Potential structural motifs for reverse transcriptases.
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Amino Acid Sequence↗
Biomedical subjects
T A Webster
Publications and source records attributed to T A Webster.
Pattern descriptors and the unidentified reading frame 6 human mtDNA dinucleotide-binding site.
In an effort to identify the structural elements essential to a given protein function a new pattern-directed inference system has been developed. It has been employed to identify a potential dinucleotide-binding domain within the human mitochondrial unidentified reading frame 6 product, thereby supporting an earlier study that this gene may encode a NADH dehydrogenase subunit.
Binding Sites↗
Prediction of a common structural domain in aminoacyl-tRNA synthetases through use of a new pattern-directed inference system.
The aminoacyl-tRNA synthetases are united by a common function with little evidence of a common structural relationship. Outside of an 11 amino acid stretch called the "signature sequence", no global primary sequence similarity exists. The signature sequence matches 4-11 amino acids in several aminoacyl-tRNA synthetases. High-resolution X-ray data are available for two of these enzymes, revealing that their signature sequence regions are small segments of a common mononucleotide binding foldlike structure. A new methodology for the analysis of dissimilar primary sequences supports the expectation that all of the signature sequence regions form a common structure. In our analysis, two complex pattern descriptors were constructed to describe the synthetase mononucleotide binding fold. These were compared to primary sequences annotated with predicted secondary structures and hydropathy profiles. Regions in 8 out of 12 (67%) heterologous aminoacyl-tRNA synthetase groups (where each group is specific for the same amino acid) match the first descriptor, and 7 of these (58%) also match the second descriptor. In contrast, only 4 regions in a set of 54 control proteins (7.4%) match the first descriptor, and only 2 regions (3.7%) match both. Alignment of these 8 regions to the descriptor (1) positions all known signature sequence regions as the first loop of a mononucleotide binding foldlike structure, (2) extends the previous alignments by another 40-odd amino acids, and (3) identifies potential sites in 3 out of 6 heterologous aminoacyl-tRNA synthetases with no previous alignments. Potential sites are also proposed for two additional heterologous synthetases on the basis of matches to less specific descriptors.
Amino Acid Sequence↗
Evidence for dispensable sequences inserted into a nucleotide fold.
Previous experimental results along with the structural modeling presented indicate that a nucleotide fold starts in the amino-terminal part of Escherichia coli isoleucyl-transfer RNA synthetase, a single chain polypeptide of 939 amino acids. Internal deletions were created in the region of the nucleotide fold. A set of deletions that collectively span 145 contiguous amino acids yielded active enzymes. Further extensions of the deletions yielded inactive or unstable proteins. The three-dimensional structure of an evidently homologous protein suggests that the active deletions lack portions of a segment that connects two parts of the nucleotide fold. Therefore, the results imply that removal of major sections of the polypeptide that connects these two parts of the fold does not result in major perturbation of the nucleotide binding site.
Amino Acid Sequence↗
Now that we have pulse oximeters and capnographs, we don't need precordial and esophageal stethoscopes.
One clinician argues that precordial and esophageal stethoscopes are obsolete. Current technology, including pulse oximetry, electrocardiography, and capnography, is both easier to use and more accurate. Another clinician argues that these stethoscopes have an important place in safe patient management. They are an inexpensive but effective extension of the anesthesiologist's own senses.
Carbon Dioxide↗
Polyethylene glycol-induced heteroassociation of malate dehydrogenase and citrate synthase.
Studies by dynamic and total intensity light scattering, ultracentrifugation, electron microscopy, and chemical crosslinking on solutions of the pig heart mitochondrial enzymes, malate dehydrogenase and citrate synthase (separately and together) demonstrate that polyethylene glycol induces very large homoassociations of each enzyme, and still larger heteroenzyme complexes between these two enzymes in the solution phase. Specificity of this heteroassociation is indicated by the facts that heteroassociations with bovine serum albumin were not observed for either the mitochondrial dehydrogenase or the synthase or between cytosolic malate dehydrogenase and citrate synthase. The weight fraction of the enzymes in the mitochondrial dehydrogenase-synthase associated particles in the solution phase was less than 0.03% with the dilute conditions used in the dynamic light scattering measurements. Neither palmitoyl-CoA nor other solution conditions tested significantly increased this weight fraction of associated enzymes in the solution phase. Because of the extremely low solubility of the associated species, however, the majority of the enzymes can be precipitated as the heteroenzyme complex. This precipitation is a classical first-order transition in spite of the large particle sizes and broad size distribution. Ionic effects on the solubility of the heteroenzyme complex appear to be of general electrostatic nature. Polyethylene glycol was found to be more potent in precipitating this complex than dextrans, polyvinylpyrrolidones, ficoll, and beta-lactoglobulin.
Animals↗
Consensus topography in the ATP binding site of the simian virus 40 and polyomavirus large tumor antigens.
The location and sequence composition of a consensus element of the nucleotide binding site in both simian virus 40 (SV40) and polyomavirus (PyV) large tumor antigens (T antigens) can be predicted with the assistance of a computer-based pattern-matching system, ARIADNE. The latter was used to optimally align elements of T antigen primary sequence and predicted secondary structure with a "descriptor" for a mononucleotide binding fold. Additional consensus elements of the nucleotide binding site in these two proteins were derived from comparisons of T antigen primary and predicted secondary structures with x-ray structures of the nucleotide binding sites in four otherwise unrelated proteins. Each of these elements was predicted to be encompassed within a 110-residue segment that is highly conserved between the two T antigens residues 418-528 in SV40 T antigen and residues 565-675 in PyV). Results of biochemical and immunologic experiments on the nucleotide binding behavior of these proteins were found to be consistent with these predictions. Taken together, the latter have resulted in a topological model of the ATP binding site in these two oncogene products.
Adenosine Triphosphate↗