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MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites.

The three-dimensional environments of ligand binding sites have been derived from the parsing and loading of the PDB entries into a relational database. For each bound molecule the biological assembly of the quaternary structure has been used to determine all contact residues and a fast interactive search and retrieval system has been developed. Prosite pattern and short sequence search options are available together with a novel graphical query generator for inter-residue contacts. The database and its query interface are accessible from the Internet through a web server located at: http://www.ebi.ac.uk/msd-srv/msdsite.

Amino Acid Sequence↗

Catalytic activity of cytochrome P4501A2 in reconstituted system with Emulgen 913.

Physicochemical properties and catalytic activity of cytochrome P4501A2 in the reconstituted system with Emulgen 913 were studied. The formation of cytochrome P4501A2 monomers was shown by gel filtration at an Emulgen concentration of 8 g/liter. The catalytic activity of the monomeric monooxygenase system was low. The maximum rate of the 7-ethoxyresorufin O-deethylation reaction, 150 pmol resorufin min-1 nmol-1 cytochrome P4501A2, was observed at an Emulgen concentration of 0.1 g/liter when cytochrome P4501A2 pentamers predominated. The effects of Emulgen on cytochrome P4501A2 cumene hydroperoxide-dependent peroxidase activity, on its affinity to substrate and to cytochrome b5, and on the rate constants of dithionite-dependent reduction were insignificant. Study of the NADPH-dependent reduction of cytochrome P4501A2 in the reconstituted system showed that the rate constant and reduction level of cytochrome P4501A2 were always higher when the reaction was initiated by NADPH than when it was initiated by NADPH-cytochrome P450 reductase. This indicated that the reduction reaction initiated by the reductase was limited by a step in the cytochrome P4501A2 and reductase interaction. Correlation between 7-ethoxyresorufin O-deethylase activity and reduction level of cytochrome P4501A2 was found.

Animals↗

Microsomal P450 2C3 is expressed as a soluble dimer in Escherichia coli following modification of its N-terminus.

A hydrophobic segment present in the N-terminus of microsomal P450s is thought to serve as a membrane anchor. A variant of P450 2C3 was constructed, P450 2C3d, that lacked the putative membrane-spanning segment of the N-terminus, residues 3-20. This construct also incorporated substitutions of an alanine for 2Asp to facilitate expression in Escherichia coli and of serines for 24His and 25Gly to introduce a restriction site. P450 2C3d is expressed at relatively high levels in E. coli, 800-1200 nmol/liter of culture medium. In contrast to P450 2C3mod, which retains a membrane-spanning N-terminal sequence modified for expression in E. coli, the subcellular distribution of P450 2C3d in E. coli is dependent on the ionic strength of the buffer used for cell disruption. In low ionic strength buffers, 2C3d was mainly localized in the membrane fraction, whereas in buffers containing 1 M NaCl or 0.5 M KPi, P450 2C3d was predominantly found in the soluble fraction, indicating that deletion of the hydrophobic segment converted the intrinsic membrane protein to an extrinsic one. P450 2C3d was further modified by the incorporation of four histidine residues at the C-terminus (P450 2C3dH), and this enzyme could be purified in the absence of detergent using immobilized metal affinity chromatography following extraction from isolated membranes in high salt buffers. The catalytic properties of the purified, modified enzymes are similar to those of the native enzyme. Size-exclusion chromatography indicated that 2C3dH and 2C3d are predominantly dimers, whereas 2C3 is a larger oligomer (> 8-mer). Moreover, the detergents sodium cholate and Chaps each dissociate the dimers of 2C3dH to monomers at concentrations that do not alter the aggregation state of 2C3. These modifications are likely to facilitate attempts to crystallize the catalytic domains of microsomal P450s.

Amino Acid Sequence↗

Characterization of cDNA clones containing CCA trinucleotide repeats derived from human brain.

Expansion mutation is the cause of eight neuropsychiatric disorders. Thus far each disease is the result of expansion of a C-G rich trinucleotide repeat that is polymorphic for length in the general population. We now report the identification of seven novel cDNA clones with CCA or equivalent trinucleotide repeats obtained by screening a human frontal cortex cDNA library. The repeat lengths of two clones, CCA11 (linked to D20S101, expressed in human brain as a 3.2 kb message) and CCA38 (linked to D5S404), are highly polymorphic in a normal human population. CCA54, mapped to chromosome 19, appears to correspond to a portion of the human gene encoding the alpha 1 subunit of a P-type calcium channel. Expansion mutations at these loci should be considered as possible candidates in evaluating the genetic etiologies of diseases linked to chromosomes 5, 19, and 20.

Base Sequence↗

Antigen processing and uptake from the intestinal tract.

We have attempted, in this discussion, to summarize the processes and evidence for absorption of antigenic macromolecules in both animals and humans, comparing the infant to the adult. The mature gut retains the capacity to absorb macromolecules by an energy-dependent pinocytotic mechanism similar to that described for the transport of immunoglobulins and other enteric antigens in certain mammalian species in the neonatal state. The vast majority of adults show no ill effects as a result of this physiologic phenomenon. However, when increased (pathologic) quantities of antigenic macro-molecules gain access to the body because of a derangement in the intraluminal digestive process, or because of a defect in the mucosal barrier, both of which are present in the immature intestine, macromolecular absorption may be altered and result in either local intestinal or systemic disorders.

Animals↗

Extracellular matrix of the human optic nerve head.

Double-antibody immunofluorescent studies of sectioned human optic nerve head indicated the marked presence of collagen type IV and laminin in the extracellular matrix of the lamina cribrosa. These macromolecules were layered transversely across the nerve fascicles and appeared to constitute the cribriform plates. Relatively little collagen types III and I were present in the extracellular matrix of this tissue and fibronectin was not detected in appreciable amounts. These results indicated that the lamina cribrosa contains a specialized extracellular matrix of the central nervous system made up of plates of material resembling basement membrane. The major macromolecular components of the lamina cribrosa do not resemble those of sclera.

Adult↗

Purification and characterization of protein synthesis initiation factor eIF-3 from wheat germ.

eIF-3 from wheat germ is a large multicomponent factor. It sediments at 15 S and is comprised of ten different polypeptides with an Mr value ranging from 26 000 to 135 000; five out of the ten seem to be present in a 1 : 1 stoichiometric ratio, whereas the others appear to occur approximately in a 0.5 to 1 ratio. The factor is active in a partially purified cell-free system derived from wheat germ and in a mammalian model assay system for the synthesis of methionyl puromycin.

Cell-Free System↗

Regulation of protein synthesis in rabbit reticulocyte lysates. Requirement of initiation factor eIF-2 holoprotein for substrate specificity of heme-regulated protein kinase.

The specificity of the heme-regulated protein kinase (HRI) was investigated further by utilizing the isolated 38,000 Da subunit (alpha subunit) polypeptide of eIF-2 as the substrate. For this purpose, the three subunit polypeptides of eIF-2 (38,000 Da, alpha; 50,000 Da, beta; and 52,000 Da, gamma) were resolved by reversed-phase high performance liquid chromatography (HPLC). Results show that HRI is incapable of phosphorylating the 38,000 Da subunit separated from the other two eIF-2 polypeptides. Data suggest that the substrate specificity of HRI is determined by the quaternary structure assumed by the alpha subunit in association with the other two subunits in the eIF-2 holoprotein.

Animals↗

A 15 kDa proteolipid found in mediatophore preparations from Torpedo electric organ presents high sequence homology with the bovine chromaffin granule protonophore.

Upon SDS PAGE of isolated mediatophore, an acetylcholine-translocating protein, a doublet at 15 kDa was identified. Amino acid sequencing after CNBr cleavage gave a 17 residue-long peptide completely homologous with a sequence of the proton-translocating proteolipid from bovine chromaffin granules. A 51-mer oligodeoxynucleotide corresponding to this sequence was used to screen a library of electric lobe cDNAs constructed in lambda Zap II. A positive recombinant clone was isolated and found to encode the complete sequence of a 15.5 kDa protein highly homologous to the bovine chromaffin or yeast vacuolar ATPase proteolipid. In vitro translation of sense RNA transcripts of the clone indeed yielded a single 15 kDa proteolipid. Northern blot analysis showed that the 1.3 kb mRNA encoding this protein is significantly expressed in nervous tissues but not in electric organ or liver of Torpedo marmorata.

Acetylcholine↗

Can one measure the free energy of binding of the histone octamer to different DNA sequences by salt-dependent reconstitution?

I explain why many recently reported measurements for the "free energy" of positioning of the histone octamer on different DNA sequences are likely to be in error: i.e. because histone octamers do not equilibrate between different DNA molecules at low salt, but only at high salt. Thus, the reported "free energies" refer to an equilibrium at high salt, under nearly dissociating conditions between protein and DNA, and they are likely to be much too small on an absolute scale. There are many other lines of evidence to suggest that the preferences of the histone octamer for different DNA sequences are rather strong and of importance in biological systems.

Base Sequence↗

Effects of captopril and propanolol on bradykinin-induced changes in vascular pressures, lymph total protein concentration, and weight in canine forelimbs.

Sixty-minute local intraarterial infusions of bradykinin (0.8, 5, or 10 micrograms base/min) produced transient forelimb vasodilation and dose-related increases in lymph flow, lymph total protein concentration, total protein transport, and weight in forelimbs perfused at a controlled flow rate. Mean aortic pressure was not affected by these infusion rates of bradykinin. Following pretreatment with captopril, the local intraarterial infusion of these same doses of bradykinin produced sustained systemic hypotension. The increase in protein efflux and edema formation produced by local infusions of bradykinin following pretreatment with captopril was markedly increased during the infusion of the low dose of bradykinin (0.8 micrograms base/min, ia), but was attenuated during the local infusion of the larger dose of bradykinin (5 micrograms base/min, ia). Following pretreatment with both captopril and propranolol, the increase in protein efflux and edema formation produced by this larger dose of bradykinin (5 micrograms base/min) was greater than that produced by infusions of this dose of bradykinin alone or after pretreatment with captopril. Moreover, the increase in protein efflux and edema formation was greater during the infusion of the higher dose of bradykinin than during the infusion of the low dose of this autacoid under these conditions. The 60-min infusion of a massive dose of bradykinin into the left ventricular chamber (280 micrograms base/min) produced sustained decreases in aortic and forelimb perfusion pressure, but little edema formation relative to that produced by local intraarterial infusions of this agent. In contrast, the 60-min intravenous infusion of only 5 micrograms base/min of bradykinin following pretreatment with both captopril and propranolol produced profound systemic hypotension and marked increases in protein efflux and edema formation in forelimbs perfused at a controlled flow rate comparable to that produced by the local intraarterial infusion of this dose of bradykinin alone. These data demonstrate that endogenous kininases and catecholamines may dramatically affect the increase in protein efflux and edema formation produced by either local or systemic infusions of bradykinin by modulating the magnitude of the increase in macromolecular permeability.

Animals↗

In vitro assembly of the outer shell of bacteriophage phi 6 nucleocapsid.

Following dissociation of bacteriophage phi 6 nucleocapsid (NC) by EDTA, a particle composed of protein P8 and corresponding to the outer shell of the NC was assembled in vitro in the presence of Ca2+ and Mg2+. Assembly was obtained from soluble protein constituents above 100 micrograms/ml and was optimal within a temperature range of 22-30 degrees. Assembly did not require the presence of genomic RNA. Crosslinking results of intact NCs and in vitro-assembled outer shells suggested that protein P8 dimers are the structural subunits of the shell. Analysis of the assembly kinetics by electron microscopy suggested that ring-like particles of uniform size, packed in flat hexagonal arrays, are intermediates in outer shell assembly.

Bacteriophages↗

Non-benzodiazepine anxiolytics: potential activity of phenylpiperazines without 3H-diazepam displacing action.

Four phenylpiperazine derivatives exhibited an activity similar to benzodiazepines and meprobamate in the 4-plate test. One of these (compound IV) demonstrated anxiolytic like activity in a step-down avoidance technique, in electroshock induced aggression and in the staircase test. In contrast to benzodiazepines, compound IV was not anticonvulsant, myorelaxant or sedative. Confirmation of the anxiolytic activity of compound IV in animal models was obtained in 3 separate clinical trials in anxious patients. The mechanism of action of these phenylpiperazines appears to be different from the benzodiazepines as they do not displace 3H-diazepam binding nor do they interact with other elements of the GABA receptor macromolecular complex. Instead, compound IV interacts with both dopaminergic and serotoninergic neuron systems. Thus, from this data it would appear that an activity at the benzodiazepine recognition site is not obligatory for anxiolytic activity in man or in animals models.

Aggression↗

Isolation of separate mRNAs for alpha- and beta-tubulin and characterization of the corresponding in vitro translation products.

The messenger RNAs coding for alpha- and beta-tubulin have been isolated from embryonic chick brain. Although the mRNAs for the two tubulin subunits have been resolved on native gels, they are very similar in molecular weight (650,000 daltons) as judged by mobility on denaturing gels containing methy mercury. The mRNAs for beta- and gamma-actin have also been resolved on native gels, but migrate as an unresolved peak (molecular weight 6500,000-700,000 daltons) under denaturing conditions. Since the nonmuscle actins are substantially smaller proteins than alpha- and beta-tubulin, the large size of chick nonmuscle actin mRNAs suggests an unusually long untranslated region. Since tubulin and actin polypeptides are internal structural proteins, one would expect them to be synthesized only on free polysomes. Translation of mRNA derived directly from a purified membrane fraction or by puromycin release from that fraction, however, showed the synthesis of a small proportion of these proteins on polysomes that are membrane-associated. Peptide mapping has in all cases confirmed the identity of the products of cell-free synthesis with authentic alpha-tubulin, beta-tubulin and actin. Approximately 67% of the alpha- and 13% of the beta-tubulin chains produced by in vitro translation are competent for co-assembly into microtubules with added carrier microtubule protein.

Actins↗

A protein factor that enhances amsacrine-mediated formation of topoisomerase II-DNA complexes in murine mastocytoma cell nuclei.

Extracts of K21 murine mastocytoma cells contain a factor that enhances formation of amsacrine-induced topoisomerase II-DNA complexes (PDCs) when added to isolated K21 nuclei. The PDC-enhancing activity is reduced in extracts from 2 or 6 h cycloheximide or cordycepin-treated cells, implying that continuous protein synthesis is required to maintain the factor. The factor is heat-labile, proteinase-sensitive and has other properties that distinguish it from the two known classes of topoisomerases. The data suggest that the factor is a labile protein with a molecular weight in excess of 50,000. This appears to be the first direct evidence of a protein factor that modulates drug-induced topoisomerase II action.

Amsacrine↗