein b (smpb) are essential trans-translation system components. in the present study, we determined the crystal structure of smpb in complex with the entire trna domain of the tmrna from thermus thermophilus. overall, the ribonucleoprotein complex (trnp) mimics a long-variable-arm trna (class ii trna) in the canonical l-shaped tertiary structure. the tmrna terminus corresponds to the acceptor and t arms, or the upper part, of trna. on the other hand, the smpb protein simulate ...	2007	17488812
identification of the biosynthetic gene cluster and an additional gene for resistance to the antituberculosis drug capreomycin.	capreomycin (cmn) belongs to the tuberactinomycin family of nonribosomal peptide antibiotics that are essential components of the drug arsenal for the treatment of multidrug-resistant tuberculosis. members of this antibiotic family target the ribosomes of sensitive bacteria and disrupt the function of both subunits of the ribosome. resistance to these antibiotics in mycobacterium species arises due to mutations in the genes coding for the 16s or 23s rrna but can also arise due to mutations in a ...	2007	17496129
mechanism for expanding the decoding capacity of transfer rnas by modification of uridines.	one of the most prevalent base modifications involved in decoding is uridine 5-oxyacetic acid at the wobble position of trna. it has been known for several decades that this modification enables a single trna to decode all four codons in a degenerate codon box. we have determined structures of an anticodon stem-loop of trna(val) containing the modified uridine with all four valine codons in the decoding site of the 30s ribosomal subunit. an intramolecular hydrogen bond involving the modification ...	2007	17496902
agrobacterium para/mind-like virc1 spatially coordinates early conjugative dna transfer reactions.	agrobacterium tumefaciens translocates t-dna through a polar virb/d4 type iv secretion (t4s) system. virc1, a factor required for efficient t-dna transfer, bears a deviant walker a and other sequence motifs characteristic of para and mind atpases. here, we show that virc1 promotes conjugative t-dna transfer by stimulating generation of multiple copies per cell of the t-dna substrate (t-complex) through pairwise interactions with the processing factors vird2 relaxase, virc2, and vird1. virc1 also ...	2007	17505518
predicting helical coaxial stacking in rna multibranch loops.	the hypothesis that rna coaxial stacking can be predicted by free energy minimization using nearest-neighbor parameters is tested. the results show 58.2% positive predictive value (ppv) and 65.7% sensitivity for accuracy of the lowest free energy configuration compared with crystal structures. the probability of each stacking configuration can be predicted using a partition function calculation. based on the dependence of accuracy on the calculated probability of the stacks, a probability thresh ...	2007	17507661
cross-linked seca dimers are not functional in protein translocation.	the atpase seca is involved in post-translational protein translocation through the secy channel across the bacterial inner membrane. seca is a dimer that can dissociate into monomers with translocation activity. here, we have addressed whether dissociation of the seca dimer is required for translocation. we show that a dimer in which the two subunits are cross-linked by disulfide bridges is inactive in protein translocation, translocation atpase, and binding to a lipid bilayer. in contrast, upo ...	2007	17511989
rna chaperone activity of l1 ribosomal proteins: phylogenetic conservation and splicing inhibition.	rna chaperone activity is defined as the ability of proteins to either prevent rna from misfolding or to open up misfolded rna conformations. one-third of all large ribosomal subunit proteins from e. coli display this activity, with l1 exhibiting one of the highest activities. here, we demonstrate via the use of in vitro trans- and cis-splicing assays that the rna chaperone activity of l1 is conserved in all three domains of life. however, thermophilic archaeal l1 proteins do not display rna cha ...	2007	17517772
developing limited proteolysis and mass spectrometry for the characterization of ribosome topography.	an approach that combines limited proteolysis and matrix-assisted laser desorption/ionization mass spectrometry (maldi-ms) has been developed to probe protease-accessible sites of ribosomal proteins from intact ribosomes. escherichia coli and thermus thermophilus 70s ribosomes were subjected to limited proteolysis using different proteases under strictly controlled conditions. intact ribosomal proteins and large proteolytic peptides were recovered and directly analyzed by maldi-ms, which allows ...	2007	17521915
interactions between the lipoprotein pilp and the secretin pilq in neisseria meningitidis.	neisseria meningitidis can be the causative agent of meningitis or septicemia. this bacterium expresses type iv pili, which mediate a variety of functions, including autoagglutination, twitching motility, biofilm formation, adherence, and dna uptake during transformation. the secretin pilq supports type iv pilus extrusion and retraction, but it also requires auxiliary proteins for its assembly and localization in the outer membrane. here we have studied the physical properties of the lipoprotein ...	2007	17526700
prediction of functional sites based on the fuzzy oil drop model.	a description of many biological processes requires knowledge of the 3-d structure of proteins and, in particular, the defined active site responsible for biological function. many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localizatio ...	2007	17530916
comparative analysis of eubacterial dna polymerase iii alpha subunits.	dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...	2006	17531796
comparative analysis of eubacterial dna polymerase iii alpha subunits.	dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...	2006	17531796
spectroscopic characterization of heme iron-nitrosyl species and their role in no reductase mechanisms in diiron proteins.		2007	17534533
the first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon pyrococcus furiosus.	we report here the characterization of the first agmatine/cadaverine aminopropyl transferase (acapt), the enzyme responsible for polyamine biosynthesis from an archaeon. the gene pf0127 encoding acapt in the hyperthermophile pyrococcus furiosus was cloned and expressed in escherichia coli, and the recombinant protein was purified to homogeneity. p. furiosus acapt is a homodimer of 65 kda. the broad substrate specificity of the enzyme toward the amine acceptors is unique, as agmatine, 1,3-diamino ...	2007	17545282
collaboration between the clpb aaa+ remodeling protein and the dnak chaperone system.	clpb and hsp104, members of the aaa+ superfamily of proteins, protect cells from the devastating effects of protein inactivation and aggregation that arise after extreme heat stress. they exist as a hexameric ring and contain two nucleotide-binding sites per monomer. clpb and hsp104 are able to dissolve protein aggregates in conjunction with the dnak/hsp70 chaperone system, although the roles of the individual chaperones in disaggregation are not well understood. in the absence of the dnak/hsp70 ...	2007	17545305
long-range structural effects of a charcot-marie-tooth disease-causing mutation in human glycyl-trna synthetase.	functional expansion of specific trna synthetases in higher organisms is well documented. these additional functions may explain why dominant mutations in glycyl-trna synthetase (glyrs) and tyrosyl-trna synthetase cause charcot-marie-tooth (cmt) disease, the most common heritable disease of the peripheral nervous system. at least 10 disease-causing mutant alleles of glyrs have been annotated. these mutations scatter broadly across the primary sequence and have no apparent unifying connection. he ...	2007	17545306
type-2 isopentenyl diphosphate isomerase. mechanistic studies with cyclopropyl and epoxy analogues.		2007	17547410
viral proteomics.	viruses have long been studied not only for their pathology and associated disease but also as model systems for molecular processes and as tools for identifying important cellular regulatory proteins and pathways. recent advances in mass spectrometry methods coupled with the development of proteomic approaches have greatly facilitated the detection of virion components, protein interactions in infected cells, and virally induced changes in the cellular proteome, resulting in a more comprehensiv ...	2007	17554050
new insights into the binding mode of coenzymes: structure of thermus thermophilus delta1-pyrroline-5-carboxylate dehydrogenase complexed with nadp+.	delta(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh) is known to preferentially use nad(+) as a coenzyme. the k(cat) value of thermus thermophilus p5cdh (ttp5cdh) is four times lower for nadp(+) than for nad(+). the crystal structure of nadp(+)-bound ttp5cdh was solved in order to study the structure-activity relationships for the coenzymes. the binding mode of nadp(+) is essentially identical to that in the previously solved nad(+)-bound form, except for the regions around the additional 2'-p ...	2007	17554163
expression, purification, assay, and crystal structure of perdeuterated human arginase i.	arginase is a manganese metalloenzyme that catalyzes the hydrolysis of l-arginine to yield l-ornithine and urea. in order to establish a foundation for future neutron diffraction studies that will provide conclusive structural information regarding proton/deuteron positions in enzyme-inhibitor complexes, we have expressed, purified, assayed, and determined the x-ray crystal structure of perdeuterated (i.e., fully deuterated) human arginase i complexed with 2(s)-amino-6-boronohexanoic acid (abh) ...	2007	17562323
structural basis for recruitment of tandem hotdog domains in acyl-coa thioesterase 7 and its role in inflammation.	acyl-coa thioesterases (acots) catalyze the hydrolysis of fatty acyl-coa to free fatty acid and coa and thereby regulate lipid metabolism and cellular signaling. we present a comprehensive structural and functional characterization of mouse acyl-coa thioesterase 7 (acot7). whereas prokaryotic homologues possess a single thioesterase domain, mammalian acot7 contains a pair of domains in tandem. we determined the crystal structures of both the n- and c-terminal domains of the mouse enzyme, and inf ...	2007	17563367
cloning, expression, purification, crystallization and preliminary x-ray analysis of thermus aquaticus succinyl-coa synthetase.	succinyl-coa synthetase (scs) is an enzyme of the citric acid cycle and is thus found in most species. to date, there are no structures available of scs from a thermophilic organism. to investigate how the enzyme adapts to higher temperatures, scs from thermus aquaticus was cloned, overexpressed, purified and crystallized. attempts to crystallize the enzyme were thwarted by proteolysis of the beta-subunit and preferential crystallization of the truncated form. crystals of full-length scs were gr ...	2007	17565180
preliminary x-ray crystallographic study of glucose dehydrogenase from thermus thermophilus hb8.	thermus thermophilus is an aerobic chemoorganotroph that has been found to grow anaerobically in the presence of nitrate. crystals of glucose dehydrogenase (gdh) from t. thermophilus hb8 belong to space group p2(1), with unit-cell parameters a = 36.90, b = 132.96, c = 60.78 a, beta = 97.2 degrees. preliminary studies and molecular-replacement calculations reveal that the asymmetric unit contains two monomers.	2007	17565193
crystal structure of saccharomyces cerevisiae 6-phosphogluconate dehydrogenase gnd1.	as the third enzyme of the pentose phosphate pathway, 6-phosphogluconate dehydrogenase (6pgdh) is the main generator of cellular nadph. both thioredoxin reductase and glutathione reductase require nadph as the electron donor to reduce oxidized thioredoxin or glutathione (gssg). since thioredoxin and gsh are important antioxidants, it is not surprising that 6pgdh plays a critical role in protecting cells from oxidative stress. furthermore the activity of 6pgdh is associated with several human dis ...	2007	17570834
structural basis for recognition of cognate trna by tyrosyl-trna synthetase from three kingdoms.	the specific aminoacylation of trna by tyrosyl-trna synthetases (tyrrss) relies on the identity determinants in the cognate trna(tyr)s. we have determined the crystal structure of saccharomyces cerevisiae tyrrs (scetyrrs) complexed with a tyr-amp analog and the native trna(tyr)(gpsia). structural information for tyrrs-trna(tyr) complexes is now full-line for three kingdoms. because the archaeal/eukaryotic tyrrss-trna(tyr)s pairs do not cross-react with their bacterial counterparts, the recogniti ...	2007	17576676
a loop loop interaction and a k-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.	the lysine riboswitch is associated to the lysc gene in bacillus subtilis, and the binding of lysine modulates the rna structure to allow the formation of an intrinsic terminator presumably involved in transcription attenuation. the complex secondary structure of the lysine riboswitch aptamer is organized around a five-way junction that undergoes structural changes upon ligand binding. using single-round transcription assays, we show that a loop-loop interaction is important for lysine-induced t ...	2007	17585050
characterization and mechanistic studies of type ii isopentenyl diphosphate:dimethylallyl diphosphate isomerase from staphylococcus aureus.	the recently identified type ii isopentenyl diphosphate (ipp):dimethylallyl diphosphate (dmapp) isomerase (idi-2) is a flavoenzyme that requires fmn and nad(p)h for activity. idi-2 is an essential enzyme for the biosynthesis of isoprenoids in several pathogenic bacteria including staphylococcus aureus, streptococcus pneumoniae, and enterococcus faecalis, and thus is considered as a potential new drug target to battle bacterial infections. one notable feature of the idi-2 reaction is that there i ...	2007	17585782
protein aq_1862 from the hyperthermophilic bacterium aquifex aeolicus is a porin and contains two conductance pathways of different selectivity.	the "hypothetical protein" aq_1862 was isolated from the membrane fraction of aquifex aeolicus and identified as the major porin. in experiments with one conducting unit (molecule) a conductance of 1.4 ns was observed in 0.1 m kcl at ph 7.5. this stable (basic) conductance was superimposed by conductance fluctuations of approximately 0.25 ns. because both events were always observed simultaneously, it is suggested that they are caused by the same molecular entity. nonetheless they show very diff ...	2007	17586565
the 2.2 a resolution crystal structure of bacillus cereus nif3-family protein yqfo reveals a conserved dimetal-binding motif and a regulatory domain.	yqfo of bacillus cereus is a member of the widespread nif3 family of proteins, which has been highlighted as an important target for structural genomics. the n- and c-terminal domains are conserved across the family and contain a dimetal-binding motif in a putative active site. yqfo contains an insert in the middle of the protein, present in a minority of bacterial family members. the structure of yqfo was determined at a resolution of 2.2 a and reveals conservation of the putative active site. ...	2007	17586767
crystal structures of tm0549 and ne1324--two orthologs of e. coli ahas isozyme iii small regulatory subunit.	crystal structures of two orthologs of the regulatory subunit of acetohydroxyacid synthase iii (ahas, ec 2.2.1.6) from thermotoga maritima (tm0549) and nitrosomonas europea (ne1324) were determined by single-wavelength anomalous diffraction methods with the use of selenomethionine derivatives at 2.3 a and 2.5 a, respectively. tm0549 and ne1324 share the same fold, and in both proteins the polypeptide chain contains two separate domains of a similar size. each protein contains a c-terminal domain ...	2007	17586771
direct localization of the 51 and 24 kda subunits of mitochondrial complex i by three-dimensional difference imaging.	complex i is the largest complex in the respiratory chain, and the least understood. we have determined the 3d structure of complex i from yarrowia lipolytica lacking the flavoprotein part of the n-module, which consists of the 51 kda (nubm) and the 24 kda (nuhm) subunits. the reconstruction was determined by 3d electron microscopy of single particles. a comparison to our earlier reconstruction of the complete y. lipolytica complex i clearly assigns the two flavoprotein subunits to an outer lobe ...	2007	17591445
testing constraints on rrna bases that make nonsequence-specific contacts with the codon-anticodon complex in the ribosomal a site.	during protein synthesis, interactions between the decoding center of the ribosome and the codon-anticodon complexes maintain translation accuracy. correct aminoacyl-trnas induce the ribosome to shift into a "closed" conformation that both blocks trna dissociation and accelerates the process of trna acceptance. as part of the ribosomal recognition of cognate trnas, the rrna nucleotides g530 and a1492 form a hydrogen-bonded pair that interacts with the middle position of the codon.anticodon compl ...	2007	17592040
geranylgeranyl diphosphate synthase in fission yeast is a heteromer of farnesyl diphosphate synthase (fps), fps1, and an fps-like protein, spo9, essential for sporulation.	both farnesyl diphosphate synthase (fps) and geranylgeranyl diphosphate synthase (ggps) are key enzymes in the synthesis of various isoprenoid-containing compounds and proteins. here, we describe two novel schizosaccharomyces pombe genes, fps1(+) and spo9(+), whose products are similar to fps in primary structure, but whose functions differ from one another. fps1 is essential for vegetative growth, whereas, a spo9 null mutant exhibits temperature-sensitive growth. expression of fps1(+), but not ...	2007	17596513
advancements in the pathophysiology of friedreich's ataxia and new prospects for treatments.	on november 9-12, 2006, the friedreich's ataxia research alliance (fara) and the national institutes of health (nih) hosted the third international friedreich's ataxia (frda) scientific conference at the nih in bethesda, maryland, highlighting the exciting research leading now to a variety of clinical trials that show promise of effective treatments for this devastating disorder. nearly 150 leading frda scientists from around the world discussed their new insights and findings. the presence of s ...	2007	17596984
protein subunit interfaces: heterodimers versus homodimers.	protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ...	2005	17597849
modeling of phosphomethyl pyrimidine kinase from leptospira interrogans serovar lai strain 56601.	many microorganisms, as well as plants and fungi, synthesize thiamin, but vertebrates do not produce it. phosphomethyl pyrimidine kinase is an enzyme involved in an intermediary step of thiamin biosynthesis from purine molecules. this enzyme is absent in humans. thus, it is a potential chemotherapeutic target for antileptospiral treatment. structure of this enzyme from leptospira interrogans serovar lai strain 56601 has not yet been elucidated. we used the structural template of phosphomethyl py ...	2006	17597880
paradigm development: comparative and predictive 3d modeling of hiv-1 virion infectivity factor (vif).	obtaining structural information about vif is of interest for several reasons that include the study of the interaction of vif with apobec3g, a resistance factor. vif is a potential drug target and its function is essential for the hiv-1 infectivity process. to study vif mechanism of action, we need to decipher its structure. pivotal in this approach is the painstaking prediction of its protein structure. the three-dimensional (3d) crystal structure for vif has not been established. in order to ...	2006	17597910
use of a dominant rpsl allele conferring streptomycin dependence for positive and negative selection in thermus thermophilus.	a spontaneous rpsl mutant of thermus thermophilus was isolated in a search for new selection markers for this organism. this new allele, named rpsl1, encodes a k47r/k57e double mutant s12 ribosomal protein that confers a streptomycin-dependent (sd) phenotype to t. thermophilus. models built on the available three-dimensional structures of the 30s ribosomal subunit revealed that the k47r mutation directly affects the streptomycin binding site on s12, whereas the k57e does not apparently affect th ...	2007	17601820
mechanistic studies of the long chain acyl-coa synthetase faa1p from saccharomyces cerevisiae.	long chain acyl-coa synthetase (acsl; fatty acid coa ligase: amp forming; ec 6.2.1.3) catalyzes the formation of acyl-coa through a process, which requires fatty acid, atp and coenzymea as substrates. in the yeast saccharomyces cerevisiae the principal acsl is faa1p (encoded by the faa1 gene). the preferred substrates for this enzyme are cis-monounsaturated long chain fatty acids. our previous work has shown faa1p is a principal component of a fatty acid transport/activation complex that also in ...	2007	17604220
thermostability of proteins: role of metal binding and ph on the stability of the dinuclear cua site of thermus thermophilus.	the dinuclear copper center (ttcua) forming the electron entry site in the subunit ii of the cytochrome c oxidase in thermus thermophilus shows high stability toward thermal as well as denaturant-induced unfolding of the protein at ambient ph. we have studied the effect of ph on the stability of the holo-protein as well as of the apo-protein by uv-visible absorption, far-uv, and visible circular dichroism spectroscopy. the results show that the holo-protein both in the native mixed-valence state ...	2007	17604317
small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.	the beta-grasp fold (beta-gf), prototyped by ubiquitin (ub), has been recruited for a strikingly diverse range of biochemical functions. these functions include providing a scaffold for different enzymatic active sites (e.g. nudix phosphohydrolases) and iron-sulfur clusters, rna-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. to understand the basis for the functional versatil ...	2007	17605815
nanoscale dewetting transition in protein complex folding.	in a previous study, a surprising drying transition was observed to take place inside the nanoscale hydrophobic channel in the tetramer of the protein melittin. the goal of this paper is to determine if there are other protein complexes capable of displaying a dewetting transition during their final stage of folding. we searched the entire protein data bank (pdb) for all possible candidates, including protein tetramers, dimers, and two-domain proteins, and then performed the molecular dynamics ( ...	2007	17608515
structural characterization of the ribosome maturation protein, rimm.	the rimm protein has been implicated in the maturation of the 30s ribosomal subunit. it binds to ribosomal protein s19, located in the head domain of the 30s subunit. multiple sequence alignments predicted that rimm possesses two domains in its n- and c-terminal regions. in the present study, we have produced thermus thermophilus rimm in both the full-length form (162 residues) and its n-terminal fragment, spanning residues 1 to 85, as soluble proteins in escherichia coli and have performed stru ...	2007	17616598
use of an escherichia coli recombinant producing thermostable polyphosphate kinase as an atp regenerator to produce fructose 1,6-diphosphate.	heat-treated escherichia coli producing thermus polyphosphate kinase regenerated atp by using exogenous polyphosphate. this recombinant could be used as a platform to produce valuable compounds in combination with thermostable phosphorylating or energy-requiring enzymes. in this work, we demonstrated the production of fructose 1,6-diphosphate from fructose and polyphosphate.	2007	17616610
a computational pipeline for high- throughput discovery of cis-regulatory noncoding rna in prokaryotes.	noncoding rnas (ncrnas) are important functional rnas that do not code for proteins. we present a highly efficient computational pipeline for discovering cis-regulatory ncrna motifs de novo. the pipeline differs from previous methods in that it is structure-oriented, does not require a multiple-sequence alignment as input, and is capable of detecting rna motifs with low sequence conservation. we also integrate rna motif prediction with rna homolog search, which improves the quality of the rna mo ...	2007	17616982
crystallization and preliminary x-ray analysis of the oxygenase component (hpab) of 4-hydroxyphenylacetate 3-monooxygenase from thermus thermophilus hb8.	the 4-hydroxyphenylacetate (4hpa) 3-monooxygenase enzyme catalyzes the hydroxylation of 4hpa to 3,4-dihydroxyphenylacetate in the initial step of the degradation pathway of 4hpa. this enzyme consists of two components: an oxygenase (hpab) and a reductase (hpac). hpab hydroxylates 4hpa using an oxygen molecule and a reduced flavin, which is supplied by hpac. hpab from thermus thermophilus hb8 was overexpressed in escherichia coli and crystallized. crystals of hpab were grown in 0.4 m 1,6-hexanedi ...	2007	17620709
crystallization and preliminary x-ray crystallographic study of a putative aspartyl-trna synthetase from the crenarchaeon sulfolobus tokodaii strain 7.	genome analysis suggests that the aspartyl-trna synthetase of the crenarchaeon sulfolobus tokodaii strain 7 belongs to the nondiscriminating type that is believed to catalyze aspartylation of trna(asp) and trna(asn). this protein has been overexpressed in escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method from 100 mm sodium hepes buffer ph 7.5 containing 100 mm nacl and 1.6 m (nh4)2so4 as the crystallizing reagent. diffraction data were collected to 2.3 a ...	2007	17620724
crystal structure of hyperthermophilic esterase este1 and the relationship between its dimerization and thermostability properties.	este1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. the molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of stru ...	2007	17625021
human endonuclease viii-like (neil) proteins in the giant dna mimivirus.	endonuclease viii (nei), which recognizes and repairs oxidized pyrimidines in the base excision repair (ber) pathway, is sparsely distributed among both the prokaryotes and eukaryotes. recently, we and others identified three homologs of escherichia coli endonuclease viii-like (neil) proteins in humans. here, we report identification of human neil homologs in mimivirus, a giant dna virus that infects acanthamoeba. characterization of the two mimiviral homologs, mvnei1 and mvnei2, showed that the ...	2007	17627905
molecular breeding of polymerases for amplification of ancient dna.	in the absence of repair, lesions accumulate in dna. thus, dna persisting in specimens of paleontological, archaeological or forensic interest is inevitably damaged. we describe a strategy for the recovery of genetic information from damaged dna. by molecular breeding of polymerase genes from the genus thermus (taq (thermus aquaticus), tth (thermus thermophilus) and tfl (thermus flavus)) and compartmentalized self-replication selection, we have evolved polymerases that can extend single, double ...	2007	17632524
effects of the deletion of the escherichia coli frataxin homologue cyay on the respiratory nadh:ubiquinone oxidoreductase.	frataxin is discussed as involved in the biogenesis of iron-sulfur clusters. recently it was discovered that a frataxin homologue is a structural component of the respiratory nadh:ubiquinone oxidoreductase (complex i) in thermus thermophilus. it was not clear whether frataxin is in general a component of complex i from bacteria. the escherichia coli homologue of frataxin is coined cyay.	2007	17650323
mg2+ binding and archaeosine modification stabilize the g15 c48 levitt base pair in trnas.	the g15-c48 levitt base pair, located at a crucial position in the core of canonical trnas, assumes a reverse watson-crick (rwc) geometry. by means of bioinformatics analysis and quantum mechanics calculations we show here that such a geometry is moderately more stable than an alternative bifurcated trans geometry, involving the guanine watson-crick face and the cytosine keto group, which we have also found in known rna structures. however we also demonstrate that the rwc geometry can take advan ...	2007	17652139
changes in the conformation of 5s rrna cause alterations in principal functions of the ribosomal nanomachine.	5s rrna is an integral component of the large ribosomal subunit in virtually all living organisms. polyamine binding to 5s rrna was investigated by cross-linking of n1-azidobenzamidino (aba)-spermine to naked 5s rrna or 50s ribosomal subunits and whole ribosomes from escherichia coli cells. aba-spermine cross-linking sites were kinetically measured and their positions in 5s rrna were localized by primer extension analysis. helices iii and v, and loops a, c, d and e in naked 5s rrna were found to ...	2007	17652323
a comparative analysis of the triloops in all high-resolution rna structures reveals sequence structure relationships.	despite an increasing number of experimentally determined rna structures, the gap between the number of structures and that of rna families is still growing. to overcome this limitation, efficient and reliable rna modeling methodologies must be developed. in order to reach this goal, here, we show how triloop sequence-structure relationships have been inferred through a systematic analysis of all triloops found in available high-resolution structures. the structural annotation of all triloops al ...	2007	17652406
biosynthesis of isoprenoids in plants: structure of the 2c-methyl-d-erithrytol 2,4-cyclodiphosphate synthase from arabidopsis thaliana. comparison with the bacterial enzymes.	the x-ray crystal structure of the 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase (mcs) from arabidopsis thaliana has been solved at 2.3 a resolution in complex with a cytidine-5-monophosphate (cmp) molecule. this is the first structure determined of an mcs enzyme from a plant. major differences between the a. thaliana and bacterial mcs structures are found in the large molecular cavity that forms between subunits and involve residues that are highly conserved among plants. in some bacteri ...	2007	17660251
tertiary structure and function of an rna motif required for plant vascular entry to initiate systemic trafficking.	vascular entry is a decisive step for the initiation of long-distance movement of infectious and endogenous rnas, silencing signals and developmental/defense signals in plants. however, the mechanisms remain poorly understood. we used potato spindle tuber viroid (pstvd) as a model to investigate the direct role of the rna itself in vascular entry. we report here the identification of an rna motif that is required for pstvd to traffic from nonvascular into the vascular tissue phloem to initiate s ...	2007	17660743
negamycin binds to the wall of the nascent chain exit tunnel of the 50s ribosomal subunit.	negamycin, a small-molecule inhibitor of protein synthesis, binds the haloarcula marismortui 50s ribosomal subunit at a single site formed by highly conserved rna nucleotides near the cytosolic end of the nascent chain exit tunnel. the mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive.	2007	17664317
crystallization and preliminary x-ray diffraction analysis of a soluble domain of the putative zinc transporter czrb from thermus thermophilus.	czrb is a putative zinc transporter from thermus thermophilus. the protein is proposed to consist of a hexahelical transmembrane domain with a cytosolic extramembranal c-terminus. the latter 92-residue fragment may be expressed free and may function independently of the full-length integral membrane protein. a 6xhis-tagged form of the water-soluble fragment has been overexpressed in escherichia coli and diffraction-quality crystals of the tagged and tag-free variants have been grown. preliminary ...	2007	17671365
crystallization and preliminary x-ray diffraction analysis of the cytosolic domain of the mg2+ transporter mgte.	the mgte family of mg(2+) transporters is ubiquitously conserved in all domains of life. the cytosolic domains of the mgte mg(2+) transporters include a cystathionine-beta-synthase (cbs) domain which is known to play a regulatory function in transporter proteins. the cytosolic domain of mgte from thermus thermophilus was overexpressed, purified and crystallized in the presence and absence of mg(2+). the crystals formed in the presence of mg(2+) diffracted x-rays to 2.3 a resolution using synchro ...	2007	17671366
crystallization and preliminary x-ray diffraction analysis of the full-length mg2+ transporter mgte.	the mgte family of mg(2+) transporters are ubiquitously conserved in all three domains. the genes encoding full-length mgte from seven different species were cloned. three of the seven mgte transporters were overexpressed and purified for use in crystallization trials. only thermus thermophilus mgte was successfully crystallized using the sitting-drop vapour-diffusion method. selenomethionine-substituted (semet) crystals were obtained by cross-microseeding using the native microcrystals. the sem ...	2007	17671367
crystallization and preliminary crystallographic analysis of hygromycin b phosphotransferase from escherichia coli.	aminoglycoside antibiotics, such as hygromycin, kanamycin, neomycin, spectinomycin and streptomycin, inhibit protein synthesis by acting on bacterial and eukaryotic ribosomes. hygromycin b phosphotransferase (hph; ec 2.7.1.119) converts hygromycin b to 7''-o-phosphohygromycin using a phosphate moiety from atp, resulting in the loss of its cell-killing activity. the hph protein has been crystallized for the first time using a thermostable mutant and the hanging-drop vapour-diffusion method. the c ...	2007	17671368
identification of genes encoding trna modification enzymes by comparative genomics.	as the molecular adapters between codons and amino acids, transfer-rnas are pivotal molecules of the genetic code. the coding properties of a trna molecule do not reside only in its primary sequence. posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. despite a wealth of biophysical and structural knowledge ...	2007	17673083
complete genomic sequence and mass spectrometric analysis of highly diverse, atypical bacillus thuringiensis phage 0305phi8-36.	to investigate the apparent genomic complexity of long-genome bacteriophages, we have sequenced the 218,948-bp genome (6479-bp terminal repeat), and identified the virion proteins (55), of bacillus thuringiensis bacteriophage 0305phi8-36. phage 0305phi8-36 is an atypical myovirus with three large curly tail fibers. an accurate mode of dna pyrosequencing was used to sequence the genome and mass spectrometry was used to accomplish the comprehensive virion protein survey. advanced informatic techni ...	2007	17673272
the archaeon methanosarcina acetivorans contains a protein disulfide reductase with an iron-sulfur cluster.	methanosarcina acetivorans, a strictly anaerobic methane-producing species belonging to the domain archaea, contains a gene cluster annotated with homologs encoding oxidative stress proteins. one of the genes (ma3736) is annotated as a gene encoding an uncharacterized carboxymuconolactone decarboxylase, an enzyme required for aerobic growth with aromatic compounds by species in the domain bacteria. methane-producing species are not known to utilize aromatic compounds, suggesting that ma3736 is i ...	2007	17675382
sympatric drosophila simulans flies with distinct mtdna show age related differences in mitochondrial metabolism.	the primary causes of age-related changes in mitochondrial metabolism are not known. the goal of this study is to document the influence of naturally occurring mtdna variation on age dependent changes in mitochondrial respiration, hydrogen peroxide (h(2)o(2)) generation and antioxidant defenses in the fly drosophila simulans. possible changes include an increase in rates of reactive oxygen species production with age and/or an age dependent decrease in antioxidant response. for this study we hav ...	2007	17681231
crystal structure of the escherichia coli regulator of sigma70, rsd, in complex with sigma70 domain 4.	the escherichia coli rsd protein binds tightly and specifically to the rna polymerase (rnap) sigma(70) factor. rsd plays a role in alternative sigma factor-dependent transcription by biasing the competition between sigma(70) and alternative sigma factors for the available core rnap. here, we determined the 2.6 a-resolution x-ray crystal structure of rsd bound to sigma(70) domain 4 (sigma(70)(4)), the primary determinant for rsd binding within sigma(70). the structure reveals that rsd binding int ...	2007	17681541
discovery of novel dna gyrase inhibitors by high-throughput virtual screening.	the bacterial type ii topoisomerases dna gyrase and topoisomerase iv are validated targets for clinically useful quinolone antimicrobial drugs. a significant limitation to widely utilized quinolone inhibitors is the emergence of drug-resistant bacteria due to an altered dna gyrase. to address this problem, we have used structure-based molecular docking to identify novel drug-like small molecules that target sites distinct from those targeted by quinolone inhibitors. a chemical ligand database co ...	2007	17682095
analysis of a nuclease activity of catalytic domain of thermus thermophilus muts2 by high-accuracy mass spectrometry.	electrospray ionization with fourier-transform ion cyclotron resonance mass spectrometry (esi-ft icr ms) is a powerful tool for analyzing the precise structural features of biopolymers, including oligonucleotides. here, we described the detailed characterization of a newly discovered nuclease activity of the c-terminal domain of thermus thermophilus muts2 (ttmuts2). using this method, the length, nucleotide content and nature of the 5'- and 3'-termini of the product oligonucleotides were accurat ...	2007	17686785
hitting bacteria at the heart of the central dogma: sequence-specific inhibition.	abstract: an important objective in developing new drugs is the achievement of high specificity to maximize curing effect and minimize side-effects, and high specificity is an integral part of the antisense approach. the antisense techniques have been extensively developed from the application of simple long, regular antisense rna (asrna) molecules to highly modified versions conferring resistance to nucleases, stability of hybrid formation and other beneficial characteristics, though still pres ...	2007	17692125
identification of indole derivatives as self-growth inhibitors of symbiobacterium thermophilum, a unique bacterium whose growth depends on coculture with a bacillus sp.	symbiobacterium thermophilum is a syntrophic bacterium whose growth depends on coculture with a bacillus sp. recently, we discovered that co(2) generated by bacillus is the major inducer for the growth of s. thermophilum; however, the evidence suggested that an additional element is required for its full growth. here, we studied the self-growth-inhibitory substances produced by s. thermophilum. we succeeded in purifying two substances from an ether extract of the culture supernatant of s. thermo ...	2007	17693561
fr3d: finding local and composite recurrent structural motifs in rna 3d structures.	new methods are described for finding recurrent three-dimensional (3d) motifs in rna atomic-resolution structures. recurrent rna 3d motifs are sets of rna nucleotides with similar spatial arrangements. they can be local or composite. local motifs comprise nucleotides that occur in the same hairpin or internal loop. composite motifs comprise nucleotides belonging to three or more different rna strand segments or molecules. we use a base-centered approach to construct efficient, yet exhaustive sea ...	2007	17694311
fr3d: finding local and composite recurrent structural motifs in rna 3d structures.	new methods are described for finding recurrent three-dimensional (3d) motifs in rna atomic-resolution structures. recurrent rna 3d motifs are sets of rna nucleotides with similar spatial arrangements. they can be local or composite. local motifs comprise nucleotides that occur in the same hairpin or internal loop. composite motifs comprise nucleotides belonging to three or more different rna strand segments or molecules. we use a base-centered approach to construct efficient, yet exhaustive sea ...	2007	17694311
type i and type ii fatty acid biosynthesis in eimeria tenella: enoyl reductase activity and structure.	apicomplexan parasites of the genus eimeria are the major causative agent of avian coccidiosis, leading to high economic losses in the poultry industry. recent results show that eimeria tenella harbours an apicoplast organelle, and that a key biosynthetic enzyme, enoyl reductase, is located in this organelle. in related parasites, enoyl reductase is one component of a type ii fatty acid synthase (fas) and has proven to be an attractive target for antimicrobial compounds. we cloned and expressed ...	2007	17697396
a functional interaction of smpb with tmrna for determination of the resuming point of trans-translation.	in trans-translation, transfer-messenger rna (tmrna), possessing a dual function as a trna and an mrna, relieves a stalled translation on the ribosome with the help of smpb. here, we established an in vitro system using escherichia coli translation and trans-translation factors to evaluate two steps of trans-translation, peptidyl transfer from peptidyl-trna to alanyl-tmrna and translation of the resume codon on tmrna. using this system, the effects of several mutations upstream of the tag-encodi ...	2007	17698641
conformations of flanking bases in hiv-1 rna dis kissing complexes studied by molecular dynamics.	explicit solvent molecular dynamics simulations (in total almost 800 ns including locally enhanced sampling runs) were applied with different ion conditions and with two force fields (amber and charmm) to characterize typical geometries adopted by the flanking bases in the rna kissing-loop complexes. we focus on flanking base positions in multiple x-ray and nmr structures of hiv-1 dis kissing complexes and kissing complex from the large ribosomal subunit of haloarcula marismortui. an initial x-r ...	2007	17704156
enzymes involved in dna ligation and end-healing in the radioresistant bacterium deinococcus radiodurans.	enzymes involved in dna metabolic events of the highly radioresistant bacterium deinococcus radiodurans are currently examined to understand the mechanisms that protect and repair the deinococcus radiodurans genome after extremely high doses of gamma-irradiation. although several deinococcus radiodurans dna repair enzymes have been characterised, no biochemical data is available for dna ligation and dna endhealing enzymes of deinococcus radiodurans so far. dna ligases are necessary to seal broke ...	2007	17705817
allosteric control of the rna polymerase by the elongation factor rfah.	efficient transcription of long polycistronic operons in bacteria frequently relies on accessory proteins but their molecular mechanisms remain obscure. rfah is a cellular elongation factor that acts as a polarity suppressor by increasing rna polymerase (rnap) processivity. in this work, we provide evidence that rfah acts by reducing transcriptional pausing at certain positions rather than by accelerating rnap at all sites. we show that 'fast' rnap variants are characterized by pause-free rna ch ...	2007	17711918