The additivity of substrate fragments in enzyme-ligand binding

BACKGROUND: Enzymes have evolved to recognise their target substrates with exquisite selectivity and specificity. Whether fragments of the substrate--perhaps never available to the evolving enzyme--are bound in the same manner as the parent substrate addresses the fundamental basis of specificity. An understanding of the relative contributions of individual portions of ligand molecules to the enzyme-binding interaction may offer considerable insight into the principles of substrate recognition. RESULTS: We report 12 crystal structures of Escherichia coli thymidylate synthase in complexes with available fragments of the substrate (dUMP), both with and without the presence of a cofactor analogue. The structures display considerable fidelity of binding mode and interactions. These complexes reveal several interesting features: the cofactor analogue enhances the localisation of substrate and substrate fragments near the reactive thiol; the ribose moiety reduces local disorder through additional specific enzyme-ligand interactions; the pyrimidine has multiple roles, ranging from stereospecificity to mechanistic competence; and the glycosidic linkage has an important role in the formation of a covalent attachment between substrate and enzyme. CONCLUSIONS: The requirements of ligand-protein binding can be understood in terms of the binding of separate fragments of the ligand. Fragments which are subsystems of the natural substrate for the enzyme confer specific contributions to the binding affinity, orientation or electrostatics of the enzymatic mechanism. This ligand-binding analysis provides a complementary method to the more prevalent approaches utilising site-directed mutagenesis. In addition, these observations suggest a modular approach for rational drug design utilising chemical fragments.     

Institutions and the supply of oil: A case study of Russia

In new institutional economics, the variance in institutions explains differences in cross-country output per capita. Institutions may also explain how the supply of oil is affected within oil-producing countries. For example in the early 1970s, as nominal oil prices increased from $3 per barrel to $11 per barrel, a number of OPEC oil producers changed the institutional environment by nationalizing their oil production and putting under government control all petroleum-related capital and infrastructure. This affected oil supplies. Similar institutional changes may be happening again now that oil prices are rising. In particular, the newly democratic Russia may be following the same path. The Russian government has already effectively taken over control of much of the oil production capacity in the country and is still heavily involved in natural gas production. In this paper, we will look at the Russian upstream oil industry as it changed from central planning to a market-oriented sector and is now swaying toward re-nationalization. Some of the laws and institutional transitions will be detailed in order to elucidate what has taken place.     

Post-traumatic stress disorder and functioning and quality of life outcomes in female Vietnam veterans

OBJECTIVE: This investigation assessed whether current post-traumatic stress disorder (PTSD) was associated with impaired functioning in a nationally representative sample of female Vietnam veterans. METHODS: Logistic models were used to determine the association between PTSD and outcome while adjusting for demographic characteristics and medical and psychiatric co-morbidities. RESULTS: PTSD was associated with significantly elevated odds of poorer functioning in five of the six outcome domains; only the association between perpetration of violence in the past year and PTSD did not achieve statistical significance. After adjusting for demographics and medical and psychiatric co-morbidities, PTSD remained associated with significantly elevated odds of bed days, poorer physical health, and currently not working. CONCLUSIONS: Among female Vietnam veterans PTSD is associated with a broad profile of functional impairment. The significantly increased odds of impaired functioning and diminished quality of life suggest that PTSD may be the core problem of the set of problems afflicting female Vietnam veterans.     

Pharmacologic profile of survivors of acute myocardial infarction at United States academic hospitals

Optimal drug therapy for patients with acute myocardial infarction (AMI) is well described in the medical literature. However, data on the actual pharmacologic management of patients surviving AMI at academic hospitals is unavailable. The purpose of this study was to document treatment profiles in 500 patients surviving AMI at 12 academic hospitals in the United States. These profiles were compared with established guidelines and were evaluated for trends. Overall, thrombolytics (streptokinase > or = tissue-type plasminogen activator) were administered in 29% of the patients, with a greater proportion of patients receiving beta-blockers than calcium channel antagonists in the initial 72 hours (61% vs 40%; p < 0.005) and at discharge (51% vs 35%; p < 0.005). Further, women were less likely than men to receive thrombolytic therapy (odds ratio [OR] = 0.61; confidence interval [CI], 0.54 to 0.69) or beta-blocker therapy within the first 72 hours (OR = 0.61; CI, 0.55 to 0.67) or at hospital discharge (OR = 0.53; CI, 0.48 to 0.58). Overall, improvements could still be made in the number of patients who receive thrombolytic and acute and chronic beta-blocker therapies after AMI, particularly in women. Changes in treatment profiles may be a reflection of the publication of large clinical trials.     

Ceftiofur hydrochloride: plasma and tissue distribution in swine following intramuscular administration at various doses

Coccidioides immitis, the primary pathogenic fungus that causes coccidioidomycosis, is most commonly found in the deserts of the southwestern United States and Central and South America. During the early 1990s, the incidence of coccidioidomycosis in California increased dramatically. Even though most infections are subclinical or self-limited, the outbreak is estimated to have cost more than $66 million in direct medical expenses and time lost from work in Kern County, California, alone. In addition to the financial loss, this pathogen causes serious and life-threatening disseminated infections, especially among the immunosuppressed, including AIDS patients. This article discusses factors that may be responsible for the increased incidence of coccidioidomycosis (e.g., climatic and demographic changes and the clinical problems of coccidioidomycosis in the immunocompromised) and new approaches to therapy and prevention.     

Anatomical basis of a congenital hearing impairment: basilar papilla dysplasia in the Belgian Waterslager canary

We studied the role of proteases in apoptosis using a cell-free system prepared from a human leukemia cell line. HL60 cells are p53 null and extremely sensitive to a variety of apoptotic stimuli including DNA damage induced by the topoisomerase I inhibitor, camptothecin. We measured DNA fragmentation induced in isolated nuclei by cytosolic extracts using a filter elution assay. Cytosol from camptothecin-treated HL60 cells induced internucleosomal DNA fragmentation in nuclei from untreated cells. This fragmentation was suppressed by serine protease inhibitors. Serine proteases (trypsin, endoproteinase Glu-C, chymotrypsin A, and proteinase K) and papain by themselves induced DNA fragmentation in naive nuclei. This effect was enhanced in the presence of cytosol from untreated cells. Cysteine protease inhibitors (E-64, leupeptin, Ac-YVAD-CHO [ICE inhibitor]) did not affect camptothecin-induced DNA fragmentation. The apopain/Yama inhibitor, Ac-DEVD-CHO, and the proteasome inhibitor, MG-132, were also inactive both in the cell-free system and in whole cells. Interleukin-1 beta converting enzyme (ICE) or human immunodeficiency virus protease failed to induce DNA fragmentation in naive nuclei. Together, these results suggest that DNA damage activates serine protease(s) which in turn activate(s) nuclear endonuclease(s) during apoptosis in HL60 cells.     

Single-sided ventilation — Part II. further considerations

This paper extends an earlier report of measurements and computer predictions of flows in a cubical cavity exposed on one side to the scavenging effect of an external stream. Further measurements and photographs are presented; they are consistent with each other and with the predictions of the computational model. Specifically, comparisons are made between measured and predicted mean velocities and turbulent shear stresses, and photographs are used to elucidate features of the shear layers generated by accelerating and decelerating external flows. The computer model is used to deduce approximate relations between internal turbulent activity (measured by mean velocity, turbulence energy and shear stress) and external velocity, percentage ‘window’ opening and relative position of the plane walls upstream and downstream of the cavity.