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T A Jones

Publications and source records attributed to T A Jones.

At least 109 records · Page 6Linked to original sources
PubMed1994

The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei.

Cellulose is the major polysaccharide of plants where it plays a predominantly structural role. A variety of highly specialized microorganisms have evolved to produce enzymes that either synergistically or in complexes can carry out the complete hydrolysis of cellulose. The structure of the major cellobiohydrolase, CBHI, of the potent cellulolytic fungus Trichoderma reesei has been determined and refined to 1.8 angstrom resolution. The molecule contains a 40 angstrom long active site tunnel that may account for many of the previously poorly understood macroscopic properties of the enzyme and its interaction with solid cellulose. The active site residues were identified by solving the structure of the enzyme complexed with an oligosaccharide, o-iodobenzyl-1-thio-beta-cellobioside. The three-dimensional structure is very similar to a family of bacterial beta-glucanases with the main-chain topology of the plant legume lectins.

Binding Sites↗
PubMed1994

Crystallization and preliminary X-ray analysis of recombinant bovine cellular retinoic acid-binding protein.

Crystals of bovine cellular retinoic acid-binding protein (CRABPI) have been grown from protein expressed in E. coli. Two different crystal forms were obtained. Crystals containing protein with the ligand all-trans retinoic acid belong to space group P4(1) or P4(3), a = b = 41.36, c = 202.71 A and diffract to 2.5 A. Crystals of CRABP with the synthetic retinoid analogue Am80 diffract to 1.9 A with space group P2(1) and cell dimensions a = 37.03, b = 105.93, c = 40.31 A, beta = 110.28 degrees. Considerations in the crystallization of proteins with light-sensitive ligands are discussed.

Journal Article↗
PubMed1994

The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica.

BACKGROUND: Lipases constitute a family of enzymes that hydrolyze triglycerides. They occur in many organisms and display a wide variety of substrate specificities. In recent years, much progress has been made towards explaining the mechanism of these enzymes and their ability to hydrolyze their substrates at an oil-water interface. RESULTS: We have determined the DNA and amino acid sequences for lipase B from the yeast Candida antarctica. The primary sequence has no significant homology to any other known lipase and deviates from the consensus sequence around the active site serine that is found in other lipases. We have determined the crystal structure of this enzyme using multiple isomorphous replacement methods for two crystal forms. Models for the orthorhombic and monoclinic crystal forms of the enzyme have been refined to 1.55 A and 2.1 A resolution, respectively. Lipase B is an alpha/beta type protein that has many features in common with previously determined lipase structures and other related enzymes. In the monoclinic crystal form, lipid-like molecules, most likely beta-octyl glucoside, can be seen close to the active site. The behaviour of these lipid molecules in the crystal structure has been studied at different pH values. CONCLUSION: The structure of Candida antarctica lipase B shows that the enzyme has a Ser-His-Asp catalytic triad in its active site. The structure appears to be in an 'open' conformation with a rather restricted entrance to the active site. We believe that this accounts for the substrate specificity and high degree of stereospecificity of this lipase.

Amino Acid Sequence↗
PubMed1994

Detection, delineation, measurement and display of cavities in macromolecular structures.

A computer program, VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling program O. Additionally, VOIDOO can be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed using O. Examples of the use of VOIDOO are given for P2 myelin protein, cellular retinol-binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are given.

Journal Article↗
PubMed1994

The CL100 gene, which encodes a dual specificity (Tyr/Thr) MAP kinase phosphatase, is highly conserved and maps to human chromosome 5q34.

Expression of the human CL100 gene is induced in skin fibroblasts in response to oxidative/heat stress and growth factors. The CL100 gene encodes a dual specificity (Tyr/Thr) protein phosphatase that specifically inactivates mitogen-activated protein (MAP) kinase in vitro. In addition, CL100 is able to suppress the activation of MAP kinase by oncogenic ras in extracts of Xenopus oocytes. Thus, the CL100 phosphatase may play an important role in the negative regulation of cellular proliferation and is a likely candidate for a tumour-suppressor gene. Here, we show that DNA sequences homologous to CL100 are present in genomic DNA isolated from mouse, chicken, Xenopus and Drosophila, indicating that the CL100 gene is highly conserved. Using an assay based on the polymerase chain reaction, in conjunction with genomic DNA obtained from human-rodent somatic-cell hybrids, we have determined that the CL100 gene is situated on chromosome 5. Fluorescence in situ hybridisation using a CL100 genomic probe confirms that the CL100 mRNA is transcribed from a single genetic locus and maps the gene to 5q34.

Animals↗
PubMed1994

Released chromatin: linearized DNA for high resolution fluorescence in situ hybridization.

Free DNA was prepared from routinely harvested and fixed cells for high resolution FISH mapping using either a sodium hydroxide/ethanol mixture or 70% formamide. Hybridization signals from cosmid probes appeared as extended lines. The average length of signals on DNA prepared with sodium hydroxide was significantly greater than with formamide. A set of overlapping cosmids from the HLA class II region was used to determine how precisely the actual overlap or gap between probes can be calculated from the measured overlap or gap between their signals. Lengths of the probe signals and their known kilobase lengths were used as an internal ruler. The mean values calculated from the measured length from 30 or more signals for each probe pair showed remarkable conformity with the known kilobase lengths of their overlaps and gaps. Immediately adjacent probes could also be ordered on the released DNA. These simple procedures dramatically increase the speed with which relationships between probes can be determined during contig construction.

Chromatin↗
PubMed1994

Use-dependent growth of pyramidal neurons after neocortical damage.

Unilateral damage to the forelimb representation area of the sensorimotor cortex in adult rats increases dendritic arborization of layer V pyramidal neurons of the contralateral homotopic cortex. Arbor size was maximum at approximately 18 d postlesion, following which there was a partial elimination, or pruning, of dendritic processes. These neural changes were closely associated with behavioral events. The overgrowth of dendrites was related in time to disuse of the contralateral (to the lesion) forelimb and over-reliance on the ipsilateral forelimb for postural and exploratory movements. The pruning of dendrites was related to a return to more symmetrical use of the forelimbs. To investigate the possibility that lesion-induced asymmetries in motor behavior contributed to dendritic arborization changes, movements of the forelimb ipsilateral to the lesion were restricted during the period of dendritic overgrowth through the use of one-holed vests. This interfered with the increase in dendritic arborization. In contrast, animals that were allowed to use both forelimbs, or only the forelimb ipsilateral to the lesion, showed the expected increases. When sham-operated rats were forced to use only one forelimb, no significant increases in arborization were found. Therefore, neither a lesion nor asymmetrical limb use alone could account for the dendritic overgrowth--it depended on a lesion-behavior interaction. Furthermore, greater sensorimotor impairments were found when the dendritic growth was blocked, suggesting that the neural growth and/or associated limb-use behavior were related to functional recovery from the cortical damage. Finally, in a second experiment, immobilization of the impaired limb during the pruning period did not prevent the elimination of processes. Thus, the pruning of neural processes was not related simply to the recovery of more symmetrical forelimb use. There may be a period early after brain damage during which marked neural structural changes can occur in the presence of adequate behavioral demand.

Animals↗
PubMed1993

Crystallization and preliminary X-ray studies on the core proteins of cellobiohydrolase I and endoglucanase I from Trichoderma reesei.

The catalytic core domains of cellobiohydrolase I (CBHI) and endoglucanase I (EGI) from Trichoderma reesei have been crystallized using the hanging drop vapour diffusion method. In the case of CBHI, use of polyethylene glycol 20,000, and calcium chloride at low pH produced good quality single crystals suitable for X-ray studies. The crystals belong to a primitive orthorhombic space group with unit cell dimensions a = 84.0 A, b = 86.2 A, c = 111.8 A, and diffract beyond 2.0 A resolution. Bipyramidal crystals of EGI core were grown from ammonium sulphate at pH 7.5. The crystals are tetragonal, either P4(1)22 or the enantiomorph P4(3)22, with cell dimensions a = b = 101.8 A and c = 198.0 A, and at best diffract to a resolution of 2.5 A.

Ammonium Sulfate↗
PubMed1993

Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301.

The structure of an activated quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) from Synechococcus PCC6301 has been solved by molecular replacement. The protein crystallizes in an orthorhombic P2(1)2(1)2(1) unit cell with a complete L(8)S(8) complex consisting of 4608 residues (37 680 non-hydrogen atoms) in the asymmetric unit. Data were collected both on film and image plate using synchrotron radiation; there were 218 276 unique reflections in the final 2.2 A data set. The eightfold non-crystallographic symmetry could be used both to improve map quality and to reduce the computing requirements of refinement. The coordinates were refined using strict non-crystallographic symmetry constraints. The stereochemistry of the final model is good, and the model has an R value of 20.0% for the reflections between 7 and 2.2 A.

Journal Article↗
PubMed1993

Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding protein in complex with all-trans-retinol.

P2 myelin protein (P2) and cellular retinol binding protein (CRBP) are members of a family of cellular lipophilic transport proteins. P2 has been refined at a resolution of 2.7 A, and CRBP has been solved by molecular replacement and refined to a resolution of 2.1 A. The members of this family form a compact three-dimensional structure built up from ten antiparallel strands that fold to form an orthogonal barrel containing the ligand. In P2, the carboxylate group of an oleic acid ligand interacts with the side-chains of two arginine (106 and 126), and one tyrosine (128) residues. The ligand adopts a U-shaped conformation. In CRBP, the all-trans-retinol has a planar conformation with its alcohol group hydrogen bonding to the side-chain of glutamine 108 (equivalent to residue 106 in P2). The local interactions of glutamine 108 explain CRBP's preference for binding retinol rather than retinal. The side-chain of lysine 40 makes a close contact with the isoprene tail of the retinol.

Amino Acid Sequence↗
PubMed1993

The chronic infusion of nicotine into the developing chick embryo does not alter the density of (-)-[3H]nicotine-binding sites or vestibular function.

(-)-Nicotine (1.2 mg/day) or saline was infused into chick embryos (Gallus domesticus) for 10 days beginning 12 h beyond the eight day of incubation (E8 + 12 h). Twelve h beyond the eighteenth day of incubation (E18 + 12 h), the eggs were opened to access the embryos and subcutaneous skull electrodes placed. Short latency vestibular response thresholds and input/output functions were determined to assess neurophysiological consequences of chronic nicotine administration. Samples of serum and extraembryonic (amniotic and albumen) fluid were analyzed by gas chromatography-mass spectrometry to determine the levels of nicotine and its major metabolite, cotinine. The brains were removed and divided into diencephalon and mesencephalon and the density of (-)-[3H]nicotine binding sites in each brain area was measured. Nicotine and cotinine were found in the serum and extraembryonic fluid, but nicotinic receptors were not up-regulated in the brains of animals infused with nicotine in comparison to controls. Vestibular response thresholds also did not differ between nicotine-treated and control animals.

Animals↗
PubMed1993

A long-range restriction map of human chromosome 5q21-q23.

A long-range restriction map encompassing the APC (adenomatous polyposis coli) gene has been constructed. The map includes 35 DNA markers and consists of two segments of 10 and 2.5 Mb. Published genetic markers have been connected using additional, nonpolymorphic DNA probes. The map clarifies marker order and allows comparison of physical and genetic data.

Adenomatous Polyposis Coli↗
PubMed1993

Alpha 2-chimerin, an SH2-containing GTPase-activating protein for the ras-related protein p21rac derived by alternate splicing of the human n-chimerin gene, is selectively expressed in brain regions and testes.

n-Chimerin (alpha 1-chimerin) is a brain GTPase-activating protein (GAP) for the ras-related p21rac. We now report the occurrence of another form of chimerin, termed alpha 2-chimerin. This is the product of an alternately spliced transcript of the human n-chimerin gene encoding an N-terminal SH2 (src homology 2) domain in addition to the phorbol ester receptor and GAP domains. alpha 1- and alpha 2-chimerin mRNAs were expressed differently. In the rat brain, only alpha 1-chimerin mRNA was expressed in cerebellar Purkinje cells, although both alpha 1- and alpha 2-chimerin mRNAs occurred in neurons in the cerebral cortex, hippocampus, and thalamus. Only alpha 2-chimerin RNA was expressed in rat testes, in early pachytene spermatocytes. A 45-kDa SH2-containing chimerin corresponding to the alpha 2 form was purified from rat brain. As with Escherichia coli 45-kDa recombinant alpha 2-chimerin, purified brain alpha 2-chimerin exhibited racGAP activity which was stimulated by phosphatidylserine. The recombinant SH2 domain bound several 32P-labelled phosphoproteins of PC12 cells, whose phosphorylation increased in response to trophic factors, including nerve growth factor. To examine the relationships of alpha 1- and alpha 2-chimerin transcripts, human genomic DNA clones were characterized. In alpha 2-chimerin mRNA, a 3' splice acceptor site within exon 1 of alpha 1-chimerin mRNA was used, replacing its 5' untranslated region and N-terminal coding sequence. The single human n-chimerin gene was mapped to chromosome 2q31-q32.1, colocalizing with the CRE-BP1 transcription factor gene (2q32). It contained several splice junctions conserved with the sequence-related protein kinase C and bcr genes. alpha 2-Chimerin is only the second SH2-containing GAP and the first example of an SH2 domain generated by alternate splicing.

Alternative Splicing↗
PubMed1993

Localization of the genes encoding the catalytic subunits of protein phosphatase 2A to human chromosome bands 5q23-->q31 and 8p12-->p11.2, respectively.

The gene for the alpha isoform of the catalytic subunit of human protein phosphatase 2A (PPP2CA) was localized to chromosome 5 using somatic cell hybrids, and then more finely mapped to chromosome region 5q23-->q31 by in situ hybridization using a tritiated cDNA probe. The gene for the beta isoform of the catalytic subunit of this enzyme (PPP2CB) was mapped by the polymerase chain reaction to human chromosome 8 using somatic cell hybrids. Fluorescence in situ hybridization was then used to localize the PPP2CB gene to 8p12-->p11.2, using a mixture of three genomic probes that ranged from 3.5 to 8 kb in size. Finally, Southern blot analysis of somatic cell hybrid DNA suggested that a PPP2CB catalytic subunit pseudogene (PPP2CBP) is on chromosome 16.

Animals↗