SEARCH · PubMed Health

Results for “Docking”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 37 records · Page 2Linked to original sources

PubMed1995

Evaluation of the respiratory health of dock workers who load grain cargoes in British Columbia.

OBJECTIVES: To investigate the respiratory health of dock workers who load grain cargoes. METHODS: The respiratory health of 118 dock workers who load grain cargoes in the ports of Vancouver and Prince Rupert was compared with that of 555 grain elevator workers from the same regions. 128 civic workers were used as an unexposed control group. RESULTS: The prevalences of chronic cough and phlegm were at least as high in dock workers as those found in the elevator workers, and when adjusted for differences in duration of employment and smoking, dock workers had an eightfold higher risk of developing chronic phlegm than did civic workers. Symptoms of eye and skin irritation that were experienced at least monthly were highest for dock workers. Average percentage of the predicted FEV1 and FVC for dock workers (mean 100.6% and 105.3% respectively) were similar to the civic workers but significantly higher than those found for elevator workers. Higher subjective estimates of duration of exposure to grain dust (hours/day) were associated with lower values of FEV1. CONCLUSIONS: The more intermittent grain dust exposure patterns of dock workers may have allowed for some recovery of lung function, but chronic respiratory symptoms were less labile.

Adult↗

PubMed1982

Effect of docking on health, blood cells and metabolites and growth of Dorset lambs.

Docking by knife or elastrator had no sustained effect on growth of lambs 0 to 8 wk postpartum. However, during the 2 wk period postdocking, growth of lambs was limited or depressed, regardless of whether lambs were docked by knife at 14, 28 or 42 d of age. Blood hematocrit and hemoglobin were decreased (P less than .01) 1 d after docking by knife and 14 d after docking by elastrator. Neither method of docking proved superior. Regardless of whether lambs were docked by knife or elastrator, tail tissue was destroyed and became necrotic. Numbers of white blood cells increased (P less than .01) in response to docking. This necessitates that lambs be observed often through 2 wk postdocking and that medical treatment be administered when needed.

Age Factors↗

PubMed1998

Morphologically docked synaptic vesicles are reduced in synaptotagmin mutants of Drosophila.

Nerve terminal specializations include mechanisms for maintaining a subpopulation of vesicles in a docked, fusion-ready state. We have investigated the relationship between synaptotagmin and the number of morphologically docked vesicles by an electron microscopic analysis of Drosophila synaptotagmin (syt) mutants. The overall number of synaptic vesicles in a terminal was reduced, although each active zone continued to have a cluster of vesicles in its vicinity. In addition, there was an increase in the number of large vesicles near synapses. Examining the clusters, we found that the pool of synaptic vesicles immediately adjacent to the presynaptic membrane, the pool that includes the docked population, was reduced to 24 +/- 5% (means +/- SEM) of control in the sytnull mutation. To separate contributions of overall vesicle depletion and increased spontaneous release from direct effects of synaptotagmin on morphological docking, we examined syt mutants in an altered genetic background. Recombining syt alleles onto a second chromosome bearing an as yet uncharacterized mutation resulted in the expected decrease in evoked release but suppressed the increase in spontaneous release frequency. Motor nerve terminals in this genotype contained more synaptic vesicles than control, yet the number of vesicles immediately adjacent to the presynaptic membrane near active zones was still reduced (33 +/- 4% of control). Our findings demonstrate that there is a decrease in the number of morphologically docked vesicles seen in syt mutants. The decreases in docking and evoked release are independent of the increase in spontaneous release. These results support the hypothesis that synaptotagmin stabilizes the docked state.

Animals↗

PubMed1997

CASP2 molecular docking predictions with the LIGIN software.

Seven docking predictions were made with the LIGIN program. In six cases the location of the binding pocket was identified correctly by systematically docking everywhere within the protein structure. In two cases the ligand was docked to within 1.8 A RMSD of the experimentally determined structure. LIGIN has not been optimized to deal with highly flexible ligands that dock at the surface of proteins. Consequently, in three cases the exposed part of the ligand was docked poorly, although the buried parts were docked well, and made similar atomic contacts with the protein as in the experimentally determined structure.

Amiloride↗

PubMedDate not supplied

Molecular docking towards drug discovery.

Fueled by advances in molecular structure determination, tools for structure-based drug design are proliferating rapidly. Lead discovery through searching of ligand databases with molecular docking techniques represents an attractive alternative to high-throughout random screening. The size of commercial databases imposes severe computational constraints on molecular docking, compromising the level of calculational detail permitted for each putative ligand. We describe alternative philosophies for docking which effectively address this challenge. With respect to the dynamic aspects of molecular recognition, these strategies lie along a spectrum of models bounded by the Lock-and-Key and Induced-Fit theories for ligand binding. We explore the potential of a rigid model in exploiting species specificity and of a tolerant model in predicting absolute ligand binding affinity. Current molecular docking methods are limited primarily by their ability to rank docked complexes; we therefore place particular emphasis on this aspect of the problem throughout our validation of docking strategies.

Animals↗

PubMed1995

Atomic solvation parameters in the analysis of protein-protein docking results.

Several sets of amino acid surface areas and transfer free energies were used to derive a total of nine sets of atomic solvation parameters (ASPs). We tested the accuracy of each of these sets of parameters in predicting the experimentally determined transfer free energies of the amino acid derivatives from which the parameters were derived. In all cases, the calculated and experimental values correlated well. We then chose three parameter sets and examined the effect of adding an energetic correction for desolvation based on these three parameter sets to the simple potential function used in our multiple start Monte Carlo docking method. A variety of protein-protein interactions and docking results were examined. In the docking simulations studied, the desolvation correction was only applied during the final energy calculation of each simulation. For most of the docking results we analyzed, the use of an octanol-water-based ASP set marginally improved the energetic ranking of the low-energy dockings, whereas the other ASP sets we tested disturbed the ranking of the low-energy dockings in many of the same systems. We also examined the correlation between the experimental free energies of association and our calculated interaction energies for a series of proteinase-inhibitor complexes. Again, the octanol-water-based ASP set was compatible with our standard potential function, whereas ASP sets derived from other solvent systems were not.

Amino Acids↗

PubMed1993

Automated docking in crystallography: analysis of the substrates of aconitase.

Automated docking of substrates to proteins of known structure aids the process of crystallographic analysis in two ways. First, automated docking can be used to generate a small number of starting models for substrates using only protein coordinates from an early stage of refinement. Second, automated docking provides a method for exploring aspects of catalysis that are inaccessible to crystallography by postulating binding modes of catalytic intermediates. This paper describes the use of automated docking to explore the binding of substrates to aconitase. The technique starts with a substrate molecule in an arbitrary configuration and position and finds favorable docked configurations in a (static) protein active site based on a molecular mechanics type force field. Using protein coordinates from an early stage of refinement of an aconitase-isocitrate complex, we successfully predicted the binding configuration of isocitrate. Four configurations were found, the energetically most favorable of which fit the observed electron density well and was used as a starting model for further refinement. Two configurations were found in citrate docking experiments, the second of which approximates the mode of substrate binding in an aconitase-nitrocitrate complex. We were also able to propose two binding modes of the catalytic intermediate cis-aconitate. These correspond closely to the isocitrate and the citrate binding modes. The relation of these new results to the proposed reaction mechanism is discussed.

Aconitate Hydratase↗

PubMed1996

Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal.

Strategies for computational association of molecular components entail a compromise between configurational exploration and accurate evaluation. Following the work of Meng et al. [Proteins, 17 (1993) 266], we investigate issues related to sampling and optimization in molecular docking within the context of the DOCK program. An extensive analysis of diverse sampling conditions for six receptor-ligand complexes has enabled us to evaluate the tractability and utility of on-the-fly force-field score minimization, as well as the method for configurational exploration. We find that the sampling scheme in DOCK is extremely robust in its ability to produce configurations near to those experimentally observed. Furthermore, despite the heavy resource demands of refinement, the incorporation of a rigid-body, grid-based simplex minimizer directly into the docking process results in a docking strategy that is more efficient at retrieving experimentally observed configurations than docking in the absence of optimization. We investigate the capacity for further performance enhancement by implementing a degeneracy checking protocol aimed at circumventing redundant optimizations of geometrically similar orientations. Finally, we present methods that assist in the selection of sampling levels appropriate to desired result quality and available computational resources.

Algorithms↗

PubMed1990

Secretory organelle docking at the cell membrane of Paramecium cells: dedocking and synchronized redocking of trichocysts.

We present the first evidence that secretory organelle docking at the cell membrane can be reversed in vivo. In nondischarge (nd) mutants of Paramecium tetraurelia all trichocysts can be detached from the cell surface within 2-3 h by different means, including cytochalasin B (but not D), high cell density, or Ca2+ ionophores. Considering the well-established ultrastructural differences between nd and wild-type (wt) cells, one can conclude that trichocyst docking at the cell periphery involves two docking sites (I, II): Site I ties the organelles to the epiplasm, and site II is the connection to the cell membrane at the fusogenic zone (expressed only in wt cells); both sites are close to the cell surface and only 150 nm apart. When the trigger for detachment of cortically docked trichocysts (high cell density, cytochalasin B) is relieved, trichocysts are synchronously reattached at the cell membrane, within 40-50 min, with a rate of 20-40 organelles/min, which far exceeds spontaneous docking rates. This is therefore also the first report on synchronization of secretory organelle docking. It is shown by radioactive leucine labeling that the same organelles are redocked, because trichocyst biogenesis is minimal under the conditions of de/redocking used. Surprisingly not only redocking but also detachment of trichocysts from the cell surface can be abolished by inhibitors of protein synthesis. Since Ca2+ ionophores mimic the effects of other conditions sufficient to detach trichocysts from the cell surface, we assume that a protein-dependent mechanism sensitive to Ca2+ (or other ions in exchange) may operate in trichocyst detachment. The precise mechanism involved in attachment or detachment of trichocysts remains to be elucidated.

Animals↗

PubMed1991

Effects of local anesthesia and intravenous naloxone on the changes in behaviour and plasma concentrations of cortisol produced by castration and tail docking with tight rubber rings in young lambs.

The reliability of some behavioral and physiological indices used for the recognition and assessment of acute pain in lambs after castration and tail docking has been examined. Changes in the indices were measured after blocking neural activity with local anaesthetic (lignocaine) and after an opioid antagonist (naloxone) was administered. Six lambs, aged less than one week, were allocated randomly to each of six treatments. (i) control handling and blood sampling; (ii) castration plus tail docking with tight rubber rings; (iii) local anaesthesia; (iv) local anaesthesia followed by castration and tail docking; (v) intravenous naloxone only (0.2 mg kg-1); and (vi) intravenous naloxone followed by castration and tail docking. Local anaesthesia eliminated the behavioural and plasma cortisol changes which usually follow castration and tail docking. Naloxone had a limited effect on the increase in cortisol but altered the behaviour. The results support the view that such indices are useful for assessment of the response to acute pain and that, although endogenous opioids do reduce pain in young lambs after castration and tail docking, the effect is small.

Anesthesia, Local↗

PubMed1994

A rab protein is required for the assembly of SNARE complexes in the docking of transport vesicles.

Rab proteins are generally required for transport vesicle docking. We have exploited yeast secretion mutants to demonstrate that a rab protein is required for v-SNAREs and t-SNAREs to assemble. The absence of the rab protein in the docking complex suggests that, in a broad sense, rab proteins participate in a reaction catalyzing SNARE complex assembly. In so doing, rab proteins could help impart an additional layer of specificity to vesicle docking. This mechanism likely involves the Sec1 homolog Sly1, which we identified in isolated docking complexes. We also report the identification of a novel v-SNARE (Ykt6p) component of the yeast ER-Golgi docking complex that has a CAAX box and is predicted to be lipid anchored. The surprising finding that docking complexes can contain many distinct species of SNAREs (Sed5p, Bos1p, Sec22p, Ykt6p, and likely Bet1p, p28, and p14) suggests that multimeric interactions are features of the fusion machinery, and may also improve the fidelity of vesicle targeting.

Amino Acid Sequence↗

PubMed1995

The peptide repeat domain of nucleoporin Nup98 functions as a docking site in transport across the nuclear pore complex.

We report the cDNA deduced primary structure of a wheat germ agglutinin-reactive nuclear pore complex (NPC) protein of rat. The protein, termed Nup98 (for nucleoporin of 98 kDa), contains numerous GLFG and FG repeats and some FXFG repeats and is thus a vertebrate member of a family of GLFG nucleoporins that were previously discovered in yeast. Immunoelectron microscopy showed Nup98 to be asymmetrically located at the nucleoplasmic side of the NPC. Nup98 functions as one of several docking site nucleoporins in a cytosolic docking activity-mediated binding of a model transport substrate. The docking site of Nup98 was mapped to its N-terminal half, which contains all of the peptide repeats. A recombinant segment of this region depleted the docking activity of cytosol. We suggest that the peptide repeat domain of Nup98, together with peptide repeat domains of other nucleoporins, forms an array of sites for mediated docking of transport substrate, and that bidirectional transport across the NPC proceeds by repeated docking and undocking reactions.

Amino Acid Sequence↗

PubMed1995

Previously identified protein of uncertain function is karyopherin alpha and together with karyopherin beta docks import substrate at nuclear pore complexes.

Previously, we had purified a cytosolic protein complex, termed karyopherin, that functions in docking import substrate at the nuclear envelope in digitonin-permeabilized cells and also had molecularly cloned and sequenced its 97-kDa beta subunit. We now report that the karyopherin alpha subunit is the previously identified protein NPI-1/SRP-1 of hitherto uncertain function. Using purified recombinant karyopherin alpha or beta subunit, we showed that neither karyopherin alpha nor karyopherin beta alone was sufficient for docking of import substrate at the nuclear envelope. Docking occurred only when both subunits were present. Moreover, docking of import substrate by the two recombinant karyopherin subunits was productive, as it led to nuclear internalization of the docked substrate in the presence of additional, previously characterized cytosolic factors. In a binding assay using immobilized karyopherin alpha and beta subunits and import substrate as a ligand, we found that only karyopherin alpha bound ligand. We suggest that karyopherin beta functions as an adaptor that binds both to karyopherin alpha and to any of a large number of docking sites that are represented by a repetitive peptide motif containing nucleoporins on both the cytoplasmic and nucleoplasmic side of the nuclear pore complex (NPC), bidirectionally ferrying a complex of karyopherin alpha-substrate across the NPC.

Animals↗

PubMed1998

Initial docking of ER-derived vesicles requires Uso1p and Ypt1p but is independent of SNARE proteins.

ER-to-Golgi transport in yeast may be reproduced in vitro with washed membranes, purified proteins (COPII, Uso1p and LMA1) and energy. COPII coated vesicles that have budded from the ER are freely diffusible but then dock to Golgi membranes upon the addition of Uso1p. LMA1 and Sec18p are required for vesicle fusion after Uso1p function. Here, we report that the docking reaction is sensitive to excess levels of Sec19p (GDI), a treatment that removes the GTPase, Ypt1p. Once docked, however, vesicle fusion is no longer sensitive to GDI. In vitro binding experiments demonstrate that the amount of Uso1p associated with membranes is reduced when incubated with GDI and correlates with the level of membrane-bound Ypt1p, suggesting that this GTPase regulates Uso1p binding to membranes. To determine the influence of SNARE proteins on the vesicle docking step, thermosensitive mutations in Sed5p, Bet1p, Bos1p and Sly1p that prevent ER-to-Golgi transport in vitro at restrictive temperatures were employed. These mutations do not interfere with Uso1p-mediated docking, but block membrane fusion. We propose that an initial vesicle docking event of ER-derived vesicles, termed tethering, depends on Uso1p and Ypt1p but is independent of SNARE proteins.

Animals↗

PubMed1997

Acute cortisol responses of lambs castrated and docked using rubber rings with or without a castration clamp.

OBJECTIVE: To measure the plasma cortisol response in lambs castrated and docked by three different methods (ring castration and tail docking, ring and clamp castration and tail docking; ring and clamp castration and ring tail docking) for 4 h after treatment. DESIGN: A physiological study with controls. PROCEDURE: A rubber ring was applied to the scrotum. Then the castration clamp was placed, distal to the ring, on each spermatic cord such that there was no overlap of the crush lines. RESULTS: There were no differences in the cortisol secretion of the lambs castrated and tail docked by the ring only and by the ring plus castration clamp methods. Using the castration clamp in addition to the ring on the tail had no effect on cortisol secretion. CONCLUSIONS: Using the castration clamp did not appear to reduce the cortisol response to ring castration and docking, as demonstrated elsewhere, because the areas of uncrushed tissue between the two castration clamp crush lines allowed nociception from ischemic scrotal tissue to be transmitted cranially via undamaged nerve fibers.

Analysis of Variance↗

PubMed1994

Lamb tail docking: a controlled field study of the effects of tail amputation on health and productivity.

A detailed study of the effects of tail docking on lamb health and productivity was prompted by current concern about the welfare aspects of lamb tail amputation. Using a controlled field trial, comparing over 3000 docked and undocked lambs on seven farms, the effects of tail docking on mortality, blowfly strike and production variables were examined. The incidence of blowfly strike was strongly and consistently higher in undocked than docked lambs (rate ratio 6.03, 95 per cent confidence interval (CI) 2.99 to 12.19 for male lambs and 4.25, 95 per cent CI 2.25 to 8.01 for female lambs). The incidence of faecal soiling of the breech was slightly higher in undocked lambs and was identified as an important independent risk factor for blowfly strike. Both the mortality and production parameters were similar for docked and undocked lambs. It was concluded that tail docking protected against blowfly strike, with little evidence of any detrimental effect on lamb mortality and production.

Amputation, Surgical↗

PubMed1985

A structural and functional analysis of the docking protein. Characterization of active domains by proteolysis and specific antibodies.

Docking protein is a 73-kDa integral membrane protein of the rough endoplasmic reticulum. It is essential for translocation of nascent secretory proteins into the lumen of the endoplasmic reticulum. Monoclonal and polyclonal antibodies have been generated which, in conjunction with limited proteolysis, have been used to characterize several subspecies of docking protein. These proteolytic fragments have been analyzed with respect to the various functions ascribed to docking protein which can be assayed in vitro. Proteolytic digestion of membrane-associated or of affinity-purified intact docking protein showed that: elastase cleavage generates a 59-kDa soluble fragment and one of 14 kDa which contains the membrane anchoring domain; trypsin as well as endogenous proteolysis generates a 46-kDa fragment, leaving a 27-kDa domain containing the membrane anchor. This 27-kDa fragment can be reduced to a 13- and a 14-kDa piece by elastase digestion. The characteristics of these various subspecies were examined. The 59-kDa soluble fragment, which can reconstitute full translocation activity to docking protein-depleted microsomes (Meyer, D. I., and Dobberstein, B. (1980) J. Cell Biol. 87, 503-508) was capable of releasing a signal recognition particle-mediated translation arrest. The 46-kDa fragment was neither able to reassociate with nor to reconstitute the activity of docking protein-depleted microsomes. Moreover this fragment was unable to release a signal recognition particle-mediated arrest. This suggests that the 13-kDa fragment (the difference between 46 and 59 kDa) is both essential for association with the membrane, and for the release of translation arrests.

Animals↗

PubMed1998

Surface solid angle-based site points for molecular docking.

We are developing a new site descriptor for the DOCK molecular modeling program suite. Sphgen, the current site description program for the DOCK suite, describes the pockets of a macromolecule by filling a volume with intersecting spheres. DOCK then identifies possible ligand orientations in the pocket by overlapping the atoms of proposed ligands with the sphere centers. Sphgen limits use of the DOCK program to concave binding regions, but macromolecular binding regions can be solvent-exposed rather than buried pockets. We present a more general site descriptor, based on the surface solid angle, which generates site points by determining the solid angle of exposure for points on the surface of the molecule, then identifying patches of surface with similar solid angle values which are then built into site points. We find possible ligand orientations by matching shape-based site points on the ligand and protein and demanding complementary solid angle values. Orientations are evaluated using the DOCK's force field-based score, which evaluates the Coulombic and van der Waals energy. The surface solid angle descriptor displays the complementary characteristics of the interfaces of our test systems: trypsin/trypsin inhibitor, chymotrypsin/turkey ovomucoid third domain, and subtilisin/chymotrypsin inhibitor. The solid angle site points can be used by DOCK to generate orientations within 1.5 A r.m.s.d. of the crystal structure orientation.

Algorithms↗