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D C Rees

Publications and source records attributed to D C Rees.

At least 163 records · Page 9Linked to original sources
PubMed1984

Effects of pH on the structure and function of carboxypeptidase A: crystallographic studies.

High-resolution crystal structures are described for carboxypeptidase A (EC 3.4.17.1) in crystals grown at pH 8.5, 9.0, and 9.5 and compared with the structure at pH 7.5. The comparison shows that in the pH range of 7.5-9.5 the enzyme structure is practically unchanged, and, most importantly, that the flexible side chain of Tyr-248 remains exclusively in the "up" position, away from the Zn atom, throughout the pH range. There is no evidence for binding of Tyr-248 to Zn at any of these pH values. We conclude that the interaction of Tyr-248 with Zn is not an essential part of the mechanism of carboxypeptidase A and that its occurrence is an artifact of chemical modification of Tyr-248. It is also suggested that Tyr-248 is not uniquely associated with the observed high pK of the enzymatic hydrolysis.

Animals↗
PubMed1983

Crystallization of the Azotobacter vinelandii nitrogenase iron protein.

The iron protein from Azotobacter vinelandii nitrogenase has been crystallized in the reduced form. The needle-shaped crystals are in space group P2(1)2(1)2 (a = 94.6 A, b = 179.9 A, c = 74.1 A) and diffract to at least 3.5-A resolution. Five or six Fe-protein monomers are present in the asymmetric unit.

Azotobacter↗
PubMed1983

Refined crystal structure of carboxypeptidase A at 1.54 A resolution.

The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981). The crystallographic R factor (formula; see text) for structure factors calculated from the final model is 0.190. Bond lengths and bond angles in the carboxypeptidase A model have root-mean-square deviations from ideal values of 0.025 A and 3.6 degrees, respectively. Four examples of a reverse turn like structure (the "Asx" turn) requiring an aspartic acid or asparagine residue are observed in this structure. The Asx turn has the same number of atoms as a reverse turn, but only one peptide bond, and the hydrogen bond that closes the turn is between the Asx side-chain CO group and a main-chain NH group. The distributions of CO-N and NH-O hydrogen bond angles in the alpha-helices and beta-sheet structures of carboxypeptidase A are centered about 156 degrees. A total of 192 water molecules per molecule of enzyme are included in the final model. Unlike the hydrogen bonding geometry observed in the secondary structure of the enzyme, the CO-O(wat) hydrogen bond angle is distributed about 131 degrees, indicating the role of the lone pair electrons of the carbonyl oxygen in the hydrogen bond interaction. Twenty four solvent molecules are observed buried within the protein. Several of these waters are organized into hydrogen-bonded chains containing up to five waters. The average temperature factor for atoms in carboxypeptidase A is 8 A2, and varies from 5 A2 in the center of the protein, to over 30 A2 at the surface.

Amino Acid Sequence↗
PubMed1983

Behavioral effects of toluene are modulated by stimulus control.

Behavior that is strongly controlled by environmental stimuli is less susceptible to disruption by certain chemicals than is such behavior not under strong external control. To determine whether toluene's effects can also be minimized by environmental stimuli, two varieties of a fixed consecutive number schedule were studied. With one, a lever press response was reinforced with milk only if preceded by a minimum of eight consecutive responses on a second lever, no cues indicating that the minimum number had been reached. With the other, a combination of lights and a tone served as a discriminative stimulus signaling the completion of the minimum response number. In an experiment studying these schedules separately, rats were exposed to toluene concentrations up to 3000 ppm for 4-hr periods immediately before their performance was tested. Toluene reduced the accuracy of both types of behavior in a concentration-related fashion. Clear differential effects occurred, with the signaled behavior, i.e., that under stronger stimulus control, showing less disruption by toluene. Similar results were produced after 2-hr exposures with a multiple schedule in which the signaled and unsignaled performances alternated within a single session. Response rate changes were observed at 560 ppm, but changes in rate were independent of effects on the accuracy of performance. The EC50 for significant behavior disruption was 1081 ppm for the unsignaled component of the multiple schedule; the EC10 was 480 ppm. No performance disruption was observed in the signaled component below 1780 ppm. The finding of differential sensitivity could be useful in guiding the development of more sensitive tests of performance impairment.

Animals↗
PubMed1983

Crystallographic studies on apocarboxypeptidase A and the complex with glycyl-L-tyrosine.

The crystal structures of zinc-free carboxypeptidase A (apocarboxypeptidase A) and the complex of glycyl-L-tyrosine with apocarboxypeptidase A are described and compared to the corresponding structures of the zinc-containing enzyme. Only small conformational changes in the zinc ligands accompany removal of the metal. Interactions between the tyrosine residue of glycyl-L-tyrosine and apocarboxypeptidase A are similar to those observed in the complex with the holoenzyme. However, in the absence of zinc, the carbonyl oxygen of the glycyl moiety now receives a hydrogen bond from the side chain of arginine-127. Although not as yet observed, a similar shift of the carbonyl oxygen of a susceptible bond from the zinc to arginine-127 could stabilize tetrahedral intermediates generated during the hydrolysis of substrates by carboxypeptidase.

Apoenzymes↗
PubMed1981

Stimulus control and the effects of d-amphetamine in the rat.

External discriminative stimuli can modify the behavioral effects of d-amphetamine. Previous work with the pigeon has demonstrated that some aspects of performance on the fixed consecutive number schedule are changed less if a discriminative stimulus indicates when reinforcement is available. This effect has now been replicated with the rat using both simple and multiple schedules. Moderate doses of d-amphetamine (0.56--1.0 mg/kg) usually produced large decreases in reinforced runs when no external cue indicated the possibility of reinforcement. Adding discriminative stimuli when the number requirement was met decreased the drug effect. As was true in the pigeon, response rate measures did not differ between the two stimulus control conditions. Thus, external stimulus control diminishes the drug effect in both species, despite the fact that key pecking was studied in the pigeon and lever pressing in the rat. Evidence was also seen of a possible increase in discriminative stimulus control by d-amphetamine.

Animals↗
PubMed1981

Zinc environment and cis peptide bonds in carboxypeptidase A at 1.75-A resolution.

The structure of the metalloenzyme carboxypeptidase A (peptidyl-L-amino-acid hydrolase, EC 3.4.17.1) has been refined at 1.75 A by a restrained least-squares procedure to a conventional crystallographic R factor of 0.162. Significant results of the refined structure relative to the catalytic mechanism are described. In the native enzyme, the zinc coordination number is five (two imidazole N delta 1 nitrogens, the two carboxylate oxygens of glutamate-72, and a water molecule). In the complex (at 2.0-A resolution) of carboxypeptidase A with the dipeptide glycyl-L-tyrosine, however, the water ligand is replaced by both the carbonyl oxygen and the amino nitrogen of the dipeptide. The amino nitrogen also statistically occupies a second position near glutamate-270. Consequently, the coordination number of zinc may vary from five to six in carboxypeptidase A-substrate complexes. Implications of these results for the catalytic mechanism of carboxypeptidase A are discussed. In addition, three cis peptide bonds, none of which involves proline as the amino nitrogen donor, have been located fairly near the active site.

Animals↗
PubMed1981

Binding of ligands to the active site of carboxypeptidase A.

We compare the detailed binding modes of the 39-amino acid inhibitor from potatoes, glycyl-L-tyrosine, the ester analogue CH3OC6H4(CO)CH2CH(CO2(-))C6H5, and indole acetate to the exopeptidase carboxypeptidase A (EC 3.4.17.1). In the potato inhibitor, cleavage of the COOH-terminal glycine-39 leaves a new carboxylate anion of valine-38 having one oxygen on zinc and the other as a receptor of a hydrogen bond from tyrosine-248 of carboxypeptidase. Tyrosine-248 also receives a hydrogen bond from the amide proton of the originally penultimate peptide bond between tyrosine-37 and valine-38. This hydrogen bond suggests product stabilization which is available to peptides and depsipeptides but not to esters lacking an equivalent peptide bond (nonspecific esters). Also, this structure may represent the intermediate binding step for the uncleaved substrate as it moves along the binding subsites. In particular, this may be the binding mode for the substrate after association of the COOH-terminal region of the substrate with the residues at binding subsite S2 (tyrosine-198, phenylalanine-279, and arginine-71) and preceding entry into the catalytic site S1'. These stabilized complexes allow some understanding of the effect of indole acetate, shown here to bind in the pocket at S1', as a competitive inhibitor for esters (for which entry into S1' precedes the rate-determining catalytic step for hydrolysis) and as a noncompetitive inhibitor for peptides (for which entry into S1' is rate limiting). These results, including the binding mode of the ester analogue, are consistent with the original proposal from x-ray studies that both esters and peptides are cleaved with the carboxy terminus at S1', although not necessarily by the same chemical steps.

Binding Sites↗
PubMed1980

Structure of potato inhibitor complex of carboxypeptidase A at 5.5-A resolution.

The complex of the 39-amino inhibitor (potato) of bovine carboxypeptidase A (carboxypeptidase; peptidyl-L-amino-acid hydrolase, EC 3.4.12.2) was crystallized in space group P32. There are two protein-inhibitor complexes in the asymmetric unit. These crystals exhibited pseudo-P3221 symmetry due to twinning about the a3 axis. Heavy atom difference Patterson maps and rotation functions indicated, however, that the noncrystallographic twofold axis that relates these two complexes is nearly coincident with the a3 axis. Consequently, to a good approximation at low resolution, the space group of the complex is P3221 and the effects of twinning may be ignored. The structure was solved by using multiple isomorphous replacement and molecular replacement techniques. At 5.5-A resolution, the multiple isomorphous replacement map was readily interpretable in terms of the known native carboxypeptidase A structure plus extra density around the active site. The position of this extra density is consistent with the binding mode for extended substrate proposed from earlier model building studies with the native enzyme (Lipscomb, W.N., Hartsuck, J.A., Reeke, G.N., Quiocho, F.A. Bethge, P.H., Ludwig, M.L., Steitz, T.A., Muirhead, H. & Coppola, J.C. (1968) Brookhaven Symp. Biol. 21, 24-90).

Animals↗
PubMed1980

Structure of an actively exchanging complex between carboxypeptidase A and a substrate analogue.

An x-ray diffraction study at 2.8 A resolution has yielded the structure of a complex between bovine carboxypeptidase A (peptidyl-L-amino-acid hydrolase, EC 3.4.17.1) and (-)-2-benzyl-3-p-methoxybenzoylpropionic acid. This substrate is an analogue of N-(p-methoxy)-benzoylphenylalanine, in which the amide NH is replaced by CN2. T. Sugimoto and E T. Kaiser (1979) J. Am. Chem. Soc. 101, 39469--3951] have shown that this complex catalyzes stereospecific exchange of that proton of the CH2 group which is in the R configuration. Our structure of this complex suports the model proposed by Sugimoto and Kaiser and is very similar to the productive peptide binding mode suggested by Lipscomb et al. [Lipscomb, W. N., Hartsuck, J. A., Reeke, G. N., Quiocho, F. A., Bethge, P. A., Ludwig, M. L., Steitz, T. A., Muirhead, H. & Coppola. J. C. (1968) Brookhaven Symp. Biol. 21, 24--90]. The proposed roles of glutamic acid 270 in the proton exchange and the interaction of zinc with the carbonyl group of the substrate are consistent with the observed structure.

Animals↗
PubMed1980

Structure of the potato inhibitor complex of carboxypeptidase A at 2.5-A resolution.

The structure of the complex between the proteolytic enzyme carboxypeptidase A (peptidyl-L-amino-acid hydrolase, EC 3.4.17.1) and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution. A combination of multiple isomorphous replacement, molecular replacement, and noncrystallographic symmetry averaging techniques was used to solve the structure. The chain trace of the inhibitor and details of the binding interactions in the complex are described. A surprising aspect of the complex is that the carboxy-terminal peptide bond of the inhibitor has been hydrolyzed, and the carboxy-terminal glycine is trapped in the binding pocket of carboxypeptidase A. Consequently, the complex resembles a stage in the catalytic mechanism after hydrolysis of the peptide bond. The ring of tyrosine-248, which is known to undergo large conformational changes upon substrate binding, is in the "down" position and interacts with the inhibitor in the complex.

Binding Sites↗
PubMed1976

Linear structure of the oligosaccharide chains in alpha1-protease inhibitor isolated from human plasma.

Two glycopeptides present in equal amounts were isolated from a pronase digest of alpha1-protease inhibitor of human plasma by gel filtration on Sephadex G-50 and chromatography on DEAE-cellulose. The carbohydrate side chains in both glycopeptides are linked through asparaginyl residues. The glycopeptides were digested sequentially with specific glycosidases; and after each step, the released sugars as well as the composition of the residual peptides were determined. The linear structures of these glycopeptides deduced from these data are shown below. Based on the total carbohydrate content of the intact protein and with these structural data, it is postulated that 4 oligosaccharide units are attached to 1 molecule of the protein; 2 of these were represented as in Equation 1, the other 2 as in Equation 2.

Acetylglucosamine↗
PubMed1975

Generation of adenosine triphosphate in cytochrome-deficient mutants of Neurospora.

The fungus Neurospora crassa is known to possess a branched respiratory system consisting of the standard cytochrome chain and a cyanide-insensitive alternate oxidase. In the present experiments, the physiological function of the alternate oxidase has been analyzed by taking advantage of a number of cytochrome-deficient mutants, particularly poky f. Respiration, cellular ATP levels, and growth have been examined under the influence of three classes of inhibitors: inhibitors of the cytochrome chain (antimycin, cyanide), an inhibitor of the laternate oxidase (salicyl hydroxamic acid), and an uncoupling agent (carbonyl cyanide m-chlorophenylhydrazone). The results indicate that the over-all efficiency of the alternate oxidase in producing ATP and supporting growth is much less than that of the cytochrome chain. Depending upon the amount of oxidative phosphorylation at Sites II and III in the cytochrome chain, which varies from strain to strain, the efficiency of the alternate oxidase relative to that of the cytochrome chain ranges from 13% in wild type Neurospora to 18 to 21% in poky f, 35% in mi-3, and 57% in cyt-2. A comparison of the short term effects of cyanide and carbonyl cyanide m-chlorophenylhydrazone on cellular ATP in poky f suggests that, during respiration through the alternate oxidase, ATP can be produced both by substrate-level phosphorylation (accompanying glycolysis and the oxidation of alpha-ketoglutarate) and by oxidative phosphorylation at Site I. When cells are grown on sucrose, as much as 22% of ATP synthesis in the presence of cyanide occurs at Site I. When cells are grown on acetate to diminish the rate of glycolysis, the contribution of Site I becomes proportionately larger. Both the growth experiments and the short term inhibitor experiments reveal that ATP levels in Neurospora are kept high be a feedback process which depresses ATP breakdown (and growth) very quckly after ATP synthesis is inhibited. Thus, poky f grows more slowly that wild type Neurospora and is inhibited still further when either the cytochrome chain or the alternate oxidase is blocked. Under all of these conditions, however, cellular ATP in poky f is maintained at a high level (about 3 mmol per kg of cell water, slightly above the values measured in the wild type strain). Continue.

Acetates↗
PubMedDate not supplied

Effects of intraperitoneal carbon monoxide on fixed-ratio and screen-test performance in the mouse.

The behavioral effects of carbon monoxide (CO) administered via IP injection were investigated in the mouse. Mice were trained to lever press under a fixed-ratio (FR) 100 schedule of water reinforcement. Thirty-min test sessions were conducted either immediately or 30 min following IP injections of air (100 ml/kg) or CO (7.5, 15, 30, 50 or 100 ml/kg). CO produced a decrease in rates of responding which was exhibited earlier and lasted longer with increasing doses. Motor performance was also measured with the inverted-screen test following the same doses of CO at either 5, 15, 30, 60, 120 min or 24 hr post-injection. Performance was affected in a dose- and time-dependent fashion. Peak carboxyhemoglobin (COHb) levels were observed at 15 or 30 min and were 20%, 32%, 42%, 51% and 60% for 7.5, 15, 30, 50 and 100 ml/kg CO, respectively. COHb saturation alone was not always a good predictor of behavioral effects since both level and duration of exposure contributed to behavioral impairment. The results also show that the IP route can be used to study the toxicity of CO.

Animals↗