| the membrane protein data bank. | the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ... | 2005 | 16314922 |
| the membrane protein data bank. | the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ... | 2005 | 16314922 |
| multiplexed tandem pcr: gene profiling from small amounts of rna using sybr green detection. | multiplexed tandem pcr (mt-pcr) is a process for highly multiplexed gene expression profiling. in the first step, multiple primer pairs are added to the rna to be analysed together with reverse transcriptase and taq dna polymerase. following reverse transcription, the multiplexed amplicons are simultaneously amplified for a small number of cycles so as to avoid competition between amplicons. the reaction product is then diluted and analysed in multiple individual pcrs using primers nested inside ... | 2005 | 16314310 |
| miniseed3 (mini3), a wrky family gene, and haiku2 (iku2), a leucine-rich repeat (lrr) kinase gene, are regulators of seed size in arabidopsis. | we have identified mutant alleles of two sporophytically acting genes, haiku2 (iku2) and miniseed3 (mini3). homozygotes of these alleles produce a small seed phenotype associated with reduced growth and early cellularization of the endosperm. this phenotype is similar to that described for another seed size gene, iku1. mini3 encodes wrky10, a wrky class transcription factor. mini3 promoter::gus fusions show the gene is expressed in pollen and in the developing endosperm from the two nuclei stage ... | 2005 | 16293693 |
| a mutation in the anticodon of a single trnaala is sufficient to confer auxin resistance in arabidopsis. | auxin-resistant mutants have been useful for dissecting the mechanisms that underlie auxin-mediated biological processes. here we report the isolation and molecular characterization of a novel auxin-resistant mutant in arabidopsis (arabidopsis thaliana). like known mutated aux/iaa transcription factors, the mutant described here displayed dominant resistance to exogenously supplied auxins (sirtinol, 2,4-dichlorophenoxyacetic acid, indole-3-acetic acid) and a host of pleiotropic phenotypes, inclu ... | 2005 | 16244142 |
| a colorimetric method for point mutation detection using high-fidelity dna ligase. | the present study reported proof-of-principle for a genotyping assay approach that can detect single nucleotide polymorphisms (snps) through the gold nanoparticle assembly and the ligase reaction. by incorporating the high-fidelity dna ligase (tth dna ligase) into the allele-specific ligation-based gold nanoparticle assembly, this assay provided a convenient yet powerful colorimetric detection that enabled a straightforward single-base discrimination without the need of precise temperature contr ... | 2005 | 16257979 |
| single-molecule forster resonance energy transfer study of protein dynamics under denaturing conditions. | proteins are highly complex systems, exhibiting a substantial degree of structural variability in their folded state. in the presence of denaturants, the heterogeneity is greatly enhanced, and fluctuations among vast numbers of folded and unfolded conformations occur via many different pathways. here, we have studied the structure and dynamics of the small enzyme ribonuclease hi (rnase h) in the presence of the chemical denaturant guanidinium chloride (gdmcl) using single-molecule fluorescence m ... | 2005 | 16221762 |
| amyloid formation of a protein in the absence of initial unfolding and destabilization of the native state. | in 5% (v/v) trifluoroethanol, ph 5.5, 25 degrees c one of the acylphosphatases from drosophila melanogaster (acpdro2) forms fibrillar aggregates that bind thioflavin t and congo red and have an extensive beta-sheet structure, as revealed by circular dichroism. atomic force microscopy indicates that the fibrils and their constituent protofilaments have diameters compatible with those of natural amyloid fibrils. spectroscopic and biochemical investigation, carried out using near- and far-uv circul ... | 2005 | 16169977 |
| deacylated trna is released from the e site upon a site occupation but before gtp is hydrolyzed by ef-tu. | the presence or absence of deacylated trna at the e site sharply influences the activation energy required for binding of a ternary complex to the ribosomal a site indicating the different conformations that the e-trna imparts on the ribosome. here we address two questions: (i) whether or not peptidyltransferase--the essential catalytic activity of the large ribosomal subunit--also depends on the occupancy state of the e site and (ii) at what stage the e-trna is released during an elongation cyc ... | 2005 | 16166657 |
| protein content of minimal and ancestral ribosome. | minimal genome approaches seek to define the smallest gene complement compatible with modern-type cellular life on earth. a consensus of computational and experimental approaches indicates that a minimal genome is close to 300 protein-coding genes, if a rich medium is provided for cell growth. i relate ribosomal gene content in completely sequenced genomes to ribosomal subunit structure and approximate the protein components of the putative minimal ribosome and the ribosome of the last universal ... | 2005 | 16043494 |
| the genomics of disulfide bonding and protein stabilization in thermophiles. | thermophilic organisms flourish in varied high-temperature environmental niches that are deadly to other organisms. recently, genomic evidence has implicated a critical role for disulfide bonds in the structural stabilization of intracellular proteins from certain of these organisms, contrary to the conventional view that structural disulfide bonds are exclusively extracellular. here both computational and structural data are presented to explore the occurrence of disulfide bonds as a protein-st ... | 2005 | 16111437 |
| profunc: a server for predicting protein function from 3d structure. | profunc (http://www.ebi.ac.uk/thornton-srv/databases/profunc) is a web server for predicting the likely function of proteins whose 3d structure is known but whose function is not. users submit the coordinates of their structure to the server in pdb format. profunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. a summary of the analyses provides an at-a-glance ... | 2005 | 15980588 |
| popscomp: an automated interaction analysis of biomolecular complexes. | large-scale analysis of biomolecular complexes reveals the functional network within the cell. computational methods are required to extract the essential information from the available data. the popscomp server is designed to calculate the interaction surface between all components of a given complex structure consisting of proteins, dna or rna molecules. the server returns matrices and graphs of surface area burial that can be used to automatically annotate components and residues that are inv ... | 2005 | 15980485 |
| identification of novel restriction endonuclease-like fold families among hypothetical proteins. | restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. the lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. using the consensus fold recognition method meta-basic that combines sequence profiles wi ... | 2005 | 15972856 |
| mapping the interaction of smpb with ribosomes by footprinting of ribosomal rna. | in trans-translation transfer messenger rna (tmrna) and small protein b (smpb) rescue ribosomes stalled on truncated or in other ways problematic mrnas. smpb promotes the binding of tmrna to the ribosome but there is uncertainty about the number of participating smpb molecules as well as their ribosomal location. here, the interaction of smpb with ribosomal subunits and ribosomes was studied by isolation of smpb containing complexes followed by chemical modification of ribosomal rna with dimethy ... | 2005 | 15972795 |
| 5s rrna: structure and function from head to toe. | 5s rrna is uniquely positioned so as to link together all of the functional centers of the ribosome. previous studies have supported the hypothesis that 5s rrna acts as a physical transducer of information, facilitating communication between the different functional centers and coordinating of the multiple events catalyzed by the ribosome. here, we present a synthesis of both structural and genetic information to construct a more detailed picture of how 5s rrna may act to transmit and coordinate ... | 2005 | 18074004 |
| the cryptochromes. | cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. they also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (uv-a) light in plants. cryptochromes are probably the evolutionary descendents of dna photolyases, which are light-activated dna-repair enzymes, and are classified into three groups -- plant cryptochromes, animal cryp ... | 2005 | 15892880 |
| diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays. | padlock probes (plps) are long oligonucleotides, whose ends are complementary to adjacent target sequences. upon hybridization to the target, the two ends are brought into contact, allowing plp circularization by ligation. plps provide extremely specific target recognition, which is followed by universal amplification and microarray detection. since target recognition is separated from downstream processing, plps enable the development of flexible and extendable diagnostic systems, targeting div ... | 2005 | 15860767 |
| recurrent structural rna motifs, isostericity matrices and sequence alignments. | the occurrences of two recurrent motifs in ribosomal rna sequences, the kink-turn and the c-loop, are examined in crystal structures and systematically compared with sequence alignments of rrnas from the three kingdoms of life in order to identify the range of the structural and sequence variations. isostericity matrices are used to analyze structurally the sequence variations of the characteristic non-watson-crick base pairs for each motif. we show that isostericity matrices for non-watson-cric ... | 2005 | 15860776 |
| independent binding sites of small protein b onto transfer-messenger rna during trans-translation. | stalled bacterial ribosomes are freed by transfer-messenger rna (tmrna). with the help of small protein b (smpb), protein synthesis restarts and tmrna adds a tag to the stalled protein for destruction. the conformation of a 347 nt long tmrna from a thermophile and its interactions with smpb were monitored using structural probes. the rna is highly folded, including the reading frame, with <30% of unpaired residues. footprints between smpb and tmrna are in the elbow of the trna domain, in some ps ... | 2005 | 15860775 |
| atp-sensitive k+ channel channel/enzyme multimer: metabolic gating in the heart. | cardiac atp-sensitive k(+) (k(atp)) channels, gated by cellular metabolism, are formed by association of the inwardly rectifying potassium channel kir6.2, the potassium conducting subunit, and sur2a, the atp-binding cassette protein that serves as the regulatory subunit. kir6.2 is the principal site of atp-induced channel inhibition, while sur2a regulates k(+) flux through adenine nucleotide binding and catalysis. the atpase-driven conformations within the regulatory sur2a subunit of the k(atp) ... | 2005 | 15910874 |
| the application of cluster analysis in the intercomparison of loop structures in rna. | we have developed a computational approach for the comparison and classification of rna loop structures. hairpin or interior loops identified in atomic resolution rna structures were intercompared by conformational matching. the root-mean-square deviation (rmsd) values between all pairs of rna fragments of interest, even if from different molecules, are calculated. subsequently, cluster analysis is performed on the resulting matrix of rmsd distances using the unweighted pair group method with ar ... | 2005 | 15769871 |
| towards understanding the molecular basis of bacterial dna segregation. | bacteria ensure the fidelity of genetic inheritance by the coordinated control of chromosome segregation and cell division. here, we review the molecules and mechanisms that govern the correct subcellular positioning and rapid separation of newly replicated chromosomes and plasmids towards the cell poles and, significantly, the emergence of mitotic-like machineries capable of segregating plasmid dna. we further describe surprising similarities between proteins involved in dna partitioning (para/ ... | 2005 | 15897178 |
| graphical representation of ribosomal rna probe accessibility data using arb software package. | taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. a frequently applied technology, fluorescence in situ hybridization (fish), besides single cell identification, allows the localization and functional studies of the microbial community composition. careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridiza ... | 2005 | 15777482 |
| another biological effect of tosylphenylalanylchloromethane (tpck): it prevents p47phox phosphorylation and translocation upon neutrophil stimulation. | tpck (tosylphenylalanylchloromethane), first discovered as a serine protease inhibitor, has been described to affect in diverse systems a number of physiological events probably unrelated to its antiprotease effect, such as proliferation, apoptosis and tumour formation. in the present study, we focus on its inhibition of the neutrophil respiratory burst, an important element of non-specific immunological defence. the superoxide anion-producing enzyme, nadph oxidase, is quiescent in resting cells ... | 2005 | 15498025 |
| hsp70 chaperones: cellular functions and molecular mechanism. | hsp70 proteins are central components of the cellular network of molecular chaperones and folding catalysts. they assist a large variety of protein folding processes in the cell by transient association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins. the substrate binding and release cycle is driven by the switching of hsp70 between the low-affinity atp bound state and the high-affinity adp bound state. thus, atp binding and hydrolysis a ... | 2005 | 15770419 |
| protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. | recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. these difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the di ... | 2005 | 15689503 |
| initiation of protein synthesis in bacteria. | valuable information on translation initiation is available from biochemical data and recently solved structures. we present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. the first section describes the ribosomal features relevant to the initiation process. subsequent sections describe the structure, function, and interactions of the mrna, the initiator trna, and the initiatio ... | 2005 | 15755955 |
| evolutionary profiles from the qr factorization of multiple sequence alignments. | we present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. the method, based on the multidimensional qr factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of ... | 2005 | 15741270 |
| homology-extended sequence alignment. | we present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. for each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into a position-specific pre-alignment profile. the enriched position-specific profile is used for standard progressive alignment, thereby more accura ... | 2005 | 15699183 |
| nadp-malate dehydrogenase from unicellular green alga chlamydomonas reinhardtii. a first step toward redox regulation? | the determinants of the thioredoxin (trx)-dependent redox regulation of the chloroplastic nadp-malate dehydrogenase (nadp-mdh) from the eukaryotic green alga chlamydomonas reinhardtii have been investigated using site-directed mutagenesis. the results indicate that a single c-terminal disulfide is responsible for this regulation. the redox midpoint potential of this disulfide is less negative than that of the higher plant enzyme. the regulation is of an all-or-nothing type, lacking the fine-tuni ... | 2005 | 15579663 |
| ribosomal protein l1 recognizes the same specific structural motif in its target sites on the autoregulatory mrna and 23s rrna. | the rna-binding ability of ribosomal protein l1 is of profound interest since the protein has a dual function as a ribosomal protein binding rrna and as a translational repressor binding its mrna. here, we report the crystal structure of ribosomal protein l1 in complex with a specific fragment of its mrna and compare it with the structure of l1 in complex with a specific fragment of 23s rrna determined earlier. in both complexes, a strongly conserved rna structural motif is involved in l1 bindin ... | 2005 | 15659579 |
| a vibrational spectral maker for probing the hydrogen-bonding status of protonated asp and glu residues. | hydrogen bonding is a fundamental element in protein structure and function. breaking a single hydrogen bond may impair the stability of a protein. we report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated asp or glu residues in proteins. ab initio computational studies were performed on hydrogen-bonding interactions of a cooh group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function th ... | 2005 | 15653739 |
| site-specific labeling of the ribosome for single-molecule spectroscopy. | single-molecule fluorescence spectroscopy can reveal mechanistic and kinetic details that may not be observed in static structural and bulk biochemical studies of protein synthesis. one approach requires site-specific and stable attachment of fluorophores to the components of translation machinery. fluorescent tagging of the ribosome is a prerequisite for the observation of dynamic changes in ribosomal conformation during translation using fluorescence methods. modifications of the ribosomal par ... | 2005 | 15647501 |
| 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 |
| mechanism of trna-dependent editing in translational quality control. | protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ... | 2006 | 17185419 |
| mechanism of trna-dependent editing in translational quality control. | protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ... | 2006 | 17185419 |
| a structural model reveals energy transduction in dynein. | intracellular active transport is driven by atp-hydrolyzing motor proteins that move along cytoskeletal filaments. in particular, the microtubule-associated dynein motor is involved in the transport of organelles and vesicles, the maintenance of the golgi, and mitosis. however, unlike kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery, due primarily to the lack of a high-resolution molecular structure. using homology modelin ... | 2006 | 17121997 |
| characteristics of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) rrna genes of apis mellifera (insecta: hymenoptera): structure, organization, and retrotransposable elements. | as an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) ribosomal rna (rrna)-encoding gene sequences (rdna) and related internally and externally transcribed spacer regions of apis mellifera (insecta: hymenoptera: apocrita). additionally, we predict secondary structures for the mature rrna molecules based on comparative sequence analyses with other arthropod taxa and reference to re ... | 2006 | 17069639 |
| diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-i release factor that potentially recognizes atypical mrna signals other than normal stop codons. | while all codons that specify amino acids are universally recognized by trna molecules, codons signaling termination of translation are recognized by proteins known as class-i release factors (rf). in most eukaryotes and archaea a single rf accomplishes termination at all three stop codons. in most bacteria, there are two rfs with overlapping specificity, rf1 recognizes ua(a/g) and rf2 recognizes u(a/g)a. | 2006 | 16970810 |
| the structure and function of frataxin. | frataxin, a highly conserved protein found in prokaryotes and eukaryotes, is required for efficient regulation of cellular iron homeostasis. humans with a frataxin deficiency have the cardio- and neurodegenerative disorder friedreich's ataxia, commonly resulting from a gaa trinucleotide repeat expansion in the frataxin gene. while frataxin's specific function remains a point of controversy, the general consensus is that the protein assists in controlling cellular iron homeostasis by directly bin ... | 2006 | 16911956 |
| structural basis for topoisomerase vi inhibition by the anti-hsp90 drug radicicol. | members of the ghl atpase superfamily, including type ii topoisomerases, hsp90-class chaperones, and mutl, all share a common ghkl-type atp-binding fold and act as nucleotide-controlled 'molecular clamps'. these enzymes' atp-binding sites have proven to be rich drug targets, and certain inhibitors of type ii topoisomerases and hsp90 bind to this region and competitively inhibit these enzymes. recently, it was found that radicicol, a drug known to block hsp90 function, also inhibits the archaeal ... | 2006 | 16920739 |
| a new paradigm: manganese superoxide dismutase influences the production of h2o2 in cells and thereby their biological state. | the principal source of hydrogen peroxide in mitochondria is thought to be from the dismutation of superoxide via the enzyme manganese superoxide dismutase (mnsod). however, the nature of the effect of sod on the cellular production of h(2)o(2) is not widely appreciated. the current paradigm is that the presence of sod results in a lower level of h(2)o(2) because it would prevent the non-enzymatic reactions of superoxide that form h(2)o(2). the goal of this work was to: a) demonstrate that sod c ... | 2006 | 17015180 |
| evidence for existence of "mesotogas," members of the order thermotogales adapted to low-temperature environments. | all cultivated isolates of the bacterial order thermotogales are either thermophiles or hyperthermophiles, but thermotogales 16s rrna gene sequences have been detected in many mesophilic anaerobic and microaerophilic environments, particularly within communities involved in the remediation of pollutants. here we provide metagenomic evidence for the existence of thermotogales lineages, which we informally call "mesotoga," that are adapted to growth at lower temperatures. two fosmid clones contain ... | 2006 | 16820506 |
| functional conformations of the l11-ribosomal rna complex revealed by correlative analysis of cryo-em and molecular dynamics simulations. | the interaction between the gtpase-associated center (gac) and the aminoacyl-trna.ef-tu.gtp ternary complex is of crucial importance in the dynamic process of decoding and trna accommodation. the gac includes protein l11 and helices 43-44 of 23s rrna (referred to as l11-rrna complex). in this study, a method of fitting based on a systematic comparison between cryo-electron microscopy (cryo-em) density maps and structures obtained by molecular dynamics simulations has been developed. this method ... | 2006 | 16682558 |
| the building blocks and motifs of rna architecture. | rna motifs can be defined broadly as recurrent structural elements containing multiple intramolecular rna-rna interactions, as observed in atomic-resolution rna structures. they constitute the modular building blocks of rna architecture, which is organized hierarchically. recent work has focused on analyzing rna backbone conformations to identify, define and search for new instances of recurrent motifs in x-ray structures. one current view asserts that recurrent rna strand segments with characte ... | 2006 | 16713707 |
| activation of superoxide dismutases: putting the metal to the pedal. | superoxide dismutases (sod) are important anti-oxidant enzymes that guard against superoxide toxicity. various sod enzymes have been characterized that employ either a copper, manganese, iron or nickel co-factor to carry out the disproportionation of superoxide. this review focuses on the copper and manganese forms, with particular emphasis on how the metal is inserted in vivo into the active site of sod. copper and manganese sods diverge greatly in sequence and also in the metal insertion proce ... | 2006 | 16828895 |
| evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal rna using arb software package. | availability of high-resolution rna crystal structures for the 30s and 50s ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal rna (rrna) for evaluating sequence alignments of rrna genes. furthermore, the secondary and tertiary structural features of rrna are highly useful and successfully employed in designing rrna targeted oligonucleotide probes intended for in situ hybridization ... | 2006 | 16672074 |
| dynamic protein domains: identification, interdependence, and stability. | existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. however, this information is vital for many areas of protein research. the recently developed hierarchical clustering of correlation patterns (hccp) technique provides machine-based domain identification in a computationally simple and physically consistent way. here we present the modification of this technique, which not only allows determination of the mo ... | 2006 | 16632509 |
| nuclear photosynthetic gene expression is synergistically modulated by rates of protein synthesis in chloroplasts and mitochondria. | arabidopsis thaliana mutants prors1-1 and -2 were identified on the basis of a decrease in effective photosystem ii quantum yield. mutations were localized to the 5'-untranslated region of the nuclear gene prolyl-trna synthetase1 (prors1), which acts in both plastids and mitochondria. in prors1-1 and -2, prors1 expression is reduced, along with protein synthesis in both organelles. prors1 null alleles (prors1-3 and -4) result in embryo sac and embryo development arrest. in mutants with the leaky ... | 2006 | 16517761 |
| ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of p-site trna are not essential for ef-g catalyzed translocation. | the coupled movement of trna-mrna complex through the ribosome is a fundamental step during the protein elongation process. we demonstrate that the ribosome will translocate a p-site-bound trna(met) with a break in the phosphodiester backbone between positions 17 and 18 in the d-loop. crystallographic data showed that the acceptor arms of p- and e-site trna interact extensively with the ribosomal large subunit. therefore, we used this fragmented p-site-bound trna(met) to investigate the contribu ... | 2006 | 16489185 |
| exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. | as tertiary structure is currently available only for a fraction of known protein families, it is important to assess what parts of sequence space have been structurally characterized. we consider protein domains whose structure can be predicted by sequence similarity to proteins with solved structure and address the following questions. do these domains represent an unbiased random sample of all sequence families? do targets solved by structural genomic initiatives (sgi) provide such a sample? ... | 2006 | 16549009 |
| a putative rna-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic rnai, and hypothetical mechanisms of action. | all archaeal and many bacterial genomes contain clustered regularly interspaced short palindrome repeats (crispr) and variable arrays of the crispr-associated (cas) genes that have been previously implicated in a novel form of dna repair on the basis of comparative analysis of their protein product sequences. however, the proximity of crispr and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis. | 2006 | 16545108 |
| nucleotide exchange via local protein unfolding--structure of rab8 in complex with mss4. | rab gtpases function as essential regulators of vesicle transport in eukaryotic cells. mss4 was shown to stimulate nucleotide exchange on rab proteins associated with the exocytic pathway and to have nucleotide-free-rab chaperone activity. a detailed kinetic analysis of mss4 interaction with rab8 showed that mss4 is a relatively slow exchange factor that forms a long-lived nucleotide-free complex with rabgtpase. in contrast to other characterized exchange factor-gtpase complexes, mss4:rab8 compl ... | 2006 | 16541104 |
| methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions. | although poorly understood, the properties of the denatured state ensemble are critical to the thermodynamics and the kinetics of protein folding. the most relevant conformations to cellular protein folding are the ones populated under physiological conditions. to avoid the problem of low expression that is seen with unstable variants, we used methionine oxidation to destabilize monomeric lambda repressor and predominantly populate the denatured state under nondenaturing buffer conditions. the d ... | 2006 | 16452618 |
| defining the primary route for lutein synthesis in plants: the role of arabidopsis carotenoid beta-ring hydroxylase cyp97a3. | lutein, a dihydroxy derivative of alpha-carotene (beta,epsilon-carotene), is the most abundant carotenoid in photosynthetic plant tissues where it plays important roles in light-harvesting complex-ii structure and function. the synthesis of lutein from lycopene requires at least four distinct enzymatic reactions: beta- and epsilon-ring cyclizations and hydroxylation of each ring at the c-3 position. three carotenoid hydroxylases have already been identified in arabidopsis, two nonheme diiron bet ... | 2006 | 16492736 |
| nucleic acid visualization with ucsf chimera. | with the increase in the number of large, 3d, high-resolution nucleic acid structures, particularly of the 30s and 50s ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. we describe an extension to the ucsf chimera molecular visualizat ... | 2006 | 16478715 |
| the post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5a (eif5a). | the eukaryotic translation initiation factor 5a (eif5a) is the only cellular protein that contains the unique polyamine-derived amino acid, hypusine [nepsilon-(4-amino-2-hydroxybutyl)lysine]. hypusine is formed in eif5a by a novel post-translational modification reaction that involves two enzymatic steps. in the first step, deoxyhypusine synthase catalyzes the cleavage of the polyamine spermidine and transfer of its 4-aminobutyl moiety to the epsilon-amino group of one specific lysine residue of ... | 2006 | 16452303 |
| structural biology of rna silencing and its functional implications. | we outline structure-function contributions from our laboratories on protein-rna recognition events that monitor sirna length, 5 -phosphate and 2-nucleotide 3 overhangs, as well as the architecture of argonaute, its externally bound sirna complex, and argonaute-based models involving guide-strand-mediated mrna binding, cleavage, and release. | 2006 | 17381284 |
| conserved quantitative stability/flexibility relationships (qsfr) in an orthologous rnase h pair. | many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. here we investigate an orthologous rnase h pair by using a minimal distance constraint model (dcm). the dcm is an all atom microscopic model [jacobs and dallakyan, biophys j 2005;88(2):903-915] that accurately reproduces heat capacity measurements [livesay et al., febs lett 2004;576(3):468-476], and is unique ... | 2006 | 16287093 |
| similarity search for local protein structures at atomic resolution by exploiting a database management system. | a method to search for local structural similarities in proteins at atomic resolution is presented. it is demonstrated that a huge amount of structural data can be handled within a reasonable cpu time by using a conventional relational database management system with appropriate indexing of geometric data. this method, which we call geometric indexing, can enumerate ligand binding sites that are structurally similar to sub-structures of a query protein among more than 160,000 possible candidates ... | 2007 | 27857569 |
| bis{μ-2,2'-[1,1'-(ethane-1,2-diyldinitrilo)diethyl-idyne]diphenolato}bis-[(benzoato-κo)manganese(iii)] dihydrate. | the title compound, [mn(2)(c(18)h(18)n(2)o(2))(2)(c(7)h(5)o(2))(2)]·2h(2)o, was synthesized by the reaction between manganese(ii) benzoate and the schiff base generated in situ by the condensation of ethane-1,2-diamine and o-hydroxy-aceto-phen-one. the jahn-teller-distorted manganese(iii) ions of the centrosymmetric dimer are connected through phen-oxy bridges. hydrogen-bonding inter-actions between the uncoord-in-ated c=o of the benzoate and uncoordinated water mol-ecules link the dimers into a ... | 2007 | 21200504 |
| bis{μ-2,2'-[1,1'-(ethane-1,2-diyldinitrilo)diethyl-idyne]diphenolato}bis-[(benzoato-κo)manganese(iii)] dihydrate. | the title compound, [mn(2)(c(18)h(18)n(2)o(2))(2)(c(7)h(5)o(2))(2)]·2h(2)o, was synthesized by the reaction between manganese(ii) benzoate and the schiff base generated in situ by the condensation of ethane-1,2-diamine and o-hydroxy-aceto-phen-one. the jahn-teller-distorted manganese(iii) ions of the centrosymmetric dimer are connected through phen-oxy bridges. hydrogen-bonding inter-actions between the uncoord-in-ated c=o of the benzoate and uncoordinated water mol-ecules link the dimers into a ... | 2007 | 21200504 |
| the ins and outs of translation. | | 2007 | 18086326 |
| thiostrepton inhibition of trna delivery to the ribosome. | ribosome-stimulated hydrolysis of guanosine-5'-triphosphate (gtp) by guanosine triphosphatase (gtpase) translation factors drives protein synthesis by the ribosome. allosteric coupling of gtp hydrolysis by elongation factor tu (ef-tu) at the ribosomal gtpase center to messenger rna (mrna) codon:aminoacyl-transfer rna (aa-trna) anticodon recognition at the ribosomal decoding site is essential for accurate and rapid aa-trna selection. here we use single-molecule methods to investigate the mechanis ... | 2007 | 17951333 |
| clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. | an evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in clusters of orthologous groups of proteins (cogs). rapid accumulation of genome sequences creates opportunities for refining cogs but also represents a c ... | 2007 | 18042280 |
| cryo-em study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins. | protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. chloroplast or plastid ribosomal proteins (prps) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (psrps); however, it is unclear to what extent these proteins play structural or regulatory roles during translation. we have obtained a three-dimensional cryo-em map of the spinach ... | 2007 | 18042701 |
| protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. | the number of macromolecular structures deposited in the protein data bank now exceeds 45,000, with the vast majority determined using crystallographic methods. thousands of studies describing such structures have been published in the scientific literature, and 14 nobel prizes in chemistry or medicine have been awarded to protein crystallographers. as important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as ... | 2007 | 18034855 |
| protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. | the number of macromolecular structures deposited in the protein data bank now exceeds 45,000, with the vast majority determined using crystallographic methods. thousands of studies describing such structures have been published in the scientific literature, and 14 nobel prizes in chemistry or medicine have been awarded to protein crystallographers. as important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as ... | 2007 | 18034855 |
| simple fluorescent sensors engineered with catalytic dna 'mgz' based on a non-classic allosteric design. | most nae (nucleic acid enzyme) sensors are composed of an rna-cleaving catalytic motif and an aptameric receptor. they operate by activating or repressing the catalytic activity of a relevant nae through the conformational change in the aptamer upon target binding. to transduce a molecular recognition event to a fluorescence signal, a fluorophore-quencher pair is attached to opposite ends of the rna substrate such that when the nae cleaves the substrate, an increased level of fluorescence can be ... | 2007 | 18030352 |
| a comprehensive analysis of non-sequential alignments between all protein structures. | the majority of relations between proteins can be represented as a conventional sequential alignment. nevertheless, unusual non-sequential alignments with different connectivity of the aligned fragments in compared proteins have been reported by many researchers. it is interesting to understand those non-sequential alignments; are they unique, sporadic cases or they occur frequently; do they belong to a few specific folds or spread among many different folds, as a common feature of protein struc ... | 2007 | 18005453 |
| structural basis for signal-sequence recognition by the translocase motor seca as determined by nmr. | recognition of signal sequences by cognate receptors controls the entry of virtually all proteins to export pathways. despite its importance, this process remains poorly understood. here, we present the solution structure of a signal peptide bound to seca, the 204 kda atpase motor of the sec translocase. upon encounter, the signal peptide forms an alpha-helix that inserts into a flexible and elongated groove in seca. the mode of binding is bimodal, with both hydrophobic and electrostatic interac ... | 2007 | 18022369 |
| the process of mrna-trna translocation. | in the elongation cycle of translation, translocation is the process that advances the mrna-trna moiety on the ribosome, to allow the next codon to move into the decoding center. new results obtained by cryoelectron microscopy, interpreted in the light of x-ray structures and kinetic data, allow us to develop a model of the molecular events during translocation. | 2007 | 18003906 |
| proline modulates the intracellular redox environment and protects mammalian cells against oxidative stress. | the potential of proline to suppress reactive oxygen species (ros) and apoptosis in mammalian cells was tested by manipulating intracellular proline levels exogenously and endogenously by overexpression of proline metabolic enzymes. proline was observed to protect cells against h(2)o(2), tert-butyl hydroperoxide, and a carcinogenic oxidative stress inducer but was not effective against superoxide generators such as menadione. oxidative stress protection by proline requires the secondary amine of ... | 2007 | 18036351 |
| proline modulates the intracellular redox environment and protects mammalian cells against oxidative stress. | the potential of proline to suppress reactive oxygen species (ros) and apoptosis in mammalian cells was tested by manipulating intracellular proline levels exogenously and endogenously by overexpression of proline metabolic enzymes. proline was observed to protect cells against h(2)o(2), tert-butyl hydroperoxide, and a carcinogenic oxidative stress inducer but was not effective against superoxide generators such as menadione. oxidative stress protection by proline requires the secondary amine of ... | 2007 | 18036351 |
| knotted and topologically complex proteins as models for studying folding and stability. | among proteins of known three-dimensional structure, only a few possess complex topological features such as knotted or interlinked (catenated) protein backbones. such unusual proteins offer potentially unique insights into folding pathways and stabilization mechanisms. they also present special challenges for both theorists and computational scientists interested in understanding and predicting protein-folding behavior. here, we review complex topological features in proteins with a focus on re ... | 2007 | 17967433 |
| rna catalysis: ribozymes, ribosomes, and riboswitches. | the catalytic mechanisms employed by rna are chemically more diverse than initially suspected. divalent metal ions, nucleobases, ribosyl hydroxyl groups, and even functional groups on metabolic cofactors all contribute to the various strategies employed by rna enzymes. this catalytic breadth raises intriguing evolutionary questions about how rna lost its biological role in some cases, but not in others, and what catalytic roles rna might still be playing in biology. | 2007 | 17981494 |
| detecting coevolution in and among protein domains. | correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution among all protein domains is still lacking. ... | 2007 | 17983264 |
| development of a novel one-tube isothermal reverse transcription thermophilic helicase-dependent amplification platform for rapid rna detection. | the high complexity and cost of polymerase chain reaction-based molecular diagnostics sometimes limits their use in the clinical diagnostics setting. a new helicase-based isothermal amplification method offers an alternative to standard polymerase chain reaction, allowing amplification and detection of specific dna sequences at a constant reaction temperature without thermocycling equipment. herein, we describe the development of a novel one-tube isothermal reverse transcription-thermophilic hel ... | 2007 | 17975029 |
| phenylalanyl-trna synthetase editing defects result in efficient mistranslation of phenylalanine codons as tyrosine. | translational quality control is monitored at several steps, including substrate selection by aminoacyl-trna synthetases (aarss), and discrimination of aminoacyl-trnas by elongation factor tu (ef-tu) and the ribosome. phenylalanyl-trna synthetase (phers) misactivates tyr but is able to correct the mistake using a proofreading activity named editing. previously we found that overproduction of editing-defective phers resulted in tyr incorporation at phe-encoded positions in vivo, although the misr ... | 2007 | 17804641 |
| first experimental evidence for the preferential stabilization of the natural d- over the nonnatural l-configuration in nucleic acids. | the homochirality of biomolecules is a prerequisite for the origin and evolution of terrestrial life. the unique selection of d-monosaccharides, in particular, d-ribose in rna and d-deoxyribose in dna, leads to the construction of proteins by l-amino acids. this points to the exclusive role of stereoselectivity in the most important physiological processes. so far, there is no experimental confirmation for the theoretical calculations of the energy differences between enantiomers used for the ex ... | 2007 | 17804644 |
| specific interaction between ef-g and rrf and its implication for gtp-dependent ribosome splitting into subunits. | after termination of protein synthesis, the bacterial ribosome is split into its 30s and 50s subunits by the action of ribosome recycling factor (rrf) and elongation factor g (ef-g) in a guanosine 5'-triphosphate (gtp)-hydrolysis-dependent manner. based on a previous cryo-electron microscopy study of ribosomal complexes, we have proposed that the binding of ef-g to an rrf-containing posttermination ribosome triggers an interdomain rotation of rrf, which destabilizes two strong intersubunit bridg ... | 2007 | 17996252 |
| transfer rna in the hybrid p/e state: correlating molecular dynamics simulations with cryo-em data. | transfer rna (trna) transiently occupies the hybrid p/e state (p/e-trna) when mrna-trna are translocated in the ribosome. in this study, we characterize the structure of p/e-trna and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free trna with the cryo-em map of p/e-trna. in our approach, we show that the cryo-em map may be interpreted as a conformational average. along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of t ... | 2007 | 17925437 |
| an expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. | the application of in vitro translation to the synthesis of unnatural peptides may allow the production of extremely large libraries of highly modified peptides, which are a potential source of lead compounds in the search for new pharmaceutical agents. the specificity of the translation apparatus, however, limits the diversity of unnatural amino acids that can be incorporated into peptides by ribosomal translation. we have previously shown that over 90 unnatural amino acids can be enzymatically ... | 2007 | 17912351 |
| virus-encoded aminoacyl-trna synthetases: structural and functional characterization of mimivirus tyrrs and metrs. | aminoacyl-trna synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. as such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. in contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as trnas. in this context, the discovery of four am ... | 2007 | 17855524 |
| the activities and function of molecular chaperones in the endoplasmic reticulum. | most proteins in the secretory pathway are translated, folded, and subjected to quality control at the endoplasmic reticulum (er). these processes must be flexible enough to process diverse protein conformations, yet specific enough to recognize when a protein should be degraded. molecular chaperones are responsible for this decision making process. er associated chaperones assist in polypeptide translocation, protein folding, and er associated degradation (erad). nevertheless, we are only begin ... | 2007 | 17964199 |
| molecular architecture of strictosidine glucosidase: the gateway to the biosynthesis of the monoterpenoid indole alkaloid family. | strictosidine beta-d-glucosidase (sg) follows strictosidine synthase (str1) in the production of the reactive intermediate required for the formation of the large family of monoterpenoid indole alkaloids in plants. this family is composed of approximately 2000 structurally diverse compounds. sg plays an important role in the plant cell by activating the glucoside strictosidine and allowing it to enter the multiple indole alkaloid pathways. here, we report detailed three-dimensional information d ... | 2007 | 17890378 |
| 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 |
| the primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. | it is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. new genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. in this way new metabolic pathways were built up by primordial cells. useful hints to disclose the origin and evolution of ancestral metabol ... | 2007 | 17767731 |
| 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 |
| a quantitative kinetic scheme for 70 s translation initiation complex formation. | association of the 30 s initiation complex (30sic) and the 50 s ribosomal subunit, leading to formation of the 70 s initiation complex (70sic), is a critical step of the translation initiation pathway. the 70sic contains initiator trna, fmet-trna(fmet), bound in the p (peptidyl)-site in response to the aug start codon. we have formulated a quantitative kinetic scheme for the formation of an active 70sic from 30sic and 50 s subunits on the basis of parallel rapid kinetics measurements of gtp hydr ... | 2007 | 17868692 |
| classification and regression tree (cart) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria. | classification and regression tree (cart) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. temperature optima for most of the organisms examined could be distinguished by cart analyses of tetranucleotide frequencies. this suggests that pervasive (nonlinear) qualities of genomes may reflect cer ... | 2007 | 19054742 |
| classification and regression tree (cart) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria. | classification and regression tree (cart) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. temperature optima for most of the organisms examined could be distinguished by cart analyses of tetranucleotide frequencies. this suggests that pervasive (nonlinear) qualities of genomes may reflect cer ... | 2007 | 19054742 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |