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A E Howard

Publications and source records attributed to A E Howard.

7 recordsLinked to original sources
PubMed1998

The object technology framework: an object-oriented interface to molecular data and its application to collagen.

We describe the Object Technology Framework (OTF) software system developed at the University of California, San Francisco Computer Graphics Laboratory for creating C+2 classes that facilitate rapid biomolecular application development and the application of the OTF to collagen modeling. C+2 class libraries for accessing and manipulating data from standard scientific data sources can be generated using the program genlib and its class library toolkit Molecule, thereby facilitating development of new applications. Use of the OTF for generating ideal collagen structural models (gencollagen) is described. The source code for the OTF is freely available at http:/(/)www.cgl.ucsf.edu/off/ to interested application developers.

Collagen↗
PubMed1996

Phytanic acid activation in rat liver peroxisomes is catalyzed by long-chain acyl-CoA synthetase.

In Refsum disease, disorders of peroxisome biogenesis, and rhizomelic chondrodysplasia punctata, pathological accumulation of phytanic acid results from impaired alpha-oxidation of this branched-chain fatty acid. Previous studies from this laboratory indicated that activation of phytanic acid to its CoA derivative precedes its alpha-oxidation in peroxisomes. It was reported that this reaction is catalyzed by a unique phytanoyl-CoA synthetase in human peroxisomes. We wanted to determine whether phytanic acid activation in rats required long-chain acyl-CoA synthetase (LCS), very long-chain acyl-CoA synthetase (VLCS), or a different enzyme. To test directly whether LCS could activate phytanic acid, rat liver cDNA encoding this enzyme was transcribed and translated in vitro. The expressed enzyme had both LCS activity (assayed with palmitic acid, C16: 0) and phytanoyl-CoA synthetase activity; VLCS activity (assayed with lignoceric acid, C24: 0) was not detectable. The ratio of phytanoyl-CoA synthetized activity to palmitoyl-CoA synthetase activity for LCS synthetized in vitro (approximately 205) was higher than that observed in peroxisomes isolated from rat liver (5-10%), suggesting that the expressed enzyme contained sufficient phytanoyl-Coa synthetase activity to account for all activity observed in intact peroxisomes. Further experiments were carried out to verify that phytanic acid was activated by LCS in rat liver peroxisomes. Attempts to separate LCS from phytanoyl-CoA synthetase by chromatography on several matrices were unsuccessful. Preparative isoelectric focusing revealed that phytanoyl-CoA synthetase and LCS had indistinguishable isoelectric points. Phytanoyl-CoA synthetase activity was inhibited by unlabeled palmitic acid but not by lignoceric acid. Heat treatment inactivated both phytanoyl-CoA and palmitoyl-CoA synthetase activities at similar rates. 5,8,11,14-Eicosatetraynoic acid inhibited activation of phytanic acid and palmitic acid in a parallel dose-dependent manner, whereas activation of lignoceric acid was not affected. These data support our conclusion that rat liver LCS, an enzyme known to be present in peroxisomal membranes, has phytanoyl-CoA synthetase activity.

5,8,11,14-Eicosatetraynoic Acid↗
PubMed1994

Phytanic acid must be activated to phytanoyl-CoA prior to its alpha-oxidation in rat liver peroxisomes.

alpha-Oxidation of the branched-chain fatty acid, phytanic acid, is defective in patients with Refsum's disease, the disorders of peroxisome biogenesis (e.g., Zellweger syndrome), and in rhizomelic chondrodysplasia punctata. 3H-Release from [2,3-3H]phytanic acid, which is impaired in cultured skin fibroblasts from these patients, was investigated in rat liver peroxisomes. Cofactors necessary for optimal 3H-release, ATP, Mg2+, and coenzyme A, were also necessary for optimal acyl-CoA synthetase activity, suggesting that the substrate for 3H-release might be phytanoyl-CoA. 5,8,11,14-Eicosatetraynoic acid (ETYA), an inhibitor of long-chain acyl-CoA synthetase activity, blocked phytanoyl-CoA synthesis as well as 3H-release from [2,3-3H]phytanic acid in a dose-dependent manner. However, this inhibitor had little effect on 3H-release from [2,3-3H]phytanoyl-CoA. Tetradecylglycidic acid (TDGA) inhibited 3H-release from [2,3-3H]phytanic acid in peroxisomal but not in mitochondrial fractions from rat liver. This agent inhibited 3H-release from [2,3-3H]phytanic acid and [2,3-3H]phytanoyl-CoA equally. In contrast to ETYA, which appeared to decrease 3H-release as a consequence of synthetase inhibition, TDGA appeared to act directly on the enzyme catalyzing 3H-release. This enzyme was partially purified from rat liver. The purified enzyme, which did not possess phytanoyl-CoA synthetase activity, catalyzed tritium release from [2,3-3H]phytanoyl-CoA. This enzyme catalyzed 3H-release from [2,3-3H]phytanic acid only if a source of phytanoyl-CoA synthetase was present. We conclude that in rat liver peroxisomes, phytanic acid must be activated to its coenzyme A derivative prior to subsequent alpha-oxidation.

5,8,11,14-Eicosatetraynoic Acid↗
PubMed1992

Molecular dynamics studies of a DNA-binding protein: 1. A comparison of the trp repressor and trp aporepressor aqueous simulations.

The results of two 30-ps molecular dynamics simulations of the trp repressor and trp aporepressor proteins are presented in this paper. The simulations were obtained using the AMBER molecular mechanical force field and in both simulations a 6-A shell of TIP3P waters surrounded the proteins. The trp repressor protein is a DNA-binding regulatory protein and it utilizes a helix-turn-helix (D helix-turn-E helix) motif to interact with DNA. The trp aporepressor, lacking two molecules of the L-tryptophan corepressor, cannot bind specifically to DNA. Our simulations show that the N- and C-termini and the residues in and near the helix-turn-helix motifs are the most mobile regions of the proteins, in agreement with the X-ray crystallographic studies. Our simulations also find increased mobility of the residues in the turn-D helix-turn regions of the proteins. We find the average distance separating the DNA-binding motifs to be larger in the repressor as compared to the aporepressor. In addition to examining the protein residue fluctuations and deviations with respect to X-ray structures, we have also focused on backbone dihedral angles and corepressor hydrogen-bonding patterns in this paper.

Amino Acid Sequence↗