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At least 145 records · Page 8Linked to original sources
PubMed1983

Smooth pursuit eye movements under open-loop and closed-loop conditions.

We measured smooth pursuit eye movement responses to sinusoidal target motion in the open-loop condition (target motion stabilized on the retina) and the closed-loop condition (target motion fixed in space). We also predicted the closed-loop response for each subject from the open-loop data, using the relationship for a linear system. Predictions made in this way were very accurate, for both gain and phase lag, even though responses of a given subject usually differed idiosyncratically from those of another. The accuracy of prediction was observed over a broad frequency range (0.5-3Hz) and a moderate range of target amplitudes (2-6 deg, peak-to-peak).

Eye Movements↗
PubMed2004

Roles of loop C and the loop B-C interval of the nicotinic receptor alpha subunit in its selective interactions with imidacloprid in insects.

To elucidate the mechanism of selective action of imidacloprid on insect nicotinic acetylcholine receptors (nAChRs), we examined the roles of loop C and the loop B-C interval region in receptor interactions with imidacloprid. The P242E mutation in loop C of the Drosophila SAD subunit (the second alpha-like Drosophila nicotinic acetylcholine receptor subunit, also called Dalpha2 subunit) reduced imidacloprid sensitivity of the SAD-chicken beta2 hybrid nAChR, whereas the E219P mutation of the alpha4 subunit increased the imidacloprid sensitivity of the alpha4beta2 nAChR. Deletion of the loop B-C interval region from the SAD subunit enhanced the effect of the P242E mutation on the SADbeta2 hybrid nAChR, suggesting important roles of the regions investigated in the nAChR-imidacloprid interactions.

Acetylcholine↗
PubMed2000

Structure of the Tie2 RTK domain: self-inhibition by the nucleotide binding loop, activation loop, and C-terminal tail.

BACKGROUND: Angiogenesis, the formation of new vessels from the existing vasculature, is a critical process during early development as well as in a number of disease processes. Tie2 (also known as Tek) is an endothelium-specific receptor tyrosine kinase involved in both angiogenesis and vasculature maintenance. RESULTS: We have determined the crystal structure of the Tie2 kinase domain to 2.2 A resolution. The structure contains the catalytic core, the kinase insert domain (KID), and the C-terminal tail. The overall fold is similar to that observed in other serine/threonine and tyrosine kinase structures; however, several unique features distinguish the Tie2 structure from those of other kinases. The Tie2 nucleotide binding loop is in an inhibitory conformation, which is not seen in other kinase structures, while its activation loop adopts an "activated-like" conformation in the absence of phosphorylation. Tyr-897, located in the N-terminal domain, may negatively regulate the activity of Tie2 by preventing dimerization of the kinase domains or by recruiting phosphatases when it is phosphorylated. CONCLUSION: Regulation of the kinase activity of Tie2 is a complex process. Conformational changes in the nucleotide binding loop, activation loop, C helix, and the C-terminal tail are required for ATP and substrate binding.

Amino Acid Substitution↗
PubMed1996

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme.

BACKGROUND: Group I introns self-splice via two consecutive trans-esterification reactions in the presence of guanosine cofactor and magnesium ions. Comparative sequence analysis has established that a catalytic core of about 120 nucleotides is conserved in all known group I introns. This core is generally not sufficient for activity, however, and most self-splicing group I introns require non-conserved peripheral elements to stabilize the complete three-dimensional (3D) structure. The physico-chemical properties of group I introns make them excellent systems for unraveling the structural basis of the RNA-RNA interactions responsible for promoting the self-assembly of complex RNAs. RESULTS: We present phylogenetic and experimental evidence for the existence of three additional tertiary base pairings between hairpin loops within peripheral components of subgroup IC1 and ID introns. Each of these new long range interactions, called P13, P14 and P16, involves a terminal loop located in domain 2. Although domains 2 of IC and ID introns share very strong sequence similarity, their terminal loops interact with domains 5 and 9 (subgroup IC1) and domain 6 (subgroup ID). Based on these tertiary contacts, comparative sequence analysis, and published experimental results such as Fe(II)-EDTA protection patterns, we propose 3D models for two entire group I introns, the subgroup IC1 intron in the large ribosomal precursor RNA of Tetrahymena thermophila and the SdCob.1 subgroup ID intron found in the cytochrome b gene of Saccharomyces douglasii. CONCLUSIONS: Three-dimensional models of group I introns belonging to four different subgroups are now available. They all emphasize the modular and hierarchical organization of the architecture of group I introns and the widespread use of base-pairings between terminal hairpin loops for stabilizing the folded and active structures of large and complex RNA molecules.

Animals↗
PubMed2005

Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies.

Deletion mutagenesis, biochemical, and X-ray crystallographic studies have shown that loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is required for the assembly of the active center, plays an important role in the stabilization of the ternary complex of HPPK with MgATP and 6-hydroxymethyl-7,8-dihydropterin (HP), and is essential for catalysis. Whether the critical functional importance of loop 3 is due to the interactions between residues R84 and W89 and the two substrates has been addressed by site-directed mutagenesis, biochemical, and X-ray crystallographic studies. Substitution of R84 with alanine causes little changes in the dissociation constants and kinetic constants of the HPPK-catalyzed reaction, indicating that R84 is not important for either substrate binding or catalysis. Substitution of W89 with alanine increases the K(d) for the binding of MgATP by a factor of 3, whereas the K(d) for HP increases by a factor of 6, which is due to the increase in the dissociation rate constant. The W89A mutation decreases the rate constant for the chemical step of the forward reaction by a factor of 15 and the rate constant for the chemical step of the reverse reaction by a factor of 25. The biochemical results of the W89A mutation indicate that W89 contributes somewhat to the binding of HP and more significantly to the chemical step. The crystal structures of W89A show that W89A has different conformations in loops 2 and 3, but the critical catalytic residues are positioned for catalysis. When these results are taken together, they suggest that the critical functional importance of loop 3 is not due to the interactions of the R84 guanidinium group or the W89 indole ring with the substrates.

Amino Acid Sequence↗
PubMed2005

Conserved extracellular cysteine residues and cytoplasmic loop-loop interplay are required for functionality of the heptahelical MLO protein.

We performed a structure-function analysis of the plasma membrane-localized plant-specific barley (Hordeum vulgare) MLO (powdery-mildew-resistance gene o) protein. Invariant cysteine and proline residues, located either in extracellular loops or transmembrane domains that have been conserved in MLO proteins for more than 400 million years, were found to be essential for MLO functionality and/or stability. Similarly to many metazoan G-protein-coupled receptors known to function as homo- and hetero-oligomers, FRET (fluorescence resonance energy transfer) analysis revealed evidence for in planta MLO dimerization/oligomerization. Domain-swap experiments with closely related wheat and rice as well as diverged Arabidopsis MLO isoforms demonstrated that the identity of the C-terminal cytoplasmic tail contributes to MLO activity. Likewise, analysis of a progressive deletion series revealed that integrity of the C-terminus determines both MLO accumulation and functionality. A series of domain swaps of cytoplasmic loops with the wheat (Triticum aestivum) orthologue, TaMLO-B1, provided strong evidence for co-operative loop-loop interplay either within the protein or between MLO molecules. Our data indicate extensive intramolecular co-evolution of cytoplasmic domains in the evolutionary history of the MLO protein family.

Amino Acid Sequence↗
PubMed2003

A new mutation, S1285F, within the A1 loop of von Willebrand factor induces a conformational change in A1 loop with abnormal binding to platelet GPIb and botrocetin causing type 2M von Willebrand disease.

We report the identification of a new mutation in exon 28 of the von Willebrand factor (VWF) gene in two related patients with type 2M von Willebrand disease (VWD). The molecular abnormality changes the Ser 1285 to Phe within the A1 loop of VWF. The S1285F mutation was reproduced by site-directed mutagenesis on the full-length VWF cDNA. The mutated recombinant VWF (rVWF), F1285rVWF, and the hybrid, S/F1285rVWF, were expressed in COS-7 cells. F1285rVWF exhibited a slight decrease of high-molecular-weight multimers and markedly reduced ristocetin- or botrocetin-induced binding of VWF to platelets in association with a decreased binding to botrocetin. The hybrid S/F1285rVWF showed a normal multimeric profile and bound to platelets in a similar way to the patients' plasma VWF, in the presence of ristocetin or botrocetin. Thus, the new S1285F mutation within the A1 loop was responsible for the type 2M VWD observed in these patients, and was involved in the binding of VWF to botrocetin and to platelet glycoprotein Ib (GPIb). Three anti-VWF monoclonal antibodies, with conformational epitopes within the A1 loop but distinct GPIb binding inhibitory properties, showed a different interaction with F1285rVWF. These results indicate that the S1285F substitution alters the folding of the A1 loop and prevents the correct exposure of the VWF binding sites to botrocetin and GPIb.

Adult↗
PubMed1998

Temporary decompression after colorectal surgery: randomized comparison of loop ileostomy and loop colostomy.

BACKGROUND: Loop ileostomy or loop transverse colostomy for temporary decompression of a left colonic anastomosis represents an important issue in abdominal surgery. METHODS: A randomized study, comparing loop ileostomy (n = 37; group 1) or loop transverse colostomy (n = 39; group 2), was conducted. Patients were followed from construction to closure of the stoma. RESULTS: Age, weight, sex and indication for surgery were similar in both groups. After stoma construction complications were reported in nine of 37 patients in group 1 and in one of 39 in group 2 (P < 0.01), leading to postoperative death in five of 37 in group 1 and one of 39 in group 2. In the period between stoma construction and closure significant differences were observed only in prolapse rate (one of 32 group 1, 16 of 38 group 2; P < 0.01), need for temporary adaptation of clothing (eight of 32 group 1, 22 of 38 group 2; P < 0.01) and dietary guidelines (23 of 32 group 1, four of 38 group 2; P < 0.01). One patient died in group 1 and four in group 2; the deaths were not stoma related. After stoma closure eight of 29 patients in group 1 had complications and there were two deaths compared with three of 32 and no deaths in group 2. CONCLUSION: Both types of stoma carry a high complication rate with a considerable associated mortality rate. The interval between stoma construction and closure has substantial impact on social and economic status. Based on all three phases studied, routine use of transverse colostomy is advised if decompression of the left colon is indicated.

Adult↗
PubMed2006

Open-loop and closed-loop control of dissociative ionization of ethanol in intense laser fields.

The relative yield of the C-O bond breaking with respect to the C-C bond breaking in ethanol cation C2H5OH+ is maximized in intense laser fields (10(13)-10(15) Wcm2) by open-loop and closed-loop optimization procedures. In the open-loop optimization, a train of intense laser pulses are synthesized so that the temporal separation between the first and last pulses becomes 800 fs, and the number and width of the pulses within a train are systematically varied. When the duration of 800 fs is filled with laser fields by increasing the number of pulses or by stretching all pulses in a triple pulse train, the relative yield of the C-O bond breaking becomes significantly large. In the closed-loop optimization using a self-learning algorithm, the four dispersion coefficients or the phases of 128 frequency components of an intense laser pulse are adopted as optimized parameters. From these optimization experiments it is revealed that the yield ratio of the C-O bond breaking is maximized as far as the total duration of the intense laser field reaches as long as approximately 1 ps and that the intermittent disappearance of the laser field within a pulse does not affect the relative yields of the bond breaking pathways.

Journal Article↗
PubMed2002

Loop-loop interaction of HIV-1 TAR RNA with N3'-->P5' deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription.

A hairpin RNA aptamer has been identified by in vitro selection against the transactivation-responsive element (TAR) of HIV-1. A nuclease-resistant N3' --> P5' phosphoramidate isosequential analog of this aptamer also folds as a hairpin and forms with TAR a loop-loop "kissing" complex with a binding constant in the low nanomolar range as demonstrated by electrophoretic mobility-shift assays and surface plasmon resonance experiments. The key structural determinants, which contribute to the stability of the RNA aptamer-TAR complex, loop complementarity and the GA residues closing the aptamer loop, remain crucial for the N3' --> P5' aptamer-TAR complex. Moreover, the N3' --> P5' phosphoramidate aptamer specifically interferes with the binding of a peptide derived from the transactivator protein (Tat) peptide to TAR and selectively inhibits the Tat-mediated transcription in an in vitro assay, which marks this nuclease-resistant aptamer as a relevant candidate for experiments in cells.

Amides↗
PubMed1999

The role of external loop regions in serotonin transport. Loop scanning mutagenesis of the serotonin transporter external domain.

Chimeric transporters were constructed in which the predicted external loops of the serotonin transporter (SERT) were replaced one at a time with a corresponding sequence from the norepinephrine transporter (NET). All of the chimeric transporters were expressed at levels equal to or greater than those of wild type SERT, but the transport and binding activity of the mutants varied greatly. In particular, mutants in which the NET sequence replaced external loops 4 or 6 of SERT had transport activity 5% or less than that of wild type, and the loop 5 replacement was essentially inactive. In some of these mutants, binding of a high affinity cocaine analog was less affected than transport, suggesting that the mutation had less effect on the initial binding steps in transport than on subsequent conformational changes. The more severely affected mutants also displayed an altered response to Na(+). In contrast to the dramatic reduction in transport and binding, the specificity of ligand binding was essentially unchanged. Chimeric transporters did not gain affinity for dopamine, a NET substrate, or desipramine, an inhibitor, at the expense of affinity for serotonin or paroxetine, a selective SERT inhibitor. The results suggest that external loops are not the primary determinants of substrate and inhibitor binding sites. However, they are not merely passive structures connecting transmembrane segments but rather active elements responsible for maintaining the stability and conformational flexibility of the transporter.

Base Sequence↗
PubMed2004

Soluble, oligomeric, and ligand-binding extracellular domain of the human alpha7 acetylcholine receptor expressed in yeast: replacement of the hydrophobic cysteine loop by the hydrophilic loop of the ACh-binding protein enhances protein solubility.

The N-terminal extracellular domain (ECD; amino acids 1-208) of the neuronal nicotinic acetylcholine receptor (AChR) alpha7 subunit, the only human AChR subunit known to assemble as a homopentamer, was expressed as a glycosylated form in the yeast Pichia pastoris in order to obtain a native-like model of the extracellular part of an intact pentameric nicotinic AChR. This molecule, alpha7-ECD, although able to bind the specific ligand alpha-bungarotoxin, existed mainly in the form of microaggregates. Substitution of Cys-116 in the alpha7-ECD with serine led to a decrease in microaggregate size. A second mutant form, alpha7-ECD(C116S,Cys-loop), was generated in which, in addition to the C116S mutation, the hydrophobic Cys-loop (Cys(128)-Cys(142)) was replaced by the corresponding hydrophilic Cys-loop from the snail glial cell acetylcholine-binding protein. This second mutant protein was water-soluble, expressed at a moderate level (0.5 +/- 0.1 mg/liter), and had a size corresponding approximately to a pentamer as judged by gel filtration and electron microscopy studies. It also bound (125)I-alpha-bungarotoxin with relatively high affinity (K(d) = 57 nm), the binding being inhibited by unlabeled alpha-bungarotoxin, d-tubocurarine, or nicotine (K(i) = 0.8 x 10(-7) m, K(i) = 1 x 10(-5) m, and K(i) = 0.9 x 10(-2) m, respectively). All three constructs were expressed as glycosylated forms, but in vitro deglycosylation reduced the heterogeneity without affecting their ligand binding properties. These results show that alpha7-ECD(C116S,Cys-loop) was expressed in P. pastoris as an oligomer (probably a pentamer) with a near native conformation and that its deglycosylated form seems to be suitable starting material for structural studies on the ligand-binding domain of a neurotransmitter receptor.

Binding, Competitive↗
PubMedDate not supplied

The phonological loop and memory for rhythms: an individual differences approach.

The purpose of the current study was to examine the relationship between short-term memory for rhythm and the phonological loop in working memory. Results showed that digit span scores significantly correlated with the scores on the rhythmic memory task, and that the correlation between the two scores remained significant even after the common variance with reading speed was partialled out. Partial correlation and regression analyses indicated that the relation between memory for rhythm and digit span scores is mediated by the third component in the phonological loop, the component that is responsible for regulation of timing mechanisms in immediate memory tasks.

Adult↗
PubMed1989

Sea urchin egg mitochondrial DNA contains a short displacement loop (D-loop) in the replication origin region.

Based on solution hybridization using single-stranded probes, native mitochondrial DNA extracted from sea urchin eggs contains a displacement-loop (D-loop) of approximately 70-80 nt. This maps to the single extended unassigned sequence of the genome, between the genes for tRNA(thr) and tRNA(pro), which also appears to contain the origin of first-strand replication. The D-loop commences at or close to a site of supercoil-dependent S1 nuclease hypersensitivity, adjacent to a run of 20 consecutive C residues, terminates near to the boundary of tRNA(thr), and appears to be composed at least partly of RNA, based on the sensitivity of the assays to RNase H. These experiments imply that the mechanisms of replication initiation in sea urchin and vertebrate mtDNAs are very similar, and suggest that the developmental restriction on mtDNA synthesis in eggs and embryos is maintained at the level of D-loop extension.

Animals↗
PubMed1996

The loop B domain is physically separable from the loop A domain in the hairpin ribozyme.

In order to understand the catalysis mechanism of the hairpin ribozyme, mutant ribozymes were constructed. The distance between the loop A domain and the loop B domain was extended by inserting various lengths of nucleotide linkers at the hinge region in cis mutants, or the domains were separated physically in a trans mutant. All the mutant ribozymes, including the trans mutant, could cleave substrate RNA at the predicted site. A cis mutant with a single nucleotide insertion exhibited cleavage activity about twice as high as that of the wild-type (wt) ribozyme. The insertion of 2-5 nucleotides (nt) gradually reduced the activity to the level of the wt ribozyme. Insertion of a longer linker, up to 11 nt, resulted in the reduction of activity to one half of that of the wt ribozyme. The ribozyme with a single nucleotide insertion at the hinge region seems to form a more suitable conformation for catalysis by three-dimensional fold-back of the loop B to loop A containing the cleavage site. The trans mutant, in which the A and B domains were physically separated, maintained a significant level of activity, suggesting that both domains are necessary for catalysis, but separable. These results demonstrate that interaction between the A and B domains results in catalysis.

Base Sequence↗
PubMed2005

Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix.

The spatial organization of an approximately 170 kb region of human chromosome 19, including CD22 and GPR40-GPR43 genes, was studied using in situ hybridization of a set of cosmid and PAC probes with nuclear halos prepared from proliferating and differentiated HL60 cells. The whole region under study was found to be looped out into the nuclear halo in proliferating cells. It is likely that the loop observed was attached to the nuclear matrix via MAR elements present at the flanks of the area under study. Upon dimethyl sulfoxide-induced differentiation of the cells the looped fragment became associated with the nuclear matrix. This change in the spatial organization correlated with the activation of transcription of at least two (CD22 and GPR43) genes present within the loop. The data obtained are discussed in the framework of the hypothesis postulating that the spatial organization of chromosomal DNA is maintained via constitutive (basic) and facultative (transcription-related) interactions of the latter with the nuclear matrix.

Base Sequence↗
PubMed1996

Protein engineering loops in aspartic proteinases: site-directed mutagenesis, biochemical characterization and X-ray analysis of chymosin with a replaced loop from rhizopuspepsin.

The loop exchange mutant chymosin 155-164 rhizopuspepsin was expressed in Trichoderma reesei and exported into the medium to yield a correctly folded and active product. The biochemical characterization and crystal structure determination at 2.5 A resolution confirm that the mutant enzyme adopts a native fold. However, the conformation of the mutated loop is unlike that in native rhizopuspepsin and involves the chelation of a water molecule in the loop. Kinetic analysis using two synthetic peptide substrates (six and 15 residues long) and the natural substrate, milk, revealed a reduction in the activity of the mutant enzyme with respect to the native when acting on both the long peptide substrate and milk. This may be a consequence of the different charge distribution of the mutated loop, its increased size and/or its different conformation.

Amino Acid Sequence↗
PubMed2001

Distribution of sizes of erased loops of loop-erased random walks in two and three dimensions.

We show that in the loop-erased random-walk problem, the exponent characterizing the probability distribution of areas of erased loops is superuniversal. In d dimensions, the probability that the erased loop has an area A varies as A(-2) for large A, independent of d, for 2< or =d< or =4. We estimate the exponents characterizing the distribution of perimeters and areas of erased loops in d=2 and 3 by large-scale Monte Carlo simulations. Our estimate of the fractal dimension z in two dimensions is consistent with the known exact value 5/4. In three dimensions, we get z=1.6183+/-0.0004. The exponent for the distribution of the durations of avalanches in the three-dimensional Abelian sandpile model is determined from this by using scaling relations.

Journal Article↗