Biomedical subjects

M C Yee

Publications and source records attributed to M C Yee.

12 recordsLinked to original sources

PubMed2001

The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan.

The crystal structure of anthranilate synthase (AS) from Serratia marcescens, a mesophilic bacterium, has been solved in the presence of its substrates, chorismate and glutamine, and one product, glutamate, at 1.95 A, and with its bound feedback inhibitor, tryptophan, at 2.4 A. In comparison with the AS structure from the hyperthermophile Sulfolobus solfataricus, the S. marcescens structure shows similar subunit structures but a markedly different oligomeric organization. One crystal form of the S. marcescens enzyme displays a bound pyruvate as well as a putative anthranilate (the nitrogen group is ambiguous) in the TrpE subunit. It also confirms the presence of a covalently bound glutamyl thioester intermediate in the TrpG subunit. The tryptophan-bound form reveals that the inhibitor binds at a site distinct from that of the substrate, chorismate. Bound tryptophan appears to prevent chorismate binding by a demonstrable conformational effect, and the structure reveals how occupancy of only one of the two feedback inhibition sites can immobilize the catalytic activity of both TrpE subunits. The presence of effectors in the structure provides a view of the locations of some of the amino acid residues in the active sites. Our findings are discussed in terms of the previously described AS structure of S. solfataricus, mutational data obtained from enteric bacteria, and the enzyme's mechanism of action.

Amino Acid Sequence↗

PubMed2000

Improving the catalytic activity of a thermophilic enzyme at low temperatures.

Enzymes from thermophilic organisms often are barely active at low temperatures. To obtain a better understanding of this sluggishness, we used DNA shuffling to mutagenize the trpC gene, which encodes indoleglycerol phosphate synthase, from the hyperthermophile Sulfolobus solfataricus. Mutants producing more active protein variants were selected by genetic complementation of an Escherichia coli mutant bearing a trpC deletion. Single amino acid changes and combinations of these changes improved growth appreciably. Five singly and doubly altered protein variants with changes at the N- and C-termini, or at the phosphate binding site, were purified and characterized with regard to their kinetics of enzymatic catalysis, product binding, cleavage by trypsin, and inactivation by heat. Turnover numbers of the purified variant proteins correlated with the corresponding growth rates, showing that the turnover number was the selected trait. Although the affinities for both the substrate and the product decreased appreciably in most protein variants, these defects were offset by the accumulation of high levels of the enzyme's substrate. Rapid mixing of the product indoleglycerol phosphate with the parental enzyme revealed that the enzyme's turnover number at low temperatures is limited by the dissociation of the enzyme-product complex. In contrast, representative protein variants bind and release the product far more rapidly, shifting the bottleneck to the preceding chemical step. The turnover number of the parental enzyme increases with temperature, suggesting that its structural rigidity is responsible for its poor catalytic activity at low temperatures. In support of this interpretation, the rate of trypsinolysis or of thermal denaturation is accelerated significantly in the activated protein variants.

Amino Acid Sequence↗

PubMed1996

On the role of helix 0 of the tryptophan synthetase alpha chain of Escherichia coli.

The role of helix 0 of the alpha chain (TrpA) of the tryptophan synthetase alpha2beta2 multi-functional enzyme complex of Escherichia coli was examined by deleting amino-terminal residues 2-6, 2-11, or 2-19 of TrpA. Selected substitutions were also introduced at TrpA positions 2-6. The altered genes encoding these polypeptides were overexpressed from a foreign promoter on a multicopy plasmid and following insertion at their normal chromosomal location. Each deletion polypeptide was functional in vivo. However all appeared to be somewhat more labile and insoluble and less active enzymatically than wild type TrpA. The deletion polypeptides were overproduced and solubilized from cell debris by denaturation and refolding. Several were partially purified and assayed in various reactions in the presence of tryptophan synthetase beta2 (TrpB). The purified TrpADelta2-6 and TrpADelta2-11 deletion polypeptides had low activity in both the indole + serine --> tryptophan reaction and the indoleglycerol phosphate + serine --> tryptophan reaction. Poor activity in each reaction was partly due to reduced association of TrpA with TrpB. The addition of the TrpA ligands, alpha-glycerophosphate or indoleglycerol phosphate, during catalysis of the indole + serine --> tryptophan reaction increased association and activity. These findings suggest that removal of helix 0 of TrpA decreases TrpA-TrpB association as well as the activity of the TrpA active site. Alignment of the TrpA sequences from different species indicates that several lack part or all of helix 0. In some of these polypeptides, extra residues at the carboxyl end may substitute for helix 0.

Amino Acid Sequence↗

PubMed1993

Partial revertants of tryptophan synthetase alpha chain active site mutant Asp60-->Asn.

Residue Asp60 of the tryptophan synthetase alpha chain of Escherichia coli is though to interact with the pyrrole NH of substrate indole-3-glycerol phosphate and facilitate its cleavage to indole and glyceraldehyde 3-phosphate. Two distinguishable partial revertants of DN60 tryptophan synthetase alpha mutant trpA34 were analyzed. The slower growing partial revertant, PR1, had the second-site change, YD102. The other partial revertant, PR2, lacked three consecutive base pairs, resulting in replacement of Ala59 and Asn60 of the DN60 mutant alpha polypeptide by Asp. Inspection of the three-dimensional structure of the enzyme-substrate analog complex revealed that Tyr102 is in the vicinity of the pyrrole NH of the substrate. The PR1 alpha chain has a near normal Km for substrate, whereas the PR2 polypeptide has greatly reduced substrate affinity. The PR2 polypeptide is more active than the PR1 polypeptide in the alpha beta reaction in vitro and appears to be more active than the PR1 polypeptide in vivo. Attempts to obtain repeat occurrences of the PR2 deletion mutation were unsuccessful. A third type of trpA34 partial revertant, PR3, that grows very poorly in minimal medium, also has a Tyr102 replacement: YF102. These findings demonstrate that each of the second-site mutations affects a residue located in the vicinity of the active site residue altered by the primary mutation. Slightly leaky mutant trpA89, genetically altered near the site of the trpA34 mutation, was found to have a GS61 substitution.

Amino Acid Sequence↗

PubMed1993

Generation of phosphatidic acid during calcium-loading of human erythrocytes. Evidence for a phosphatidylcholine-hydrolyzing phospholipase D.

We have studied the mechanism by which calcium-loading of human erythrocytes stimulates phospholipid turnover and generates diacylglycerol and phosphatidic acid. Using quantitative measurement of individual phospholipid classes, we have demonstrated that the amount of phosphatidic acid generated during calcium-loading of intact red cells exceeds the amount of diacylglycerol formed by phospholipase-C-mediated hydrolysis of the polyphosphoinositol lipids and that addition of the diacylglycerol kinase inhibitor, R59022, only partly inhibited this increase. Thus, in contrast to current explanations, the phosphatidic acid generated following calcium-loading of erythrocytes cannot be solely explained by the action of a polyphosphoinositol-lipid-specific phospholipase C with subsequent phosphorylation of diacylglycerol to phosphatidic acid. Our data demonstrate that calcium-loading of intact erythrocytes, but not of red cell ghost membranes, causes a small but significant decrease in the relative amount of phosphatidylcholine (PtdCho). In order to identify the mechanisms responsible for calcium-mediated hydrolysis of PtdCho, we encapsulated Ptd[Me-14C]Cho-containing rat liver microsomes into erythrocytes and studied the generation of [Me-14C]choline and phospho[Me-14C]choline. We found that choline was the only detectable 14C-labeled product. Furthermore, incubation of erythrocytes with calcium under hypotonic conditions and in the presence of [14C]PtdCho vesicles and ethanol resulted in the formation of [14C]phosphatidylethanol. Together, these results suggest that the loss of PtdCho during calcium-loading of human erythrocytes is caused by a previously unrecognized PtdCho-hydrolyzing phospholipase D, resulting in direct generation of phosphatidic acid. Analysis of the molecular species composition of PtdCho, phosphatidic acid, and diradylglycerol, confirm the simultaneous actions of PtdCho-hydrolyzing and polyphosphoinositol-lipid-hydrolyzing phospholipases in calcium-loaded human erythrocytes.

Adult↗

PubMed1993

Molecular species analysis of phospholipids from Trypanosoma brucei bloodstream and procyclic forms.

We present a quantitative description of the molecular species composition of the major phospholipid classes in bloodstream and procyclic forms of Trypanosoma brucei. Phospholipid classes were resolved by 2-dimensional thin-layer chromatography. Diradylglycerols were released from individual phospholipid classes by phospholipases C, converted into benzoate derivatives and separated into diacyl, alkylacyl and alk-1-enylacyl subclasses. Individual molecular species were quantitated and identified by HPLC and the assignments were confirmed by mass spectrometry. Comparison of the diacyl species of PC, PE and PI in bloodstream trypanosomes showed major differences in the relative amounts of individual molecular species between the different classes but not striking changes in the degree of saturation or overall chain length. In contrast, in procyclic trypanosomes the relative amounts of diacyl molecular species with polyunsaturated fatty acyl chains decreased in the order of PC > PE >> PI. Also, the alkylacyl and alk-1-enylacyl subclasses of PC and PE in bloodstream trypanosomes comprised a single molecular species, 18:0 18:2. Such exclusivity was not observed in procyclic trypanosomes among the same phospholipid subclasses, although 18:0 18:2 was the predominant species. Almost all the PI of bloodstream forms contained one 18:0 acyl species, which is consistent with the composition of the PI used for glycosylphosphatidylinositol synthesis.

Acetylglucosamine↗

PubMed1993

Simultaneous measurement of heart rate and body motion to quantitate physical activity.

None of the various methods used to measure habitual physical activity over days, weeks, or years in the general population have yet proven entirely satisfactory. A major problem is that no "gold standard" exists for the validation of various questionnaires, logs, or diaries that can be used in large sample population studies. Attempts have been made to accurately measure the activity profile by using heart rate or various motion sensors or accelerometers, but each approach has had significant limitations. The availability of new solid state recording techniques and computer-based analytic and display procedures now makes it possible to simultaneously record heart rate and body movement continuously for days and to combine the analysis of these data using customized software. Preliminary evaluation of this concept of simultaneous recording and analysis of heart rate and body motion via movement sensors on an arm and leg were conducted in 19 men. Subjects performed a variety of exercises in the laboratory during which heart rate, leg motion, arm motion, and oxygen uptake were recorded. Various issues regarding the prediction of energy expenditure from heart rate and body movement independently and in combination were evaluated. The results demonstrate that the accuracy of estimating oxygen uptake during a wide range of activities is improved when individualized heart rate--oxygen uptake regressions are used and heart rate and body movement are analyzed simultaneously rather that separately.

Adult↗

PubMed1991

Characterization of the complement sensitivity of calcium loaded human erythrocytes.

A deficiency of membrane proteins having a glycosylphosphatidylinositol (GPI) anchor is characteristic of the erythrocytes of paroxysmal nocturnal hemoglobinuria (PNH) and is currently believed to be the basis for the enhanced susceptibility to lysis by activated complement observed in these cells. Our recent observation that GPI-anchored proteins are preferentially lost into membrane vesicles shed from normal erythrocytes after calcium loading led us to examine the hypothesis that the remnant erythrocytes might also have increased sensitivity to complement-mediated hemolysis. Indeed, red blood cells treated in such a manner became more sensitive to lysis by antibody and complement or to lysis initiated by activated cobra venom factor complexes (CoFBb). As a consequence of membrane vesiculation, the erythrocytes lost up to approximately 50% of their immunoreactive decay-accelerating factor and 25% to 30% of their immunoreactive membrane inhibitor of reactive lysis (MIRL). Closer examination of the defect responsible for the marked increase in sensitivity to CoFBb-initiated hemolysis seen in calcium-loaded erythrocytes showed that a complex combination of factors produced the defect. These included a decrease in both functional and immunoreactive MIRL and depletion of intracellular potassium and adenosine triphosphate (ATP). These results suggest the possibility that loss of DAF and MIRL via membrane vesiculation, as well as decreases in intracellular potassium and/or ATP, might contribute to the phenotype of PNH erythrocytes. Further, normal or pathologic red blood cells might develop a PNH-like defect after membrane vesiculation if sufficient decreases in potassium and ATP also occurred.

Adenosine Triphosphate↗

PubMed1989

Effects of 3-(3,4-Dichlorophenyl)-1,1-Dimethylurea on the Cell Cycle in Euglena gracilis.

The cell cycle of the photosynthetic unicellular alga Euglena gracilis growing in phototrophic medium is regulated by light. To investigate the relationship of this cell cycle response to light stimulated photosynthesis, we have tested the effect of the photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) on Euglena cell cycle transit. While DCMU does not block light stimulated cells from entering the S phase of the cell cycle, it does inhibit the transit through G(2)/M. The specificity of this response and its relationship to photosynthesis was studied by looking at the effect of DCMU on dark grown wild-type cells, and on two bleached variants of Euglena (W(3)BUL and W(10)BSmL) that lack chloroplasts. The drug does block G(2)/M in these cells, but not entrance into the cell cycle. Our studies show that entrance of cells into the cell cycle from a quiescent state does not require active photosynthesis, and that DCMU has effects on G(2)/M transit that are independent of the photosynthetic capacity of the cells.

Journal Article↗

PubMed1988

Light regulation of the cell cycle in Euglena gracilis bacillaris.

We have studied the light regulation of the cell division cycle in the photosynthetic alga Euglena gracilis bacillaris. Euglena grown under phototrophic conditions are easily synchronized to a 12 h light-12 h dark regime. By inoculating stationary phase, nondividing cells into fresh media and exposing the diluted cells to either light or darkness, we have determined that initiation of DNA synthesis for the cell division cycle is light dependent. By varying the length of time in light to which synchronized cells are exposed, we have shown that commitment to the cell cycle requires exposure to more than 6 h of light. We propose that this is to allow the accumulation, through photosynthetic electron transport, of an initiating factor that will enable DNA synthesis to begin. Flow cytometry analysis also shows that once cells are committed to the cell cycle, they complete the cycle in the dark, so mitosis is a light-independent step.

Animals↗

PubMed1986

Red cell vesiculation--a common membrane physiologic event.

Loss of red blood cell membrane material in the form of microvesicles has been noted in sickle cells, in Ca++-loaded and adenosine triphosphate (ATP)-depleted normal red blood cells; and during storage of normal red blood cells. To further understand the vesiculation process, we have studied vesicles generated by a variety of perturbations of the red blood cell membrane. Vesicles were isolated by centrifugation at 30,000 X g from plasma of heparinized pathologic blood samples (sickle cell anemia, hemoglobin H disease, hereditary spherocytosis, hereditary elliptocytosis, and protein 4.1 deficiency) incubated overnight at 4 degrees C. Vesicle formation also was induced in normal erythrocytes by ATP depletion, by heating to 49 degrees C, by incubation at pH 5.4, and by incubation in 5 mmol/L diamide. Membrane protein composition was characterized on denaturing polyacrylamide gels and by immunoblot. The vesicles all contained band 3, glycophorin A, and band 4.1. Spectrin was depleted in all vesicles. Thiol disulfide exchange chromatography revealed evidence of oxidative cross-linking of spectrin in pathologic and normal red blood cells that had undergone vesiculation. This suggests that the mechanism of vesiculation may be related to cross-linking of membrane proteins. Membrane phospholipid composition of sickle cell and acid-induced vesicles was similar to that of normal red cells as determined by thin-layer chromatography. Possible pathophysiologic effects of vesiculation were assessed by using a modified Russell's viper venom assay. All vesicles examined shortened Russell's viper venom clotting time by 55% to 70% of control values. In addition, ektacytometer studies reveal that cells remaining after acid-induced vesiculation are rigid. These observations indicate that the vesicles may play a role in the hypercoagulation seen in some hemolytic disorders and that the process of vesiculation itself may contribute to increased rigidity of red cells and their subsequent removal from the circulation.

Chromatography↗

PubMedDate not supplied

Xenopus ATR is a replication-dependent chromatin-binding protein required for the DNA replication checkpoint.

BACKGROUND: The DNA replication checkpoint ensures that mitosis is not initiated before DNA synthesis is completed. Recent studies using Xenopus extracts have demonstrated that activation of the replication checkpoint and phosphorylation of the Chk1 kinase are dependent on RNA primer synthesis by DNA polymerase alpha, and it has been suggested that the ATR kinase-so-called because it is related to the product of the gene that is mutated in ataxia telangiectasia (ATM) and to Rad3 kinase-may be an upstream component of this response. It has been difficult to test this hypothesis as an ATR-deficient system suitable for biochemical studies has not been available. RESULTS: We have cloned the Xenopus laevis homolog of ATR (XATR) and studied the function of the protein in Xenopus egg extracts. Using a chromatin-binding assay, we found that ATR associates with chromatin after initiation of replication, dissociates from chromatin upon completion of replication, and accumulates in the presence of aphidicolin, an inhibitor of DNA replication. Its association with chromatin was inhibited by treatment with actinomycin D, an inhibitor of RNA primase. There was an early rise in the activity of Cdc2-cyclin B in egg extracts depleted of ATR both in the presence or absence of aphidicolin. In addition, the premature mitosis observed upon depletion of ATR was accompanied by the loss of Chk1 phosphorylation. CONCLUSIONS: ATR is a replication-dependent chromatin-binding protein, and its association with chromatin is dependent on RNA synthesis by DNA polymerase alpha. Depletion of ATR leads to premature mitosis in the presence and absence of aphidicolin, indicating that ATR is required for the DNA replication checkpoint.

Amino Acid Sequence↗