Biomedical subjects

P R David

Publications and source records attributed to P R David.

At least 19 recordsLinked to original sources

PubMed2000

Architecture of RNA polymerase II and implications for the transcription mechanism.

A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.

Amino Acid Motifs↗

PubMed1999

Yeast RNA polymerase II at 5 A resolution.

Appropriate treatment of X-ray diffraction from an unoriented 18-heavy atom cluster derivative of a yeast RNA polymerase II crystal gave significant phase information to 5 A resolution. The validity of the phases was shown by close similarity of a 6 A electron density map to a 16 A molecular envelope of the polymerase from electron crystallography. Comparison of the 6 A X-ray map with results of electron crystallography of a paused transcription elongation complex suggests functional roles for two mobile protein domains: the tip of a flexible arm forms a downstream DNA clamp; and a hinged domain may serve as an RNA clamp, enclosing the transcript from about 8-18 residues upstream of the 3'-end in a tunnel.

Crystallography, X-Ray↗

PubMed1999

Acute urinary retention due to ectopic pregnancy.

Two cases of ectopic pregnancy are presented in which acute urinary retention was a salient clinical feature. The emergency physician must consider ectopic pregnancy in the differential diagnosis in any woman of child-bearing age with abdominal, pelvic, or urinary complaints.

Abdominal Pain↗

PubMed1998

Repeated tertiary fold of RNA polymerase II and implications for DNA binding.

X-ray diffraction data from two forms of yeast RNA polymerase II crystals indicate that the two largest subunits of the polymerase, Rpb1 and Rpb2, may have similar folds, as is suggested by secondary structure predictions. DNA may bind between the two subunits with its 2-fold axis aligned to a pseudo 2-fold axis of the protein.

Amino Acid Sequence↗

PubMed1994

Low-resolution real-space envelopes: the application of the condensing-protocol approach to the ab initio macromolecular phase problem of a variety of examples.

A recently reported method - the improved condensing protocol [Subbiah (1991). Science, 252, 128-133; (1993). Acta Cryst. D49, 108-119] - for obtaining low-resolution macromolecular envelopes is applied to five varied test cases. These examples were chosen to illustrate the general applicability of the method to the wide range that typical macromolecular crystals adopt. The cases include small and large asymmetric unit volumes (4.7 x 10(4) to 1.17 x 10(6) A(3)), low and high symmetry (2 to 12 symmetry elements), small and large proteins (1570 to 12 216 non-H atoms), orthogonal and non-orthogonal unit cells, a wide variety of space groups (P2(1) to P6(3)22), small and large solvent contents (33-80%), and a case of non-crystallographic symmetry (threefold). In all five cases the inherent ambiguity of the condensing protocol in differentiating between bulk matter and bulk solvent is then resolved by use of the recently reported sign-fixing method (Subbiah, 1993).

Journal Article↗

PubMed1993

[8 years outcome of 243 trials of coronary angiography performed in the Montreal Institute of Cardiology].

This study reports the long-term outcome of the first 243 patients who underwent coronary angioplasty at the Montreal Heart Institute between February 1980 and March 1983. The average age of the patients was 50 +/- 9 years; one quarter of cases were unstable angina; three quarters of the patients were men. Single vessel coronary disease was present in 83% of patients; the mean ejection fraction was 62%. One segment was dilated in 216 patients and 2 segments in 27 patients. The LAD was dilated in 179 patients, the right coronary in 63 and the left circumflex artery in 20 patients. The average severity of stenosis was 83 +/- 9.5%. Angioplasty was successful in 68.7% of patients. There were no fatalities: 25.5% of patients underwent coronary bypass surgery; 6.2% of patients suffered myocardial infarction. Restenosis was observed in 28% of patients. The average follow-up period was 99 +/- 10 months (average 8 years) and ranged from 7 to 10 years. The survival rate was 98.4% and 90.5% at 5 and 10 years respectively. Survival rates without infarction were 91.8% and 81.3% at 5 and 10 years, and survival without infarction or revascularisation was 73.2% and 60.3% at 5 and 10 years, respectively. During follow-up, 80% of patients were asymptomatic. Nearly a half of patients required antianginal therapy (monotherapy in 65.7% of them). Factors associated with absence of mortality infarction or revascularisation were: female sex, absence of restenosis and less severe stenosis before angioplasty. Using a multivariate analysis, only the degree of stenosis was correlated to the absence of these complications.(ABSTRACT TRUNCATED AT 250 WORDS)

Actuarial Analysis↗

PubMed1992

Structure determination and refinement of bovine lens leucine aminopeptidase and its complex with bestatin.

The three-dimensional structure of bovine lens leucine aminopeptidase (EC 3.4.11.1) complexed with bestatin, a slow-binding inhibitor, has been solved to 3.0 A resolution by the multiple isomorphous replacement method with phase combination and density modification. In addition, this structure and the structure of the isomorphous native enzyme have been refined at 2.25 and 2.32 A resolution, respectively, with crystallographic R-factors of 0.180 and 0.159, respectively. The current structural model for the enzyme includes the two zinc ions and 481 of the 487 amino acid residues comprising the asymmetric unit. The enzyme is physiologically active as a hexamer, which has 32 symmetry, and is triangular in shape with a triangle edge length of 115 A and maximal thickness of 90 A. Monomers are crystallographically equivalent. Each is folded into two unequal alpha/beta domains connected by an alpha-helix to give a comma-like shape with approximate maximal dimensions of 90 A x 55 A x 55 A. The secondary structural composition is 35% alpha-helix and 23% beta-strand. The N-terminal domain (160 amino acid residues) mediates trimer-trimer interactions and does not appear to participate directly in catalysis, while the C-terminal domain (327 amino acid residues) is responsible for catalysis and binds the two zinc ions, which are less than 3 A apart. These two metal ions are located near the edge of an eight-stranded, saddle-shaped beta-sheet. The zinc ion that has the lower temperature factor is co-ordinated by one carboxylate oxygen atom from each of Asp255, Asp332 and Glu334, and the carbonyl oxygen of Asp332. The other zinc ion, presumed to be readily exchangeable, is co-ordinated by one carboxylate oxygen atom of each of Asp273 and Glu334 and the side-chain amino group of Lys250. The active site also contains two positively charged residues, Lys262 and Arg336. The six active sites are themselves located in the interior of the hexamer, where they line a disk-shaped cavity of radius 15 A and thickness 10 A. Access to this cavity is provided by solvent channels that run along the 2-fold symmetry axes. Bestatin binds to one of the active site zinc ions, and its phenylalanine and leucine side-chains occupy hydrophobic pockets adjacent to the active site. Finally, the relationship between bovine lens leucine aminopeptidase and the homologous enzyme pepA from Escherichia coli is discussed.

Amino Acid Sequence↗

PubMed1991

Leucine aminopeptidase: bestatin inhibition and a model for enzyme-catalyzed peptide hydrolysis.

The three-dimensional structures of native bovine lens leucine aminopeptidase (EC 3.4.11.1) and its complex with bestatin, a slow-binding inhibitor, have been solved and exhaustively refined. The mode of binding of bestatin to leucine aminopeptidase may be similar to that of a tetrahedral intermediate that is thought to form during peptide bond hydrolysis. Bestatin binds in the active site with its alpha-amino group and hydroxyl group coordinated to the zinc ion located in the readily exchangeable divalent cation binding site. Its phenylalanyl side chain is stabilized by van der Waals interactions with Met-270, Thr-359, Gly-362, Ala-451, and Met-454, which appear to form a terminal hydrophobic pocket. The leucyl side chain binds in another hydrophobic cleft lined by Asn-330, Ala-333, and Ile-421. Hydrogen bonds involving active site residues Lys-262, Asp-273, Gly-360, and Leu-362 are responsible for stabilizing the backbone nitrogen and oxygen atoms of bestatin. The mode of bestatin inhibition of leucine aminopeptidase is discussed and correlated with biochemical studies of bestatin analogues. In addition, features of a mechanism of catalysis of peptide hydrolysis by leucine aminopeptidase are discussed.

Amino Acid Sequence↗

PubMed1990

Molecular structure of leucine aminopeptidase at 2.7-A resolution.

The three-dimensional structure of bovine lens leucine aminopeptidase (EC 3.4.11.1) complexed with bestatin, a slow-binding inhibitor, has been solved to 3.0-A resolution by the multiple isomorphous replacement method with phase combination and density modification. In addition, the structure of the isomorphous native enzyme has been refined at 2.7-A resolution, and the current crystallographic R factor is 0.169 for a model that includes the two zinc ions and all 487 amino acid residues comprising the asymmetric unit. The enzyme is physiologically active as a hexamer, which has 32 symmetry and is triangular in shape with a triangle edge length of 115 A and maximal thickness of 90 A. The monomers are crystallographically equivalent and each is folded into two unequal alpha/beta domains connected by an alpha-helix to give a comma-like shape with approximate maximal dimensions of 90 x 55 x 55 A3. The secondary structural composition is 40% alpha-helix and 19% beta-strand. The N-terminal domain (160 amino acids) mediates trimer-trimer interactions and does not appear to participate directly in catalysis. The C-terminal domain (327 amino acids) is responsible for catalysis and binds the two zinc ions, which are 2.88 A apart. The pair of metal ions is located near the edge of an eight-stranded, saddle-shaped beta-sheet. One zinc ion is coordinated by carboxylate oxygen atoms of Asp-255, Asp-332, and Glu-334 and the carbonyl oxygen of Asp-332. The other zinc ion is coordinated by the carboxylate oxygen atoms of Asp-255, Asp-273, and Glu-334. The active site also contains two positively charged residues, Lys-250 and Arg-336. The six active sites are themselves located in the interior of the hexamer, where they line a disk-shaped cavity of radius 15 A and thickness 10 A. Access to this cavity is provided by solvent channels that run along the twofold symmetry axes.

Amino Acid Sequence↗

PubMed1988

Aspirin and dipyridamole in the prevention of restenosis after percutaneous transluminal coronary angioplasty.

To examine the role of antiplatelet therapy in the prevention of arterial restenosis after percutaneous transluminal coronary angioplasty (PTCA), we conducted a randomized, double-blind, placebo-controlled study in 376 patients. The active treatment consisted of an oral aspirin-dipyridamole combination (330 mg-75 mg) given three times daily, beginning 24 hours before PTCA. Eight hours before PTCA, the oral dipyridamole was replaced with intravenous dipyridamole at a dosage of 10 mg per hour for 24 hours, and oral aspirin was continued. Sixteen hours after PTCA, the initial combination was reinstituted. Treatment was continued in patients with a successfully dilated vessel until follow-up angiography four to seven months after PTCA--or earlier, if symptoms dictated. Of 249 patients who underwent follow-up angiography, 37.7 percent of patients receiving the active drug had restenosis in at least one segment, as compared with 38.6 percent of patients taking placebo (P not significant). The number of stenotic segments was virtually the same in the two groups. Among the 376 randomized patients, there were 16 periprocedural Q-wave myocardial infarctions--13 in the placebo group and 3 in the active-drug group (6.9 percent vs. 1.6 percent, P = 0.0113). Although the use of this antiplatelet regimen before and after PTCA did not reduce the six-month rate of restenosis after successful coronary angioplasty, it markedly reduced the incidence of transmural myocardial infarction during or soon after PTCA. Thus, the short-term use of antiplatelet agents in relation to PTCA can be recommended.

Administration, Oral↗

PubMed1988

Multiple coronary angioplasty: a model to discriminate systemic and procedural factors related to restenosis.

To assess the interrelation of clinical and procedural factors responsible for restenosis, 119 patients undergoing coronary arteriography were studied a mean of 5.8 +/- 3 months after successful multiple percutaneous transluminal coronary angioplasty. In all clinical, angiographic and procedural variables, the 119 patients undergoing repeat catheterization were similar to the 87 patients that did not. Overall, restenosis occurred in 74 (34%) of 215 lesions. Sixty-three patients had no restenosis, 44 had at least one restenosis and 12 had restenosis at all angioplasty sites. The statistical distribution of restenoses did not follow a binomial model, suggesting that restenosis is more than a lesion-specific phenomenon. Of all the clinical and procedural variables assessed by multivariate logistic regression analysis, only percent stenosis before angioplasty (p less than 0.01), diabetes mellitus (p less than 0.01) and percent stenosis after angioplasty (p less than 0.05) were predictive of restenosis in the entire group. Patients with no restenosis and patients with restenosis at all sites were not different with respect to procedural variables; however, patients with restenosis at all sites more often (p less than 0.05) had diabetes and recent onset angina. In contrast, patients with no restenosis differed from patients with isolated restenosis with respect to procedural variables: severity of stenosis before and after angioplasty, balloon/artery lumen ratio and maximal inflation pressure. Thus, procedural factors may be more related to isolated restenosis, but patient-related factors such as diabetes and recent onset angina may play a more important role in patients with multiple restenoses.

Aged↗

PubMed1987

Early results, complications and restenosis rates after multilesion and multivessel percutaneous transluminal coronary angioplasty.

Initial results, complications, restenosis rates and clinical outcomes were compared in 78 patients undergoing multilesion and 128 patients undergoing multivessel percutaneous transluminal coronary angioplasty (PTCA). Multilesion PTCA was defined as a procedure in which a proximal PTCA site had to be crossed to dilate a distal severe narrowing and multivessel PTCA as multiple dilatations without having to cross 1 severe narrowing to dilate another. The clinical and angiographic features of the 2 groups were similar. More sites per patient were attempted among those who underwent multilesion PTCA. Primary success rate per lesion was 86% (236 of 274) among those who underwent multivessel and 73% (155 of 211) among those who underwent multilesion PTCA (p less than 0.001). A success rate of 81% (101 of 124) for proximal lesions among those with multilesion PTCA was not significantly worse than that for those with multivessel PTCA; however, lesions distal to proximal sites had a success rate of only 62% (54 of 87), worse than either those with proximal stenoses or multivessel PTCA (p less than 0.005). Arterial diameter, severity of stenosis or procedural variables did not account for this difference. Complication rates were similar in the 2 groups. Despite a poorer success rate among patients with multilesion PTCA, clinical improvement to functional class 0 or 1 occurred in more than 70% of patients in both groups and was equal in patients with and without successful distal dilatations. Restenosis rates per lesion in patients with multivessel (31%) and multilesion (30%) PTCA were similar.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1987

Restenosis after successful percutaneous transluminal coronary angioplasty: the Montreal Heart Institute experience.

Repeat coronary angiography was performed within 6 months after successful percutaneous transluminal coronary angioplasty (PTCA) in 178 of our first 181 patients (98%). The remaining 3 patients were symptom free, had negative treadmill exercise test results and were considered not to have had restenosis. A second follow-up angiogram was performed in 107 patients (59%), including all patients with persistent or recurrent anginal symptoms, between 7 and 18 months after PTCA. Fifty-one of the 181 patients (28%) had restenosis on 51 of 205 successfully dilated segments (25%). The stenosis was greater than or equal to 70% in 49 of these 51 segments; it was 65% and 55%, respectively, in the 2 remaining patients. Restenosis was documented angiographically at a median time of 4.7 +/- 4 months. However, 47 patients (92%) had restenosis documented within 6 months, 2 between 7 and 12 months and 2 between 13 and 18 months after PTCA. Stepwise logistic regression analysis selected the following factors as independent predictors of restenosis after PTCA: variant angina, multivessel disease, severity of residual stenosis and less reduction in the diameter of the stenosis on the angiogram immediately after PTCA. Of these 4 factors, the degree of residual stenosis immediately after PTCA was by far the most significant. It is concluded that restenosis occurs in approximately 25% of patients, almost always within the first 6 months, after successful PTCA. The degree of residual stenosis after PTCA is the most important predictor of restenosis. Increased experience and improved instrumentation may eventually lead to less residual stenosis and better late results after PTCA.

Angioplasty, Balloon↗

PubMed1987

Mechanism of carboxypeptidase A: hydration of a ketonic substrate analogue.

The structure of the complex between carboxypeptidase A alpha (EC 3.4.17.1) and the ketonic substrate analogue 5-benzamido-2-benzyl-4-oxopentanoic acid (BOP) has been determined by x-ray crystallographic methods to a resolution of 1.7 A (final R = 0.191). Interestingly, BOP was observed to bind to the active site of carboxypeptidase A alpha as the covalent hydrate adduct. Because BOP is probably less than 0.2% hydrated in aqueous solution, this result was unexpected. One possibility is that the zinc-bound water of the native enzyme added to the ketone carbonyl. Alternatively, the enzyme may preferentially scavenge the hydrated ketone as it is continuously maintained at equilibrium in the solution in which the carboxypeptidase A alpha crystals were immersed. In either case, this mode of binding of BOP to carboxypeptidase A alpha provides an example of the preferred binding of a model of a structure along the reaction coordinate of a hydrolytic reaction.

Carboxypeptidases↗

PubMed1987

Restenosis and its determinants in first and repeat coronary angioplasty.

Restenosis is the main problem limiting long-term success of percutaneous transluminal coronary angioplasty (PTCA) and is most accurately evaluated by follow-up angiography. We compared the primary and long-term results of angioplasty in 268 consecutive patients (293 segments) with first PTCA (PTCA 1, angiographic follow-up 98%) and in 66 patients (76 segments) with repeat PTCA after restenosis (PTCA 2, angiographic follow-up 92%). Forty clinical, angiographic and procedural factors were assessed in relation to outcome. Primary success rate was higher in PTCA 2 (91% vs 67.5%) and major complications were fewer (4.5% vs 16%). Higher inflation pressure (7.9 +/- 2.3 vs 6.8 +/- 1.8 atm, P less than 0.005) and larger balloons (3.5 +/- 0.5 vs 3.2 +/- 0.5 mm, P less than 0.005) were used for PTCA 2, resulting in lesser residual stenosis (33 +/- 16% vs 40 +/- 18%, P less than 0.05). Restenosis rate (greater than or equal to 70%) after PTCA 1 and after PTCA 2 (27% vs 36%, P = NS) and the mean time to recurrence (4.7 vs 5.3 months, P = NS) were similar. Procedural factors were the main determinants of long-term success in primary PTCA. The restenosis risk was independently related to residual stenosis greater than or equal to 45% (P less than 0.001), variant angina (P less than 0.05) and multivessel disease (P less than 0.05) after PTCA 1 and to male sex (P less than 0.001) and higher inflation pressure (P less than 0.05) after PTCA 2. Mild to moderate intimal tearing was associated with less restenosis after PTCA 1, but not after PTCA 2. Including 9 patients (10 segments) with a third PTCA, 70% of the 66 patients with repeat PTCA had a successful long-term outcome. Repeat angioplasty should therefore be considered as an integral part of PTCA therapy. Restenosis however remains a major concern. An optimal primary result with a minimal residual stenosis is decisive for first PTCA, whereas avoidance of a dissection by using lower inflation pressure on a restenosis might improve the long-term outcome of repeat PTCA.

Adult↗

PubMed1986

Risk of preangioplasty occlusion and myocardial infarction in one-vessel-disease patients scheduled for percutaneous transluminal coronary angioplasty.

Coronary occlusion or myocardial infarction occurred in 50 of 394 (13%) one-vessel-disease patients awaiting percutaneous transluminal coronary angioplasty (PTCA). To identify risk factors for these events, we first matched the 37 patients who demonstrated occlusion on the immediate preangioplasty repeat angiogram with 37 patients who did not. Matching was based on the time interval between angiograms, the date of the procedure, and the site of the lesion. Preangioplasty occlusion patients did differ from controls by age (47 +/- 11 vs 54 +/- 8 years, P less than .01), smoking status (34/37 vs 24/37, P less than .01), and angina class (2.6 +/- 1.0 vs 2.3 +/- 0.7, P less than .10) at the time of the first angiogram. Second, we pooled the data of the 37 preangioplasty occlusion patients with those of the 13 patients with preangioplasty myocardial infarction. The 50 cases with complication (coronary occlusion or myocardial infarction) were younger (47 +/- 12 vs 54 +/- 8 years, P less than .01), more often smokers (42/50 vs 24/37, P less than .05), and more symptomatic (2.7 +/- 0.8 vs 2.3 +/- 0.7, P less than .05) than the 37 controls. This study suggests that young smokers with severe angina are at high risk of preangioplasty occlusion and/or myocardial infarction; prompt management of these patients, when considered for PTCA, seems advisable.

Angiography↗

PubMed1985

[Developmental atherosclerosis of the coronary arteries treated by successive transluminal angioplasties].

The authors present the case of a 62 year old patient with advanced coronary artery disease who underwent three successive percutaneous transluminal coronary angioplasties for five stenoses over a period of 30 months. Three of these stenoses appeared after the first operation. This case illustrates the advantage of this new technique of revascularisation which has an encouraging future in the field of "operative cardiology". The coronary angioplasty can be repeated several times in the same patient, not only in the case of recurrent stenoses, but also when new stenoses appear, provided the technical expertise of the operator can guarantee a minimal risk for the patient.

Angioplasty, Balloon↗

PubMed1985

Prognostic significance of progression of coronary artery disease.

Angiographically documented coronary artery disease (CAD) can progress. Although progression itself is frequently recognized in patients who have undergone repeat cardiac catheterization, its prognostic significance remains unclear. To evaluate the influence of progression on survival, 313 patients with CAD who underwent catheterization twice (39 +/- 25 months apart) were followed for 3 to 129 months (mean 41 +/- 30) after the second angiogram. At the time of the second angiogram, 21, 91, 113 and 88 patients had 0-, 1-, 2- and 3-vessel CAD, respectively. The mean ejection fraction (EF) of the group was 55 +/- 13%. Progression was noted in 139 patients (44%). Of the 313 patients, 33 died and 39 had acute myocardial infarction (AMI) during follow-up. Four-year survival was estimated at 94% and 83% in the nonprogression and progression groups, respectively. Progression was predictive of survival by (univariate) long-rank test (p less than 0.01), but only EF (p less than 0.001), number of diseased vessels (p less than 0.01) and percent stenosis in the left main coronary artery (p less than 0.05) were independently significant by (multivariate) Cox regression analysis. Four-year survival without AMI was 89% and 73% in the nonprogression and progression groups, respectively. Progression was related to survival without AMI (p less than 0.001) by log-rank test. Cox regression analysis provided 3 independent predictors of survival without AMI: number of diseased vessels (p less than 0.01), progression (p less than 0.01), relative risk = 2.28) and EF (p less than 0.01). Results were similar when analyzing only the 39 AMIs.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗