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Biomedical subjects

J B Cooper

Publications and source records attributed to J B Cooper.

At least 19 recordsLinked to original sources
PubMed1992

Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.

The three-domain structure of porphobilinogen deaminase, a key enzyme in the biosynthetic pathway of tetrapyrroles, has been defined by X-ray analysis at 1.9 A resolution. Two of the domains structurally resemble the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins. The X-ray structure and results from site-directed mutagenesis provide evidence for a single catalytic site. Interdomain flexibility may aid elongation of the polypyrrole product in the active-site cleft of the enzyme.

Binding Sites↗
PubMed1992

X-ray analyses of peptide-inhibitor complexes define the structural basis of specificity for human and mouse renins.

X-ray analyses have defined the three-dimensional structures of crystals of mouse and human renins complexed with peptide inhibitors at resolutions of 1.9 and 2.8 A, respectively. The exquisite specificity of renin arises partly from ordered loop regions at the periphery of the binding cleft. Although the pattern of main-chain hydrogen bonding in other aspartic proteinase inhibitor complexes is conserved in renins, differences in the positions of secondary structure elements (particularly helices) also lead to improved specificity in renins for angiotensinogen substrates.

Amino Acid Sequence↗
PubMed1992

Crystallization and preliminary X-ray investigation of Escherichia coli porphobilinogen deaminase.

Porphobilinogen deaminase, the polymerase that catalyses the synthesis of preuroporphyrinogen, the linear tetrapyrrole precursor of uroporphyrinogen III, has been crystallized from sodium acetate buffer with polyethylene glycol 6000 as precipitant. The crystals are orthorhombic and the space group is P2(1)2(1)2, with unit cell dimensions a = 88.01 A, b = 75.86 A, c = 50.53 A and alpha = beta = gamma = 90 degrees, indicating a single molecule of 34 kDa in the asymmetric unit. The crystals grow to dimensions of 1 mm x 2 mm x 0.5 mm within two weeks in the dark and are stable in the X-ray beam for at least 40 hours. Diffraction data beyond 1.7 A resolution, observed with a synchrotron radiation source, indicate that a high resolution structure analysis is feasible.

Crystallization↗
PubMed1992

Crystallization and preliminary X-ray analysis of complexes of peptide inhibitors with human recombinant and mouse submandibular renins.

Inhibitor-complexed crystals of mouse and human renins suitable for X-ray analysis have been prepared. The mouse renin is complexed with a non-hydrolysable decapeptide analogue of rat angiotensinogen containing a hydroxyethylene isostere in place of the scissile bond. The crystals are monoclinic, space group P2(1) with cell dimensions a = 78.3 A, b = 117.8 A, c = 85.9 A, beta = 101.18 degrees containing four molecules per asymmetric unit. The human renin is fully glycosylated and complexed with a tetrapeptide containing norstatine. The complex crystallises in the cubic space group P2(1)3 with a = 143.1 A and has two molecules in the asymmetric unit. The rotation function of the mouse renin complex indicates pseudo 222 symmetry while that of human renin indicates a pseudo 2-fold axis. Full structural analyses of the two complexes are underway.

Amino Acid Sequence↗
PubMed1992

Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases.

We report the X-ray analysis at 2.0 A resolution for crystals of the aspartic proteinase endothiapepsin (EC 3.4.23.6) complexed with a potent difluorostatone-containing tripeptide renin inhibitor (CP-81,282). The scissile bond surrogate, an electrophilic ketone, is hydrated in the complex. The pro-(R) (statine-like) hydroxyl of the tetrahedral carbonyl hydrate is hydrogen-bonded to both active-site aspartates 32 and 215 in the position occupied by a water in the native enzyme. The second hydroxyl oxygen of the hydrate is hydrogen-bonded only to the outer oxygen of Asp 32. These experimental data provide a basis for a model of the tetrahedral intermediate in aspartic proteinase-mediated cleavage of the amide bond. This indicates a mechanism in which Asp 32 is the proton donor and Asp 215 carboxylate polarizes a bound water for nucleophilic attack. The mechanism involves a carboxylate (Asp 32) that is stabilized by extensive hydrogen bonding, rather than an oxyanion derivative of the peptide as in serine proteinase catalysis.

Amino Acid Sequence↗
PubMed1992

Domain flexibility in aspartic proteinases.

Comparison of the three-dimensional structures of native endothiapepsin (EC 3.4.23.6) and 15 endothiapepsin oligopeptide inhibitor complexes defined at high resolution by X-ray crystallography shows that endothiapepsin exists in two forms differing in the relative orientation of a domain comprising residues 190-302. There are relatively few interactions between the two parts of the enzyme; consequently, they can move as separate rigid bodies. A translational, librational, and screw analysis of the thermal parameters of endothiapepsin also supports a model in which the two parts can move relative to each other. In the comparison of different aspartic proteinases, the rms values are reduced by up to 47% when the two parts of the structure are superposed independently. This justifies description of the differences, including those between pepsinogen and pepsin (EC 3.4.34.1), as a rigid movement of one part relative to another although considerable distortions within the domains also occur. The consequence of the rigid body movement is a change in the shape of the active site cleft that is largest around the S3 pocket. This is associated with a different position and conformation of the inhibitors that are bound to the two endothiapepsin forms. The relevance of these observations to a model of the hydrolysis by aspartic proteinases is briefly discussed.

Aspartic Acid Endopeptidases↗
PubMed1992

Effect of pulse oximetry, age, and ASA physical status on the frequency of patients admitted unexpectedly to a postoperative intensive care unit and the severity of their anesthesia-related complications.

Unanticipated intensive care unit admission (UIA) associated with anesthesia served as an outcome measure to assess the quality of anesthesia care in a large teaching hospital. We characterized the patient population and types of problems associated with UIAs, attempted to identify patterns of care that could have led to specific adverse outcomes, and determined if a specific intervention, pulse oximetry, reduced UIAs. During a consecutive 65-wk period (July 1985-September 1986), 17,093 surgical patients were expected to enter the recovery room and then return to floor care. Seventy-one patients (0.42%) experienced a UIA from either the recovery room or operating room, and the circumstances of their admissions were analyzed in detail. After introduction of pulse oximetry in all anesthetizing locations (not including the recovery room) in the 29th week, the overall rate of UIAs and, specifically, the rate of UIA to rule out myocardial infarction, decreased significantly. Increasing ASA physical status (ASA-PS) and age significantly increased the probability of UIA. UIA patients with ASA-PS III/IV had a significantly higher acuity in the intensive care unit and were far more likely to die during their hospitalization than ASA-PS I/II patients. Retrospective review of UIAs alone did not identify patterns of care requiring remediation, which leads us to question the utility of UIAs as a generic screen for quality assurance.

Adult↗
PubMed1992

Effects of forage and protein source on feedlot performance and carcass traits of Holstein and crossbred beef steers.

Fifty-eight Holstein and 58 crossbred beef steers were individually fed one of four isonitrogenous diets to evaluate the effects of forage source (corn silage and alfalfa haylage) and protein source (soybean meal and fish meal) on feedlot performance. Phase 1 diets (up to 354 kg of BW) were 40% forage and 60% concentrates and were fed for 70 to 136 d (depending on diet and breed group). Phase 2 diets (354 kg of BW until slaughter) were 20% forage and 80% concentrates and were fed for 127 to 150 d (depending on diet and breed group). Slaughter end points were .6 cm of 12th rib fat for Holsteins and 1.0 cm of rib fat for crossbreds using real-time ultrasonic estimates. The steers were fed for a maximum of 330 d each year. Forage source was a significant component of variation for most growth, efficiency, and carcass traits. Holstein and crossbred steers fed alfalfa haylage had significantly lower average daily gain, feed efficiency, dressing percentage, and empty body fat and required more days on feed to reach slaughter end points, but had higher total feed energy intake available for production. Steers fed corn silage diets had significantly greater energetic efficiency (P less than .05) than those fed alfalfa haylage, due to increased use of ME to produce fat in the carcass. Protein type did not influence gain, feed or energetic efficiency, energy intake, or most carcass traits. A significant protein system x forage source interaction among the four diets was detected for crossbred steers fed corn silage and fish meal, for which there was significantly greater feed conversion with lower energy intake above maintenance, possibly due to better fiber digestion and(or) amino acid flow to the lower tract. Alfalfa haylage plus soybean meal diets decreased (P less than .05) the percentage of Holsteins grading USDA Choice or higher. These results indicate that corn silage, because of greater energy concentration, was a more desirable forage in feedlot diets composed of less than or equal to 40% forage and that protein type (soybean meal and fish meal) in growing diets is not an important factor in feedlot performance or carcass traits of Holstein or crossbred steers that are fed these diets.

Animal Feed↗
PubMed1992

Predicting body weight and wither height in Holstein heifers using body measurements.

Relationships between body weight, wither height, and various other body traits, including heart girth, body length, and hip width, were studied using data from six experiments with 2625 observations. Body weight and wither height were regressed on the other body traits. Regressions of body weight including the linear, quadratic, and cubic effects of a single independent variable (heart girth, wither height, hip width or body length) indicated that each measurement would be useful in predicting body weight (R2 > .95); the regression of body weight on heart girth had the highest R2, followed by hip width. Similarly, regressions of wither height on heart girth, wither height, hip width, or body length, including linear, quadratic, and cubic effects, yielded R2 > .99. Regressions considering multiple traits as independent variables showed that the addition of a second body trait added little to the already high multiple correlations found with a single variable. In management situations for which body weight or wither height cannot be measured, various other traits can be used to estimate these body measurements accurately.

Animals↗
PubMed1992

Multidisciplinary cycles for protein engineering: site-directed mutagenesis and X-ray structural studies of aspartic proteinases.

The specificity and pH profile of aspartic proteinases have evolved to include not only pepsin with a broad specificity and an optimal activity in acid media, but also renin, with high specificity for angiotensinogen and activity close to neutral pH. Comparisons of the structures and catalytic activities of aspartic proteinases provide helpful clues for engineering new activity profiles. We illustrate an approach that involves recombinant DNA techniques, biochemistry, structure determination and biocomputing. We use the 3-D structures of inhibitor complexes of several aspartic proteinases to define likely intermediates and specificity sub-sites. The multidisciplinary research is organised as cycles, in which each cycle tests a design hypothesis proposed in the previous cycle. We use one member of the aspartic proteinase family, chymosin, to illustrate these ideas in engineering enzymes with altered pH optima and specificities.

Amino Acid Sequence↗
PubMed1991

Evaluation of feed conversion in steers from a diallel of Simmental, Limousin, Polled Hereford, and Brahman beef cattle.

A total of 269 steers produced in a four-breed diallel mating design of Simmental, Limousin, Polled Hereford, and Brahman breeds were evaluated for the unadjusted and maintenance-adjusted total feed intake to total weight gain ratio. Time on feed ranged from 184 to 251 d. Covariate adjustments were made separately for age- and 12th rib fat-constant end points. Purebred, general combining ability, and maternal effects and heterosis were estimated. Effects of year, breed of dam, slaughter group, and days on feed accounted for most of the variation in feed conversion. Significantly higher unadjusted cumulative feed/gain ratios were found for steers from Brahman sires and for those from Simmental, Limousin, and Brahman dams. Adjustment to either fat- or age-constant values did not rerank breed groups, but a small reduction in the differences between these groups was detected for fat-constant efficiency. For maintenance-adjusted feed intake, progeny of Simmental and Limousin dams were less efficient than those of Polled Hereford and Brahman dams. Negative values for general combining ability, maternal effects, and heterosis would indicate less feed required per unit of weight gain. General combining ability for Polled Hereford crosses was negative and significant for cumulative feed/gain ratios, but no difference among dam breeds was found for the maintenance-adjusted ratio. Maternal effects for Limousin dams were positive and significant for all maintenance-adjusted ratios. Heterosis estimates for specific breed crosses were generally negative and ranged from -.87 to .22.

Animals↗
PubMed1990

X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution.

The aspartic proteinase, endothiapepsin (EC 3.4.23.6), was complexed with a highly potent renin inhibitor, H-261 (t-Boc-His-Pro-Phe-His-LeuOHVal-Ile-His), where OH denotes a hydroxyethylene (-(S) CHOH-CH2-) transition-state isostere in the scissile bond surrogate. Crystals were grown in a form that has the same space group P2(1) as the uncomplexed enzyme, but with a 10 A decrease in the length of the alpha-axis and a 13 degrees decrease in the beta-angle. X-ray data have been collected to a resolution of 1.6 A. The rotation and translation parameters defining the position of the enzyme in the unit cell were determined previously using another enzyme-inhibitor complex that crystallized isomorphously with that of H-261. The molecule was refined using restrained least-squares refinement and the positions of non-hydrogen atoms of the inhibitor and water molecules were defined by difference Fourier techniques. The enzyme-inhibitor complex and 322 water molecules were further refined to a crystallographic R-factor of 0.14. Apart from a small rigid group rotation of a domain comprising residues 190 to 302 and small movements in the flap, there is little difference in conformation between the complexed and uncomplexed forms of the enzyme. The inhibitor is bound in an extended conformation along the active site cleft, and the hydroxyl group of the hydroxyethylene moiety is hydrogen-bonded to both catalytic aspartate carboxylates. The complex is stabilized by hydrogen bonds between the main-chain of the inhibitor and the enzyme. All side-chains of the inhibitor are in van der Waals' contact with groups in the enzyme and define a series of specificity pockets along the active site cleft. The study provides useful clues as to how this potent renin inhibitor (IC50 value of 0.7 x 10(-9) M) may bind renin. In particular it defines the interactions of the hydroxyethylene transition-state isostere with the enzyme more precisely than has been previously possible and therefore provides a useful insight into interactions in the transition state complex.

Aspartic Acid Endopeptidases↗
PubMed1990

X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution.

The molecular structure of the hexagonal crystal form of porcine pepsin (EC 3.4.23.1), an aspartic proteinase from the gastric mucosa, has been determined by molecular replacement using the fungal enzyme, penicillopepsin (EC 3.4.23.6), as the search model. This defined the space group as P6522 and refinement led to an R-factor of 0.190 at 2.3 A resolution. The positions of 2425 non-hydrogen protein atoms in 326 residues have been determined and the model contains 371 water molecules. The structure is bilobal, consisting of two predominantly beta-sheet lobes which, as in other aspartic proteinases, are related by a pseudo 2-fold axis. The strands of the mixed beta-sheets (1N and 1C) of each lobe are related by an intra-lobe topological 2-fold symmetry. Two further beta-sheets, 2N and 2C, are each composed of two topologically related beta-hairpins folded below the 1N and 1C sheets. A further six-stranded sheet (3) spans the two lobes and forms a structure resembling an arch upon which the four other sheets reside. The interface between sheets 1N and 1C forms the catalytic centre consisting of absolutely conserved aspartate residues 32 and 215, which are shielded from solvent by a beta-hairpin loop (75 to 78). The crystal structure of a mammalian aspartic proteinase indicates that interactions with substrate may be more extensive on the prime side of the active site cleft than in the fungal enzymes and involve Tyr189 and the loop 290 to 295, perhaps contributing to the transpeptidase activity of pepsin and the specificity of the renins. Comparison with the high-resolution structure of pepsinogen gives a root-mean-square deviation of 0.9 A and reveals that, in addition to local rearrangement at the active site, there appears to be a rigid group movement of part of the C-terminal lobe of pepsin towards the cleft on activation. A large proportion of the absolutely conserved residues in aspartic proteinases are polar and buried. An examination of the pepsin structure reveals that these side-chains are involved in hydrogen-bond interactions with either the main chain of the protein or other conserved side-chains of the enzyme or propart.

Amino Acid Sequence↗