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M E Baker

Publications and source records attributed to M E Baker.

At least 55 records · Page 3Linked to original sources
PubMed1997

Steroid receptor phylogeny and vertebrate origins.

Vertebrates appear about 500 million years ago in the fossil record. This is only 25-50 million years after the great explosion of multicellular invertebrate body plans in the early Cambrian. On a geological time scale, this interval is a 'blink of an eye', suggesting that the evolution of regulatory genes is likely to be important in the origins of vertebrates. Here we present evidence for a role of steroid receptors in this process based on a phylogenetic analysis suggesting that receptors for androgens, glucocorticoids, mineralocorticoids, and progesterone evolved from an ancestral steroid receptor gene by two successive duplications over a brief time that could have coincided with the origins of vertebrates. Moreover, the duplications of these steroid receptors may be additional evidence for the two duplications on a genome-scale that have been proposed to be important in the evolution of vertebrates. The two successive duplications of steroid receptor genes and their subsequent sequence divergence leading to steroid-specific receptors that regulate growth, development, reproduction and homeostasis in vertebrates may have been one of the events important in vertebrate survival after the Cambrian during global extinctions that occurred about 440 and 370 million years ago.

Animals↗
PubMed1997

Physiological "constants" for PBPK models for pregnancy.

Physiologically based pharmacokinetic (PBPK) models for pregnancy are inherently more complex than conventional PBPK models due to the growth of the maternal and embryo/fetal tissues. Physiological parameters such as compartmental volumes or flow rates are relatively constant at any particular time during gestation when an acute experiment might be conducted, but vary greatly throughout the course of gestation (e.g., contrast relative fetal weight during the first month of gestation with the ninth month). Maternal physiological parameters change during gestation, depending upon the particular system; for example, cardiac output increases by approximately 50% during human gestation; plasma protein concentration decreases during pregnancy; overall metabolism remains fairly constant. Maternal compartmental volumes may change by 10-30%; embryo/fetal volume increases over a billionfold from conception to birth. Data describing these physiological changes in the human are available from the literature. Human embryo/fetal growth can be well described using the Gompertz equation. By contrast, very little of these same types of data is available for the laboratory animal. In the rodent there is a dearth of information during organogenesis as to embryo weights, and even less organ or tissue weight or volume data during embryonic or fetal periods. Allometric modeling offers a reasonable choice to extrapolate (approximately) from humans to animals; validation, however, is confined to comparisons with limited data during the late embryonic and fetal periods of development (after gestation d 11 in the rat and mouse). Embryonic weight measurements are limited by the small size of the embryo and the current state of technology. However, the application of the laser scanning confocal microscope (LSCM) to optically section intact embryos offers the capability of precise structural measurements and computer-generated three-dimensional reconstruction of early embryos. Application of these PBPK models of pregnancy in laboratory animal models at teratogenically sensitive periods of development provides exposure values at specific target tissues. These exposures provide fundamentally important data to help design and interpret molecular probe investigations into mechanisms of teratogenesis.

Animals↗
PubMed1997

MLN64 contains a domain with homology to the steroidogenic acute regulatory protein (StAR) that stimulates steroidogenesis.

MLN64 is a protein that is highly expressed in certain breast carcinomas. The C terminus of MLN64 shares significant homology with the steroidogenic acute regulatory protein (StAR), which plays a key role in steroid hormone biosynthesis by enhancing the intramitochondrial translocation of cholesterol to the cholesterol side-chain cleavage enzyme. We tested the ability of MLN64 to stimulate steroidogenesis by using COS-1 cells cotransfected with plasmids expressing the human cholesterol side-chain cleavage enzyme system and wild-type and mutant MLN64 proteins. Wild-type MLN64 increased pregnenolone secretion in this system 2-fold. The steroidogenic activity of MLN64 was found to reside in the C terminus of the protein, because constructs from which the C-terminal StAR homology domain was deleted had no steroidogenic activity. In contrast, removal of N-terminal sequences increased MLN64's steroidogenesis-enhancing activity. MLN64 mRNA was found in many human tissues, including the placenta and brain, which synthesize steroid hormones but do not express StAR. Western blot analysis revealed the presence of lower molecular weight immunoreactive MLN64 species that contain the C-terminal sequences in human tissues. Homologs of both MLN64 and StAR were identified in Caenorhabditis elegans, indicating that the two proteins are ancient. Mutations that inactivate StAR were correlated with amino acid residues that are identical or similar among StAR and MLN64, indicating that conserved motifs are important for steroidogenic activity. We conclude that MLN64 stimulates steroidogenesis by virtue of its homology to StAR.

Amino Acid Sequence↗
PubMed1997

Hidden Markov model analysis of motifs in steroid dehydrogenases and their homologs.

The increasing size of protein sequence databases is straining methods of sequence analysis, even as the increased information offers opportunities for sophisticated analyses of protein structure, function, and evolution. Here we describe a method that uses artificial intelligence-based algorithms to build models of families of protein sequences. These models can be used to search protein sequence databases for remote homologs. The MEME (Multiple Expectation-maximization for Motif Elicitation) software package identifies motif patterns in a protein family, and these motifs are combined into a hidden Markvov model (HMM) for use as a database searching tool. Meta-MEME is sensitive and accurate, as well as automated and unbiased, making it suitable for the analysis of large datasets. We demonstrate Meta-MEME on a family of dehydrogenases that includes mammalian 11 beta-hydroxysteroid and 17 beta-hydroxysteroid dehydrogenase and their homologs in the short chain alcohol dehydrogenase family. We chose this dataset because it is large and phylogenetically diverse, providing a good test of the sensitivity and selectivity of Meta-MEME on a protein family of biological interest. Indeed, Meta-MEME identifies at least 350 members of this family in Genpept96 and clearly separates these sequences from non-homologous proteins. We also show how the MEME motif output can be used for phylogenetic analysis.

Algorithms↗
PubMed1997

An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases.

MEME (Multiple Expectation-maximization for Motif Elicitation) is a unique new software tool that uses artificial intelligence techniques to discover motifs shared by a set of protein sequences in a fully automated manner. This paper is the first detailed study of the use of MEME to analyse a large, biologically relevant set of sequences, and to evaluate the sensitivity and accuracy of MEME in identifying structurally important motifs. For this purpose, we chose the short-chain alcohol dehydrogenase superfamily because it is large and phylogenetically diverse, providing a test of how well MEME can work on sequences with low amino acid similarity. Moreover, this dataset contains enzymes of biological importance, and because several enzymes have known X-ray crystallographic structures, we can test the usefulness of MEME for structural analysis. The first six motifs from MEME map onto structurally important alpha-helices and beta-strands on Streptomyces hydrogenans 20beta-hydroxysteroid dehydrogenase. We also describe MAST (Motif Alignment Search Tool), which conveniently uses output from MEME for searching databases such as SWISS-PROT and Genpept. MAST provides statistical measures that permit a rigorous evaluation of the significance of database searches with individual motifs or groups of motifs. A database search of Genpept90 by MAST with the log-odds matrix of the first six motifs obtained from MEME yields a bimodal output, demonstrating the selectivity of MAST. We show for the first time, using primary sequence analysis, that bacterial sugar epimerases are homologs of short-chain dehydrogenases. MEME and MAST will be increasingly useful as genome sequencing provides large datasets of phylogenetically divergent sequences of biomedical interest.

Alcohol Dehydrogenase↗
PubMed1997

Meta-MEME: motif-based hidden Markov models of protein families.

MOTIVATION: Modeling families of related biological sequences using Hidden Markov models (HMMs), although increasingly widespread, faces at least one major problem: because of the complexity of these mathematical models, they require a relatively large training set in order to accurately recognize a given family. For families in which there are few known sequences, a standard linear HMM contains too many parameters to be trained adequately. RESULTS: This work attempts to solve that problem by generating smaller HMMs which precisely model only the conserved regions of the family. These HMMs are constructed from motif models generated by the EM algorithm using the MEME software. Because motif-based HMMs have relatively few parameters, they can be trained using smaller data sets. Studies of short chain alcohol dehydrogenases and 4Fe-4S ferredoxins support the claim that motif-based HMMs exhibit increased sensitivity and selectivity in database searches, especially when training sets contain few sequences.

Alcohol Dehydrogenase↗
PubMed1997

Spiral noncontrast CT versus combined plain radiography and renal US after extracorporeal shock wave lithotripsy: cost-identification analysis.

PURPOSE: To investigate the costs of spiral computed tomography (CT) versus those of combined plain radiography and renal ultrasound (US) in screening for postprocedural complications after extracorporeal shock wave lithotripsy (ESWL). MATERIALS AND METHODS: Twenty-five adult patients who had undergone ESWL were prospectively examined with spiral CT, renal US, and plain abdominal radiography. Each examination was timed, and direct technical costs were calculated by using a procedural-based cost-accounting system. The combined cost of US and plain radiography was compared with the cost of spiral CT. RESULTS: The average time for spiral CT was 15.3 minutes compared with 37.2 minutes for combined US and plain radiography. The direct technical cost of spiral CT was $36.86 compared with $57.60 for combined US and plain radiography. Average examination times were varied to assess the effect on overall costs. Within reasonable time ranges, combined US and plain radiography cannot be cost equivalent to spiral CT. CONCLUSION: Spiral CT is faster and is associated with less direct technical cost than combined US and plain radiography when used to examine patients after ESWL, given the dependence of this model on time of examination. Further studies are needed to assess the relative accuracy of these alternative approaches.

Adult↗
PubMed1997

Timed barium swallow: a simple technique for evaluating esophageal emptying in patients with achalasia.

OBJECTIVE: Our purpose was to define a simple technique for timing a barium swallow by which radiologists can assess esophageal emptying in patients with achalasia before and after minimally invasive therapy. Our purpose was also to determine the best method of quantifying the degree of emptying using this timed technique. MATERIALS AND METHODS: In the barium swallow technique, upright frontal spot films of the esophagus are obtained at 1, 2, and 5 min after ingestion of 100-200 ml of low-density (45% weight in volume) barium sulfate (volume of barium determined by patient tolerance). Forty-two of these barium swallows done by 23 patients with achalasia were retrospectively reviewed. The examination served either as a baseline study or as a 1-month follow-up study after patients had undergone pneumatic dilatation or Clostridium botulinum toxin injection. The spot films were digitized, and a region of interest was drawn around the column of barium by two observers. The change in area seen in the region of interest on the 1- and 5-min films served as the gold standard for percentage of emptying. The spot films were then analyzed by four other observers, each of whom independently, subjectively, and qualitatively estimated the percentage of emptying between the 1- and 5-min spot films. Percentages were divided into quintiles. On a separate occasion, each of these four observers also independently measured the height and width of the barium column on the 1- and 5-min spot films. The product of height times width seen on the 1- and 5-min films became the quantitative estimate for percentage of emptying. RESULTS: We found no statistically significant difference between the percentage of emptying as measured on the digitized images by the two observers and the height-times-width calculations or qualitative emptying percentage as estimated by the four observers. Interobserver agreement for the area evaluated on the digitized films as well as the height-times-width measurements and qualitative estimates of emptying was almost perfect (the correlation coefficients being 0.99, 0.87, and 0.93, respectively). CONCLUSION: The timed barium swallow is a simple and reproducible technique. Both qualitative assessment and estimated change in area based on height-times-width measurements of the barium column are accurate methods of estimating esophageal emptying.

Adolescent↗
PubMed1996

Structures important in NAD(P)(H) specificity for mammalian retinol and 11-Cis-retinol dehydrogenases.

Mammalian retinol and 11-cis retinol dehydrogenases catalyze the formation of retinaldehyde from retinol and 11-cis retinaldehyde from 11-cis retinol, respectively. Although their amino acid sequences are 54% identical, these enzymes have different cofactor specificities: rat retinol dehydrogenase uses NADP+, while cow 11-cis retinol dehydrogenase uses NAD+. We used their close sequence similarity and the availability of 3D structures of their homologs to construct a 3D model of the two retinol dehydrogenases to investigate the determinants for cofactor specificity. The structure of rat retinol dehydrogenase shows that lysine-64 is important in stabilizing binding of 2'-phosphate on NADP+ in two ways: lysine's positively charged side chain has a coulombic attraction to the 2'-phosphate and partially compensates for the negative charge of aspartic acid-38. Cow 11-cis retinol dehydrogenase has threonine-61 at the position homologous to lysine-64. Threonine-61 does not have a stabilizing coulombic interaction with NADP+, nor can threonine-61 counteract the repulsive interaction between NADP+ and aspartic acid-37 in 11-cis retinol dehydrogenase. This suggests that aspartic acid-37 and threonine-61 are important in the specificity of 11-cis retinol dehydrogenase for NAD+.

Alcohol Oxidoreductases↗
PubMed1996

Unusual evolution of 11beta- and 17beta-hydroxysteroid and retinol dehydrogenases.

11beta-hydroxysteroid dehydrogenases regulate glucocorticoid concentrations and 17beta-hydroxysteroid dehydrogenases regulate estrogen and androgen concentrations in mammals. Phylogenetic analysis of the sequences from two 11beta-hydroxysteroid dehydrogenases and four mammalian 17beta-hydroxysteroid dehydrogenases indicates unusual evolution in these enzymes. Type 1 11beta- and 17beta-hydroxysteroid dehydrogenases are on the same branch; Type 2 enzymes cluster on another branch with beta-hydroxybutyrate dehydrogenase,11-cis-retinol dehydrogenase and retinol dehydrogenase; Type 3 17beta-hydroxysteroid dehydrogenase is on a third branch; while the pig dehydrogenase clusters with a yeast multifunctional enzyme on a fourth branch. Pig 17beta-hydroxysteroid dehydrogenase appears to have evolved independently from the other three 17beta-hydroxysteroid dehydrogenases; in which case, the evolution of 17beta-hydroxysteroid dehydrogenase activity is an example of functional convergence. The phylogeny also suggests that independent evolution of specificity toward C11 substituents on glucocorticoids and C17 substituents on androgens and estrogens has occurred in Types 1 and 2 11beta- and 17beta-hydroxysteroid dehydrogenases.

11-beta-Hydroxysteroid Dehydrogenases↗
PubMed1996

Regeneration of a transplanted liver after right hepatic lobectomy.

Liver regeneration has been described after heterotopic liver transplantation, small-for-size orthotopic liver transplantation and reduced-size liver transplantation. In this report, we document the regenerative response of a whole liver transplant to major resection for the first time. A right hepatic lobectomy for liver ischemia was performed in a 30-year-old female after transplantation for autoimmune disease of the liver. Volumetric analysis of computed tomography (CT) scans revealed a preoperative liver volume of 1,961 mL, whereas analysis of the 6-week posthepatectomy CT scan showed a volume of 1,820 mL. Factors influencing regeneration in the setting of a liver transplant include rejection, ischemia/thrombosis, infection, or cyclosporine hepatotrophic/hepatotoxic effects. These factors, balanced with the intrinsic ability of hepatocytes to achieve a standard liver volume, determine the extent of regeneration.

Adult↗
PubMed1995

Structures stabilizing the dimer interface on human 11 beta-hydroxysteroid dehydrogenase types 1 and 2 and human 15-hydroxyprostaglandin dehydrogenase and their homologs.

Human 11 beta-hydroxysteroid dehydrogenase-types 1 and 2 and human 15-hydroxyprostaglandin dehydrogenase belong to a large family of oxidoreductases that includes human dihydropteridine reductase and Streptomyces hydrogenans 20 beta-hydroxysteroid dehydrogenase, for which 3D structures are available. Almost all of these enzymes are either dimers or tetramers. The dimer interface of rat dihydropteridine reductase consists of alpha-helices E and F from each monomer arranged in a four alpha-helix bundle [Varughese et al. (1992) Proc. Natl. Acad. Sci. USA 89, 6080-6084]. Alpha-helix F contains tyrosine-146 and lysine-150, residues that are highly conserved in this protein superfamily and have been proposed to be at the catalytic site. We have examined the dimer interface between alpha-helix F in human and rat dihydropteridine reductase and Streptomyces hydrogenans 20 beta-hydroxysteroid dehydrogenase as well as modeled 3D structures of steroid and prostaglandin dehydrogenases and homologs for stabilizing interactions. We find a site in the middle of alpha-helix F that stabilizes the dimer. This anchor is adjacent to conserved lysine on alpha-helix F. Our analysis suggests that sequence variation in the anchor may be important in substrate specificity.

11-beta-Hydroxysteroid Dehydrogenases↗
PubMed1995

Licorice-derived compounds inhibit linoleic acid (C:18:2 omega 6) desaturation in soybean chloroplasts.

Although glycyrrhizic acid, a major constituent of licorice root, has important pharmacological effects in humans, the biological activity of glycyrrhizic acid and its aglycone glycyrrhetinic acid in plants is unknown. Here we report that these licorice-derived compounds and the analog carbenoxolone inhibit desaturation of linoleic acid (C18:2 omega 6) in soybean chloroplasts using monogalactosyldiacylglycerol and phosphatidylcholine substrates in an in vitro assay for desaturase activity. At 10 nM glycyrrhetinic acid, there is significant inhibition of desaturation of linoleic acid suggesting that licorice-derived compounds could prove useful in investigating biochemical pathways of linoleic acid desaturation in plant chloroplasts and plant desaturase regulation, which has application in modification of plant response to environmental stress, as well as optimization of oil seed composition.

Carbohydrate Sequence↗
PubMed1995

Amino acids important in enzyme activity and dimer stability for Drosophila alcohol dehydrogenase.

We have determined the nucleotide sequences of eight ethyl methanesulphonate-induced mutants in Drosophila alcohol dehydrogenase (ADH), of which six were previously characterized by Hollocher and Place [(1988) Genetics 116, 253-263 and 265-274]. Four of these ADH mutants contain a single amino acid change: glycine-17 to arginine, glycine-93 to glutamic acid, alanine-159 to threonine, and glycine-184 to aspartic acid. Although these mutants are inactive, three mutants (Gly17Arg, Gly93Glu and Gly184Asp) form stable homodimers, as well as heterodimers with wild-type ADH, in which the wild-type ADH subunit retains full enzyme activity [Hollocher and Place (1988) Genetics 116, 265-274]. Interestingly, the Ala159Thr mutant does not form either stable homodimers or heterodimers with wild-type ADH, suggesting that alanine-159 is important in stabilizing ADH dimers. The mutations were analysed in terms of a three-dimensional model of ADH using bacterial 20 beta-hydroxysteroid dehydrogenase and rat dihydropteridine reductase as templates. The model indicates that mutations in glycine-17 and glycine-93 affect the binding of NAD+. It also shows that alanine-159 is part of a hydrophobic anchor on the dimer interface of ADH. Replacement of alanine-159 with threonine, which has a larger side chain and can hydrogen bond with water, is likely to reduce the strength of the hydrophobic interaction. The three-dimensional model shows that glycine-184 is close to the substrate binding site. Replacement of glycine-184 with aspartic acid is likely to alter the position of threonine-186, which we propose hydrogen bonds to the carboxamide moiety of NAD+. Also, the negative charge on the aspartic acid side chain may interact with the substrate and/or residues in the substrate binding site. These mutations provide information about ADH catalysis and the stability of dimers, which may also be useful in understanding homologous dehydrogenases, which include the human 17 beta-hydroxysteroid, 11 beta-hydroxysteroid and 15-hydroxyprostaglandin dehydrogenases.

Alcohol Dehydrogenase↗
PubMed1995

Structures important in mammalian 11 beta- and 17 beta-hydroxysteroid dehydrogenases.

We have used the X-ray crystallographic structures of rat and human dihydropteridine reductase and Streptomyces hydrogenans 20 beta-hydroxysteroid dehydrogenase to model parts of the 3-dimensional structure of human 11 beta- and 17 beta-hydroxysteroid dehydrogenases. We use this information along with previous results from studies of Drosophila alcohol dehydrogenase mutants to analyze the structures in binding sites for NAD(H) and NADP(H) in 11 beta-hydroxysteroid dehydrogenase-types 1 and 2. We also examine the structure of an alpha-helix at catalytic site of 17 beta-hydroxysteroid dehydrogenase-types 1, 2, 3, and 4. This alpha-helix contains a highly conserved tyrosine and lysine. Adjacent to the carboxyl side of this lysine is a site proposed to be important in subunit association. We find that 11 beta- and 17 beta-hydroxysteroid dehydrogenases-type 1 have the same residues at the "anchor site" and conserve other stabilizing features, despite only 20% sequence identity between their entire sequences. Similar conservation of stabilizing structures is found in the 11 beta- and 17 beta-hydroxysteroid dehydrogenases-type 2. We suggest that interactions of the dimerization surface of alpha-helix F with proteins or membranes may be important in regulating activity of hydroxysteroid dehydrogenases.

11-beta-Hydroxysteroid Dehydrogenases↗