Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Loops are regions of non-repetitive conformation connecting regular secondary structures. They are both the most difficult and error prone regions of a protein to solve by X-ray crystallography and the hardest regions to model using comparative procedures. Although a loop can sometimes be modelled from a homologue, very often it must be selected from outside the family. The loop prediction procedure, SLoop, attempts to identify the conformational class of the loop rather than to select a specific loop from a set of fragments extracted from known structures or generated ab initio. Templates are constructed for each of the 161 loop conformational classes that have been identified from the clustering of the structures of some 2024 loops of one to eight residues in length. A class template describes both sequence preferences and relative disposition of bounding secondary structures. During comparative modelling, the conformation of a loop can be predicted by identifying a loop class with which its sequence and disposition of bounding secondary structures are compatible. The procedure is tested on an unrelated non-redundant set of 1785 loops under stringent and lax evaluation schemes. Optimal sequence score cut-offs are identified such that the prediction rate is equal to the percentage of loops assigned to acceptable classes. Under the stringent evaluation, at the optimal sequence score cut-off, a conformation is predicted for 50% of loops of which 47% are correct, while under the lax evaluation a conformation is predicted for 63% of loops of which 54% are correct. Sequence score is shown to be a good indicator of the probability of a prediction being correct. Loop length also has a strong affect on prediction outcomes. Considering only loops of two to five residues in length, under the stringent evaluation 62% of loops are predicted with 52% of these predictions being correct while under the lax evaluation predictions are provided for 75% of loops of which 57% are correct.
J Mol Biol 1997 Mar 28
PMID:Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling. 909 31

The heptadecapeptide orphanin FQ (OFQ) has been identified as the endogenous ligand for a G protein-coupled receptor (OFQ-R), which, despite its high degree of sequence similarity to opioid receptors, fails to bind opioid ligands. We developed two radioligands for the OFQ-R: a tritiated native OFQ peptide ([3H]OFQ) and a radioiodinated form in which Leu14 was substituted by tyrosine (125I-Tyr14-OFQ). Their binding properties were examined in human embryonic kidney (HEK) 293 and Chinese hamster ovary (CHO) cells heterologously expressing the OFQ-R at different levels (HEK 293 expressed 40-fold more OFQ-R than did CHO). Both ligands exhibited rapid, monophasic association kinetics in each cell line. Dissociation of both ligands from OFQ-R expressed in HEK 293 cells was biphasic, whereas dissociation of 125I-Tyr14-OFQ from OFQ-R expressed in CHO cells was monophasic and slow. Saturation binding analysis revealed two affinity states in HEK 293 cells with binding parameters in accord with those determined kinetically. In CHO cells, 125I-Tyr14-OFQ detected a single affinity state with an intermediate Kd value of 54 pM. Optimal binding of the radioligands required 1-5 mM MgCl2, whereas millimolar concentrations of ZnCl2, CaCl2, MnCl2, and NaCl reduced specific binding of both ligands. A nonhydrolyzable GTP analog [guanosine-5'-(beta,gamma-imido)triphosphate] reduced the affinity of both OFQ ligands to their receptor without significant changes in the total binding capacity, indicating functional interactions between the OFQ-R and G proteins. In rat brain membranes, specific, saturable binding of 125I-Tyr14-OFQ was demonstrated to be pharmacologically identical to the heterologously expressed OFQ-R. Taken together, these results indicate that 125I-Tyr14-OFQ and [3H]OFQ exhibit virtually identical characteristics and are suitable for the pharmacological analysis of the OFQ-R.
Mol Pharmacol 1997 May
PMID:Interaction of [3H]orphanin FQ and 125I-Tyr14-orphanin FQ with the orphanin FQ receptor: kinetics and modulation by cations and guanine nucleotides. 914 20

Perfluorocarbon affinity emulsions have been generated by immobilizing concanavalin A onto the surface of triazine-activated perfluorocarbon droplets. Immobilized concanavalin A densities of 0.1, 0.7 and 2.1 mg/ml were obtained by varying the concentration of cyanuric chloride used for activation. The affinity emulsions were found to adsorb Saccharomyces cerevisiae cells from solution with adsorption capacities of 1 x 10(9) cells, 4.6 x 10(9) and 6 x 10(9) cell/ml, respectively. Optimal conditions for the elution of bound cells were obtained by studying inhibition curves of concanavalin A-mannan precipitation using simple sugars. Methyl alpha-D-mannopyranoside showed the greatest inhibitory power with 50 per cent inhibition displayed at a concentration of 0.05 mM. Experiments carried out examining the concentrations of methyl alpha-D-mannopyranoside necessary to dissociate a concanavalin A-mannan precipitate demonstrated that at least a seven-fold higher concentration of methyl alpha-D-mannopyranoside was required for dissociation than that required for inhibition of its formation. The efficiency of elution of bound yeast cells was found to be dependent on the concentration of methyl alpha-D-mannopyranoside used, the time of elution and the immobilized ligand density. Thus, 100 per cent elution was obtained with a concanavalin A affinity emulsion (0.1 mg/ml) by incubation with 500 mM methyl alpha-D-mannopyranoside for 1 h.
J Mol Recognit
PMID:Affinity adsorption of Saccharomyces cerevisiae on concanavalin A perflurocarbon emulsions. 917 46

One of the major goals of rational design of combinatorial libraries is to design libraries with maximum diversity to enhance the potential of finding active compounds in the initial rounds of high-throughput screening programs. We present strategies to visualize and optimize the structural diversity of sets of molecules, which can be either potential substituents to be attached at specific positions of the library scaffold, or entire molecules corresponding to enumerated libraries. The selection of highly diverse subsets of molecules from the library is based on the stochastic optimization of 'Diversity' functions using a single-point-mutation Monte Carlo technique. The Diversity functions are defined in terms of the distances among molecules in multidimensional property space resulting from the calculation of 2D and 3D molecular descriptors. Several Diversity functions, including an implementation of D-Optimal design, are applied to select diverse subsets and the results are compared. The diversity of the selected subsets of molecules is visualized by embedding the intermolecular distances, defined by the molecules in multidimensional property space, into a three-dimensional space.
Mol Divers 1996 Oct
PMID:Optimization and visualization of molecular diversity of combinatorial libraries. 923 35

Differential display (DD) is a powerful instrument to detect differences in gene expression of malignant and normal cells. An optimized silver staining protocol was used to compare mRNA expression of keratinocytes and squamous cell carcinoma cells of the head and neck. Optimal concentration for upstream and downstream primer was 0.2 microM. Best primer concentrations for reamplification were between 40 and 60 pM. With this optimized protocol nearly 50 differentially expressed transcripts have been identified and differential display can be applied safer, easier, and faster, than by radioactive labeling.
Res Commun Mol Pathol Pharmacol 1997 Aug
PMID:Optimized differential display and reamplification parameters for silver staining. 934 36

This study is a phylogenetic analysis of the avian family Ciconiidae, the storks, based on two molecular data sets: 1065 base pairs of sequence from the mitochondrial cytochrome b gene and a complete matrix of single-copy nuclear DNA-DNA hybridization distances. Sixteen of the nineteen stork species were included in the cytochrome b data matrix, and fifteen in the DNA-DNA hybridization matrix. Both matrices included outgroups from the families Cathartidae (New World vultures) and Threskiornithidae (ibises, spoonbills). Optimal trees based on the two data sets were congruent in those nodes with strong bootstrap support. In the best-fit tree based on DNA-DNA hybridization distances, nodes defining relationships among very recently diverged species had low bootstrap support, while nodes defining more distant relationships had strong bootstrap support. In the optimal trees based on the sequence data, nodes defining relationships among recently diverged species had strong bootstrap support, while nodes defining basal relationships in the family had weak support and were incongruent among analyses. A combinable-component consensus of the best-fit DNA-DNA hybridization tree and a consensus tree based on different analyses of the cytochrome b sequences provide the best estimate of relationships among stork species based on the two data sets.
Mol Phylogenet Evol 1997 Dec
PMID:Phylogeny of the avian family Ciconiidae (storks) based on cytochrome b sequences and DNA-DNA hybridization distances. 941 89

Optimal cutting temperature (OCT) is a widely used embedding medium for tissues for histopathologic analysis. This investigation examined the effects that OCT storage can have upon the ability to perform subsequent molecular biological analyses. Tumor material was dissected into small pieces and stored at approximately 20 degrees C both with and without OCT. DNA and RNA were then extracted from the tissue fragments and analyzed by the polymerase chain reaction (PCR), using primer sets designed to amplify a range of product sizes, and also by reverse transcriptase-PCR (RT-PCR). The storage of pathological specimens in OCT compound was found to affect significantly and irreversibly the ability to amplify DNA in the PCR, particularly as the size of the amplified fragment increased. This effect appeared to occur as a result of greater degradation of DNA extracted from tissue embedded in OCT compared to DNA extracted from tissue stored without OCT. RNA quality appeared unaffected, which may be because of the extraction protocol employed. Our results suggest that OCT-embedded frozen-tissue samples may be used for RNA isolation for subsequent RT-PCR and for the in vitro amplification of DNA targets of approximately < 300 base pairs only. We strongly advise against the routine storage of any tissue biopsy material in OCT if molecular analyses may be required.
Diagn Mol Pathol 1997 Oct
PMID:The use of optimal cutting temperature compound can inhibit amplification by polymerase chain reaction. 945 90

Purified membrane-bound alkaline phosphatase from rat osseous plate hydrolyzed pyrophosphate in the presence of magnesium ions, with a specific activity of 92.7 U/mg. Optimal apparent pH for pyrophosphatase activity was 8.0 and it remained unchanged on increasing the pyrophosphate concentration. In the absence of magnesium ions the enzyme had a Km = 88 microM and V = 36.7 U/mg for pyrophosphate and no inhibition by excess substrate was observed. Pyrophosphatase activity was rapidly destroyed at temperatures above 40 degrees C, but magnesium ions apparently protected the enzyme against denaturation. Sodium metavanadate (Ki = 1.0 mM) was a competitive inhibitor of pyrophosphatase activity, while levamisole (Ki = 8.2 mM) and theophylline (Ki = 7.4 mM) were uncompetitive inhibitors. Magnesium ions (K0.5 = 1.7 microM) stimulated pyrophosphatase activity, while cobalt (Ki = 48.5 microM) and zinc (Ki = 22.0 microM) ions were non-competitive inhibitors. Manganese and calcium ions had no effect on pyrophosphatase activity. The Mw of the pyrophosphatase protein was 130 kDa by gel filtration, but a value of 65 kDa was obtained by dissociative gel electrophoresis, suggesting that it was a dimer of apparently identical subunits. These results suggested that pyrophosphatase activity stems from the membrane-bound osseous plate alkaline phosphatase and not from a different protein.
Cell Mol Biol (Noisy-le-grand) 1998 Mar
PMID:Inorganic pyrophosphate-phosphohydrolytic activity associated with rat osseous plate alkaline phosphatase. 959 80

Association of the Golgi-specific adaptor protein complex 1 (AP-1) with the membrane is a prerequisite for clathrin coat assembly on the trans-Golgi network (TGN). The AP-1 adaptor is efficiently recruited from cytosol onto the TGN by myristoylated ADP-ribosylation factor 1 (ARF1) in the presence of the poorly hydrolyzable GTP analog guanosine 5'-O-(3-thiotriphosphate) (GTPgammaS). Substituting GTP for GTPgammaS, however, results in only poor AP-1 binding. Here we show that both AP-1 and clathrin can be recruited efficiently onto the TGN in the presence of GTP when cytosol is supplemented with ARF1. Optimal recruitment occurs at 4 microM ARF1 and with 1 mM GTP. The AP-1 recruited by ARF1.GTP is released from the Golgi membrane by treatment with 1 M Tris-HCl (pH 7) or upon reincubation at 37 degreesC, whereas AP-1 recruited with GTPgammaS or by a constitutively active point mutant, ARF1(Q71L), remains membrane bound after either treatment. An incubation performed with added ARF1, GTP, and AlFn, used to block ARF GTPase-activating protein activity, results in membrane-associated AP-1, which is largely insensitive to Tris extraction. Thus, ARF1. GTP hydrolysis results in lower-affinity binding of AP-1 to the TGN. Using two-stage assays in which ARF1.GTP first primes the Golgi membrane at 37 degreesC, followed by AP-1 binding on ice, we find that the high-affinity nucleating sites generated in the priming stage are rapidly lost. In addition, the AP-1 bound to primed Golgi membranes during a second-stage incubation on ice is fully sensitive to Tris extraction, indicating that the priming stage has passed the ARF1.GTP hydrolysis point. Thus, hydrolysis of ARF1.GTP at the priming sites can occur even before AP-1 binding. Our finding that purified clathrin-coated vesicles contain little ARF1 supports the concept that ARF1 functions in the coat assembly process rather than during the vesicle-uncoating step. We conclude that ARF1 is a limiting factor in the GTP-stimulated recruitment of AP-1 in vitro and that it appears to function in a stoichiometric manner to generate high-affinity AP-1 binding sites that have a relatively short half-life.
Mol Biol Cell 1998 Jun
PMID:ADP-ribosylation factor 1 transiently activates high-affinity adaptor protein complex AP-1 binding sites on Golgi membranes. 961 77

Previously, we reported that unaggressive, growth factor-dependent FET human colon carcinoma cells downregulated their transforming growth factor alpha (TGFalpha) expression in a quiescent state (G0/G1) induced by growth factor and nutrient deprivation (Mulder, 1991, Cancer Res., 51:2256-2262). In contrast, highly aggressive, growth factor-independent HCT116 human colon carcinoma cells aberrantly upregulated this autocrine activity in the quiescent state (Mulder, 1991, Cancer Res., 51:2256-2262; Howell et al., 1998, Mol. Cell. Biol., 18:303-313). In this report, the role of autocrine TGFalpha and the mechanism of its regulation of expression during reentry into the cell cycle from a noncycling growth state were determined in FET cells. Optimal induction of DNA synthesis from a quiescent state in FET cells is dependent upon autocrine TGFalpha as well as exogenous transferrin and insulin. Reentry into the cell cycle resulting from treatment with exogenous transferrin and insulin resulted in approximately 3-fold induction of TGFalpha expression within 1 hr. TGFalpha induction was controlled at the transcription level, and the cis-controlling element was localized to the region between bp -370 - -201 relative to the translation start codon within the TGFalpha promoter. Thus neutralization of autocrine TGFalpha protein revealed that the induced TGFalpha autocrine activity was necessary for DNA synthesis and acted only in the early G1 phase of the cell cycle. Blockade of autocrine TGFalpha expression early in the cell cycle resulted in the reduction of DNA synthesis, whereas treatment with neutralization antibody at later times had no effect. This suggested that autocrine TGFalpha functions to initiate cell growth from noncycling states. This was further confirmed by the dependence of FET cells upon autocrine TGFalpha for colony formation in experiments where the plating density was sufficiently low to generate a lag phase in tissue culture. In contrast, TGFalpha autocrine activity was not required for exponential phase cells, as evidenced by the failure of TGFalpha neutralizing antibody to inhibit proliferation in this growth state. Taken together, these results suggest that autocrine TGFalpha acts primarily in the process of growth initiation by moving cells from a noncycling state back into the cell cycle, rather than supporting cell growth already initiated.
 ...
PMID:Autocrine TGFalpha expression in the regulation of initiation of human colon carcinoma growth. 980 47


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