Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “HOPS”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed2004

The gene for soluble N-ethylmaleimide sensitive factor attachment protein alpha is mutated in hydrocephaly with hop gait (hyh) mice.

The spontaneous autosomal recessive mouse mutant for hydrocephaly with hop gait (hyh) exhibits dramatic cystic dilation of the ventricles at birth and invariably develops hopping gait. We show that the gene for soluble N-ethylmaleimide sensitive factor attachment protein alpha, also known as alpha-SNAP, is mutated in hyh mice. alpha-SNAP plays a key role in a wide variety of membrane fusion events in eukaryotic cells, including the regulated exocytosis of neurotransmitters. Homozygous mutant mice harbor a missense mutation M105I in a conserved residue in one of the alpha-helical domains. We demonstrate that the hyh mutant is not a null allele and is expressed; however, the mutant protein is 40% less abundant in hyh mice. The hyh mutant provides a valuable in vivo model to study vesicle/membrane trafficking and provides insight into the potential roles of alpha-SNAP in embryogenesis and brain development.

Amino Acid Sequence↗
PubMed2002

Ligand discrimination by TPR domains. Relevance and selectivity of EEVD-recognition in Hsp70 x Hop x Hsp90 complexes.

Protein-protein interaction modules containing so-called tetratricopeptide repeats (TPRs) mediate the assembly of Hsp70/Hsp90 multi-chaperone complexes. The TPR1 and TPR2A domains of the Hsp70/Hsp90 adapter protein p60/Hop specifically bind to short peptides corresponding to the C-terminal tails of Hsp70 and Hsp90, respectively, both of which contain the highly conserved sequence motif EEVD-COOH. Here, we quantitatively assessed the contribution of TPR-mediated peptide recognition to Hsp70.Hop.Hsp90 complex formation. The interaction of TPR2A with the C-terminal pentapeptide of Hsp90 (MEEVD) is identified as the core contact for Hop binding to Hsp90. (In peptide sequences, italics are used to highlight residues specific for Hsp70 or Hsp90.) In contrast, formation of the Hsp70.Hop complex depends not only on recognition of the C-terminal Hsp70 heptapeptide (PTIEEVD) by TPR1 but also on additional contacts between Hsp70 and Hop. The sequence motifs for TPR1 and TPR2A binding were defined by alanine scanning of the C-terminal octapeptides of Hsp70 and Hsp90 and by screening of combinatorial peptide libraries. Asp0 and Val-1 of the EEVD motif are identified as general anchor residues, but the highly conserved glutamates of the EEVD sequence, which are critical in Hsp90 binding by TPR2A, do not contribute appreciably to the interaction of Hsp70 with TPR1. Rather, TPR1 prefers hydrophobic amino acids in these positions. Moreover, the TPR domains display a pronounced tendency to interact preferentially with hydrophobic aliphatic and aromatic side chains in positions -4 and -6 of their respective peptide ligands. Ile-4 in Hsp70 and Met-4 in Hsp90 are most important in determining the specific binding of TPR1 and TPR2A, respectively.

Amino Acid Motifs↗
PubMed2003

Construction of gene expression system in hop (Humulus lupulus) lupulin gland using valerophenone synthase promoter.

The promoter region of the valerophenone synthase (VPS) gene was isolated from hop (Humulus lupulus). VPS, a member of the chalcone synthase (CHS) super-family, catalyzes the biosynthesis reaction of the hop resin that significantly accumulates in the cone's secretory gland called the "lupulin gland". The typical H-box and G-box sequences, which exist in many plants' CHS promoters and act as cis-elements for tissue specificity, UV-light induction, etc., were not found in the isolated VPS promoter, although the H-box-like sequence (CCTTACC, CCTAACC) and the core sequence (ACGT) of the G-box were observed. The transformation experiment using the VPS promoter-UIDA gene fusion revealed that the promoter acts not only in the lupulin gland but also in the glands of leaf and stem. On the other hand, the VPS promoter activity was not induced by UV-irradiation.

Acyltransferases↗
PubMed1994

Developmental sequences for hopping as assessment instruments: a generalizability analysis.

The purpose of this study was to investigate the generalizability with which undergraduate kinesiology and elementary education students can rate children's hopping performances according to prelongitudinally validated developmental sequences for the arms, legs, and total body. Twenty observers were assigned to one of four training groups (n = 5): (a) kinesiology students/total-body sequence, (b) kinesiology students/component sequences, (c) elementary education students/total-body sequence, and (d) elementary education students/component sequences. The observers rated five trials of videotaped hopping performances by 10 boys and 10 girls between the ages of 3.5 and 9.0 years. The results suggested that when kinesiology students receive 2 hours of training, one observer can reliably assess leg action in one trial (.80) and arm action in five trials (.80). In contrast, one elementary education student can reliably assess leg action within five trials (.80), but the average score of two observers assessing three trials each is needed to assess arm action (.81). Reliable assessment of total-body action requires two observers for both the kinesiology students (four trials each = .80) and the elementary education students (two trials each = .84).

Arm↗
PubMed2005

The vacuolar kinase Yck3 maintains organelle fragmentation by regulating the HOPS tethering complex.

The regulation of cellular membrane flux is poorly understood. Yeast respond to hypertonic stress by fragmentation of the normally large, low copy vacuole. We used this phenomenon as the basis for an in vivo screen to identify regulators of vacuole membrane dynamics. We report here that maintenance of the fragmented phenotype requires the vacuolar casein kinase I Yck3: when Yck3 is absent, salt-stressed vacuoles undergo fission, but reassemble in a SNARE-dependent manner, suggesting that vacuole fusion is disregulated. Accordingly, when Yck3 is deleted, in vitro vacuole fusion is increased, and Yck3 overexpression blocks fusion. Morphological and functional studies show that Yck3 modulates the Rab/homotypic fusion and vacuole protein sorting complex (HOPS)-dependent tethering stage of vacuole fusion. Intriguingly, Yck3 mediates phosphorylation of the HOPS subunit Vps41, a bi-functional protein involved in both budding and fusion during vacuole biogenesis. Because Yck3 also promotes efficient vacuole inheritance, we propose that tethering complex phosphorylation is a part of a general, switch-like mechanism for driving changes in organelle architecture.

Adaptor Proteins, Vesicular Transport↗
PubMed1992

Fractionation by SFE and microcolumn analysis of the essential oil and the bitter principles of hops.

Supercritical fluid extraction (SFE) is evaluated and optimized for the enrichment and fractionation of the essential oil and the bitter principles of hops (Humulus lupulus), both of which contribute to the flavor of beer. Profiles of the essential oil of different hop varieties are compared. The bitter principles, the humulones and lupulones, are analyzed by miniaturized liquid chromatography (micro-LC) and by micellar electrokinetic chromatography (MEKC).

Chromatography↗
PubMed2001

Co-chaperones Bag-1, Hop and Hsp40 regulate Hsc70 and Hsp90 interactions with wild-type or mutant p53.

Using highly purified proteins, we have identified intermediate reactions that lead to the assembly of molecular chaperone complexes with wild-type or mutant p53R175H protein. Hsp90 possesses higher affinity for wild-type p53 than for the conformational mutant p53R175H. The presence of Hsp90 in a complex with wild-type p53 inhibits the binding of Hsp40 and Hsc70 to p53, consequently preventing the formation of wild-type p53-multiple chaperone complexes. The conformational mutant p53R175H can form a stable heterocomplex with Hsp90 only in the presence of Hsc70, Hsp40, Hop and ATP. The anti-apoptotic factor Bag-1 can dissociate Hsp90 from a pre- assembled complex wild-type p53 protein, but it cannot dissociate a pre-assembled p53R175H-Hsp40- Hsc70-Hop-Hsp90 heterocomplex. The results presented here provide possible molecular mechanisms that can help to explain the observed in vivo role of molecular chaperones in the stabilization and cellular localization of wild-type and mutant p53 protein.

Adenosine Triphosphate↗
PubMed2006

The prenylflavonoid isoxanthohumol from hops (Humulus lupulus L.) is activated into the potent phytoestrogen 8-prenylnaringenin in vitro and in the human intestine.

Hops, an essential beer ingredient, are a source of prenylflavonoids, including 8-prenylnaringenin (8-PN), one of the most potent phytoestrogens. Because 8-PN concentrations in beers are generally low, its health effects after moderate beer consumption were considered negligible. However, human intestinal microbiota may activate up to 4 mg/L isoxanthohumol (IX) in beer into 8-PN. Depending on interindividual differences in the intestinal transformation potential, this conversion could easily increase the 8-PN exposure 10-fold upon beer consumption. Here, we present a further investigation of the process both in vitro and in vivo. In vitro experiments with the dynamic SHIME model showed that hop prenylflavonoids pass unaltered through the stomach and small intestine and that activation of IX into 8-PN (up to 80% conversion) occurs only in the distal colon. In vitro incubations of 51 fecal samples from female volunteers with IX enabled us to separate the fecal microbiota into high (8 of 51), moderate (11 of 51) and slow (32 of 51) 8-PN producers, clearly illustrating an interindividual variability. Three women, selected from the respective groups, received a daily dose of 5.59 mg IX for 4 d. Intestinal IX activation and urinary 8-PN excretion were correlated (R(2) = 0.6417, P < 0.01). These data show that intestinal conversion of IX upon moderate beer consumption can lead to 8-PN exposure values that might fall within the range of human biological activity.

Adult↗
PubMed1992

Novel in-frame two codon translational hop during synthesis of bovine placental lactogen in a recombinant strain of Escherichia coli.

A recombinant Escherichia coli strain was constructed for the overexpression of bovine placental lactogen (bPL), using a bPL structural gene containing 9 of the rare arginine codons AGA and AGG. When high level bPL synthesis was induced in this strain, cell growth was inhibited and bPL accumulated to less than 10% of total cell protein. In addition, about 2% of the recombinant bPL produced from this strain exhibited an altered trypsin digestion pattern. Amino acid residues 74 through 109 normally produce 2 tryptic peptides, but the altered form of bPL lacked these two peptides and instead had a new peptide which was missing arginine residue 86 and one of the two flanking leucine residues. The codon for arginine residue 86 was AGG and the codons for the flanking leucine residues 85 and 87 were TTG. When 5 of the 9 AGA and AGG codons in the bPL structural gene were changed to more preferred arginine codons, cell growth was not inhibited and bPL accumulated to about 30% of total cell protein. When bPL was purified from this modified strain, which included changing the arginine codon at position 86 from AGG to CGT, none of the altered form of bPL was produced. These observations are consistent with a model in which translational pausing occurs at the arginine residue 86 AGG codon because the corresponding arginyl-tRNA species is reduced by the high level of bPL synthesis, and a translational hop occurs from the leucine residue 85 TTG codon to the leucine residue 87 TTG codon. This observation represents the first report of an error in protein synthesis due to an in-frame translational hop within an open reading frame.

Amino Acid Sequence↗
PubMed1998

Pneumocystis carinii pneumonia incidence and chemoprophylaxis failure in ambulatory HIV-infected patients. HIV Outpatient Study (HOPS) Investigators.

BACKGROUND: Pneumocystis carinii pneumonia (PCP) remains the most frequently reported serious opportunistic infection in AIDS patients and the second highest cause of mortality among persons with AIDS in the United States, despite the availability of effective chemoprophylaxis. METHODS: To evaluate incidence of PCP and determinants of PCP chemoprophylaxis failure, we analyzed data from 2842 patients visits to infectious diseases physicians at 10 HIV clinics (eight private and two public) in eight U.S. cities from January 1992 through June 1996 as part of the HIV Outpatient Study (HOPS). We performed a time-dependent regression analysis to examine potential determinants of PCP chemoprophylaxis failure. RESULTS: The incidence of chemoprophylaxis failure was 4.6 PCP cases/100 person-years on chemoprophylaxis; these cases represent 67% of all incident episodes of PCP. In a multivariate analysis, the only significant predictors of chemoprophylaxis failure were the use of agents other than trimethoprim-sulfamethoxazole (TMP-SMX), history of prior PCP, and a CD4+ T-lymphocyte cell count of <50 cells/microl. Dosing or frequency of TMP-SMX did not seem to influence risk of chemoprophylaxis failure. DISCUSSION: Chemoprophylaxis failure, especially among those with the most advanced immunosuppression or history of prior PCP, was the most significant source of new PCP cases in the HOPS cohort and thus represents one of the largest contributors to morbidity and mortality in this cohort.

AIDS-Related Opportunistic Infections↗
PubMed2001

The molecular characterization of 16 new sequence variants of Hop stunt viroid reveals the existence of invariable regions and a conserved hammerhead-like structure on the viroid molecule.

At present isolates of Hop stunt viroid (HSVd) are divided into five groups: three major groups (plum-type, hop-type and citrus-type) each containing isolates from only a limited number of isolation hosts and two minor groups that were presumed to derive from recombination events between members of the main groups. In this work we present the characterization of 16 new sequence variants of HSVd obtained from four Mediterranean countries (Cyprus, Greece, Morocco and Turkey) where this viroid had not previously been described. Molecular variability comparisons considering the totality of the sequence variants characterized so far revealed that most of the variability is found in the pathogenic and variable domains of the viroid molecule whereas both the terminal right (T(R)) and left (T(L)) domains are regions of low or no variability, respectively, suggesting the existence of constraints limiting the heterogeneity of the sequence variants. Phylogenetic analyses revealed that sequence variants belonging to the two minor recombinant subgroups are more frequent than previously thought. When the cruciform structure alternative to the typical rod-like conformation was considered it was observed that the upper part of this structure (hairpin I) was strictly conserved whereas in the lower part a reduced variability was found. The existence of a covariation in this lower part was notable. Interestingly, a hammerhead-like sequence was found within the T(R) domain of HSVd and it was strictly conserved in all the sequence variants. The evolutionary implications of the presence of this motif on the HSVd are discussed.

Base Sequence↗
PubMed2003

Comprehensive analysis of orthologous protein domains using the HOPS database.

One of the most reliable methods for protein function annotation is to transfer experimentally known functions from orthologous proteins in other organisms. Most methods for identifying orthologs operate on a subset of organisms with a completely sequenced genome, and treat proteins as single-domain units. However, it is well known that proteins are often made up of several independent domains, and there is a wealth of protein sequences from genomes that are not completely sequenced. A comprehensive set of protein domain families is found in the Pfam database. We wanted to apply orthology detection to Pfam families, but first some issues needed to be addressed. First, orthology detection becomes impractical and unreliable when too many species are included. Second, shorter domains contain less information. It is therefore important to assess the quality of the orthology assignment and avoid very short domains altogether. We present a database of orthologous protein domains in Pfam called HOPS: Hierarchical grouping of Orthologous and Paralogous Sequences. Orthology is inferred in a hierarchic system of phylogenetic subgroups using ortholog bootstrapping. To avoid the frequent errors stemming from horizontally transferred genes in bacteria, the analysis is presently limited to eukaryotic genes. The results are accessible in the graphical browser NIFAS, a Java tool originally developed for analyzing phylogenetic relations within Pfam families. The method was tested on a set of curated orthologs with experimentally verified function. In comparison to tree reconciliation with a complete species tree, our approach finds significantly more orthologs in the test set. Examples for investigating gene fusions and domain recombination using HOPS are given.

Animals↗
PubMed2001

Stochastic exclusion processes with extended hopping.

We study the effects of extended hopping in the stochastic asymmetric simple exclusion process (ASEP) of one dimension. A modified ASEP with four parameters is proposed. The current and bulk density are calculated. Two different phases with a curved boundary are observed. The phase of maximum current is absent. We also present the unusual density fluctuations near both boundaries. The characteristic of the stochastic dynamics with extended hopping is pointed out.

Journal Article↗
PubMed2005

Barrier hopping, viscous flow, and kinetic gelation in particle-polymer suspensions.

The naive mode coupling-polymer reference interaction site model (MCT-PRISM) theory of gelation and elasticity of suspensions of hard sphere colloids or nanoparticles mixed with nonadsorbing polymers has been extended to treat the emergence of barriers, activated transport, and viscous flow. The barrier makes the dominant contribution to the single particle relaxation time and shear viscosity, and is a rich function of the depletion attraction strength via the polymer concentration, polymer-particle size asymmetry ratio, and particle volume fraction. The dependences of the barrier on these three system parameters can be accurately collapsed onto a single scaling variable, and the resultant master curve is well described by a power law. Nearly universal master curves are also constructed for the hopping or alpha relaxation time for system conditions not too close to the ideal MCT transition. Based on the calculated barrier hopping time, a theory for kinetic gel boundaries is proposed. The form and dependence on system parameters of the kinetic gel lines are qualitatively the same as obtained from prior ideal MCT-PRISM studies. The possible relevance of our results to the phenomenon of gravity-driven gel collapse is studied. The general approach can be extended to treat nonlinear viscoelasticity and rheology of polymer-colloid suspensions and gels.

Journal Article↗
PubMed2000

Hot-electron effects in two-dimensional hopping with a large localization length

We have studied nonlinear effects in the resistance of a two-dimensional system with a large localization length on both sides of the crossover from weak to strong localization. It is shown that nonlinearity in the hopping regime is due to electron overheating rather than the field effects. This qualitatively new behavior is a signature of a two-dimensional hopping transport with a large localization length.

Journal Article↗
PubMed2000

Partially suppressed shot noise in hopping conduction: observation in SiGe quantum wells

We have observed shot noise in the hopping conduction of two-dimensional carriers confined in a p-type SiGe quantum well at a temperature of 4 K. Moreover, shot noise is suppressed relative to its "classical" value 2eI by an amount that depends on the length of the sample and the carrier density. We have found a suppression factor to the classical value of about one-half for a 2 &mgr;m long sample, and of one-fifth for a 5 &mgr;m sample. In each case, the factor decreased slightly as the density increased toward the insulator-metal transition. We explain these results in terms of the characteristic length ( approximately 1 &mgr;m in our case) of the inherent inhomogeneity of hopping transport, obtained from percolation theory.

Journal Article↗
PubMed2002

Anisotropic local stress and particle hopping in a deeply supercooled liquid.

The origin of the microscopic motions that lead to stress relaxation in deeply supercooled liquid remains unclear. We show that in such a liquid the stress relaxation is locally anisotropic which can serve as the driving force for the hopping of the system on its free energy surface. However, not all hoppings are equally effective in relaxing the local stress, suggesting that diffusion can decouple from viscosity even at the local level. On the other hand, orientational relaxation is found to be always coupled to stress relaxation.

Journal Article↗
PubMed2003

Electrical conduction in native deoxyribonucleic acid: hole hopping transfer mechanism?

Measurements of the quasistatic and frequency dependent electric conductivity below 1 MHz were carried out on wet-spun, macroscopically oriented, calf thymus DNA bulk samples, thus effectively extending previous radio frequency data down to quasistatic time scales. The frequency dependence of the electrical conductivity in the frequency range of approximately 10(-3)-10(15) Hz agrees well with predictions of the hopping hole mechanism. Temperature dependence of the quasistatic electrical conductivity can be rather well described by the activated Arrhenius law with the activation energy of approximately 0.9 eV; however, based on the quality of the fits, the hopping ansatz cannot be ruled out.

Animals↗