Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Theoretical analysis of the structural deformation in Mn-doped BaTiO3

An alternative theoretical method to simulate the structural deformation induced by Mn-doping in BaTiO3 is proposed. The periodic quantum-mechanical method is based on density functional theory at B3LYP level. The structural models were obtained from Rietveld refinement of the undoped and Mn doped BaTiO3 X-ray diffraction data. This modelization gives access to the dopant General effect on the electronic structure. In fact, the influence of the doing element itself on the electronic configuration is barely local: therefore, it is not included in the simulation. The simplicity of the model makes it available for working within a wide range of materials.(C) 2004 Published bv Elsevier B.V.

Molecular models of cyclin-dependent kinase 1 complexed with inhibitors

Roscovitine and flavopiridol have been shown to potently inhibit cyclin-dependent kinase 1 and 2 (CDK1 and 2). The structures of CDK2 complexed with roscovitine and deschoroflavopiridol have been reported, however no crystallographic structure is available for complexes of CDK1 with inhibitors. The present work describes two molecular models for the binary complexes CDK1:roscovitine and CDK1:flavopiridol. These structural models indicate that both inhibitors strongly bind to the ATP-binding pocket of CDKI and structural comparison of the CDK complexes correlates the structures with differences in inhibition of these CDKs by flavopiridol and roscovitine. This article explains the structural basis for the observed differences in activity of these inhibitors. (C) 2004 Elsevier B.V. All rights reserved.

Molecular models of protein kinase 6 from Plasmodium falciparum

Cyclin-dependent kinases (CDKs) have been identified as potential targets for development of drugs, mainly against cancer. These studies generated a vast library of chemical inhibitors of CDKs, and some of these molecules can also inhibit kinases identified in the Plasmodium falciparum genome. Here we describe structural models for Protein Kinase 6 from P. falciparum (PfPK6) complexed with Roscovitine and Olomoucine. These models show clear structural evidence for differences observed in the inhibition, and may help designing inhibitors for PfPK6 generating new potential drugs against malaria.

Functional and structural analysis of two fibrinogen-activating enzymes isolated from the venoms of Crotalus durissus terrificus and Crotalus durissus collilineatus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural and geochronological studies of the Médio Coreaú domain, NE Brazil: Constraints on Brasiliano/Pan-African tectonic evolution in the NW part of the Borborema Province

Recent structural investigations and geochronological studies of rocks from the Médio Coreaú domain in the NW part of northeast Brazil's Borborema Province provide important constraints on the tectonic evolution of the region both preceeding and during the assembly of West Gondwana. Field observations of structural features and fabrics have revealed the presence of four distinct deformational phases in the MCD: D1, D2, D3 and D4. Only the early Paleoproterozoic gneisses record the D1 tectonic event and its preservation is cryptic owing to strong overprinting by the subsequent tectonic phases. The D2, D3 and D4 events affected younger supracrustal rocks and Neoproterzoic magmatic units, and U-Pb geochronological constraints show that all of these tectonic phases represent deformational events that occurred during Brasiliano collision between the West African craton and the NW part of the Borborema Province. The D2 phase, lasting between ca. 622 and 591 Ma, represents a frontal collision stage, which generated NW verging thrust-nappe systems, low-angle foliation, high-grade metamorphism and crustal anatexis. Transition to a strike-slip regime (D3) occurred at around 591 Ma when the region entered a phase of escape tectonics. During this time, the motion of crustal blocks towards NE and E was accommodated along numerous anastomosing shear zones. Syntectonic emplacement of granitoid plutons took place in transtensional domains of the shear zone system. The intrusion of late tectonic granitoids and rapid uplift and cooling of the orogen around 560 Ma as a result of D4 transpressional movements marked the end of the D3 transcurrent regime. These findings show that only the early Paleoproterozoic gneisses in the Médio Coreaú domain are polycyclic in nature. Rather than representing distinct orogenic events, the D2, D3 and D4 tectonic phases are a manifestation of progressive deformational events that developed in response to changes in the regional stress field during convergence and collision between the Borborema Province and its surrounding cratons.

SKPDB: A structural database of shikimate pathway enzymes

Background: The functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans.Description: The ShiKimate Pathway DataBase (SKPDB) is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores) are available for downloading. The modeled structures can be viewed using the Jmol program.Conclusions: The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/. © 2010 Arcuri et al; licensee BioMed Central Ltd.

Structural reforms, technological gaps and economic development: a Latin American perspective

Includes bibliography

A structural model of emotions of cognitive dissonances

Cognitive dissonance is the stress that comes from holding two conflicting thoughts simultaneously in the mind, usually arising when people are asked to choose between two detrimental or two beneficial options. In view of the well-established role of emotions in decision making, here we investigate whether the conventional structural models used to represent the relationships among basic emotions, such as the Circumplex model of affect, can describe the emotions of cognitive dissonance as well. We presented a questionnaire to 34 anonymous participants, where each question described a decision to be made among two conflicting motivations and asked the participants to rate analogically the pleasantness and the intensity of the experienced emotion. We found that the results were compatible with the predictions of the Circumplex model for basic emotions. (C) 2012 Elsevier Ltd. All rights reserved.

Air pollution and health: bridging the gap from sources to health outcomes: conference summary

Air Pollution and Health: Bridging the Gap from Sources to Health Outcomes, an international specialty conference sponsored by the American Association for Aerosol Research, was held to address key uncertainties in our understanding of adverse health effects related to air pollution and to integrate and disseminate results from recent scientific studies that cut across a range of air pollution-related disciplines. The Conference addressed the science of air pollution and health within a multipollutant framework (herein "multipollutant" refers to gases and particulate matter mass, components, and physical properties), focusing on five key science areas: sources, atmospheric sciences, exposure, dose, and health effects. Eight key policy-relevant science questions integrated across various parts of the five science areas and a ninth question regarding findings that provide policy-relevant insights served as the framework for the meeting. Results synthesized from this Conference provide new evidence, reaffirm past findings, and offer guidance for future research efforts that will continue to incrementally advance the science required for reducing uncertainties in linking sources, air pollutants, human exposure, and health effects. This paper summarizes the Conference findings organized around the science questions. A number of key points emerged from the Conference findings. First, there is a need for greater focus on multipollutant science and management approaches that include more direct studies of the mixture of pollutants from sources with an emphasis on health studies at ambient concentrations. Further, a number of research groups reaffirmed a need for better understanding of biological mechanisms and apparent associations of various health effects with components of particulate matter (PM), such as elemental carbon, certain organic species, ultrafine particles, and certain trace elements such as Ni, V, and Fe(II), as well as some gaseous pollutants. Although much debate continues in this area, generation of reactive oxygen species induced by these and other species present in air pollution and the resulting oxidative stress and inflammation were reiterated as key pathways leading to respiratory and cardiovascular outcomes. The Conference also underscored significant advances in understanding the susceptibility of populations, including the role of genetics and epigenetics and the influence of socioeconomic and other confounding factors and their synergistic interactions with air pollutants. Participants also pointed out that short-and long-term intervention episodes that reduce pollution from sources and improve air quality continue to indicate that when pollution decreases so do reported adverse health effects. In the limited number of cases where specific sources or PM2.5 species were included in investigations, specific species are often associated with the decrease in effects. Other recent advances for improved exposure estimates for epidemiological studies included using new technologies such as microsensors combined with cell phone and integrated into real-time communications, hybrid air quality modeling such as combined receptor-and emission-based models, and surface observations used with remote sensing such as satellite data.

Tenofovir or zidovudine in second-line antiretroviral therapy after stavudine failure in southern Africa

BACKGROUND There is debate over using tenofovir or zidovudine alongside lamivudine in second-line antiretroviral therapy (ART) following stavudine failure. We analyzed outcomes in cohorts from South Africa, Zambia and Zimbabwe METHODS: Patients aged ≥16 years who switched from a first-line regimen including stavudine to a ritonavir-boosted lopinavir-based second-line regimen with lamivudine or emtricitabine and zidovudine or tenofovir in seven ART programs in southern Africa were included. We estimated the causal effect of receiving tenofovir or zidovudine on mortality and virological failure using Cox proportional hazards marginal structural models. Its parameters were estimated using inverse probability of treatment weights. Baseline characteristics were age, sex, calendar year and country. CD4 cell count, creatinine and hemoglobin levels were included as time-dependent confounders. RESULTS 1,256 patients on second-line ART, including 958 on tenofovir, were analyzed. Patients on tenofovir were more likely to have switched to second-line ART in recent years, spent more time on first-line ART (33 vs. 24 months) and had lower CD4 cell counts (172 vs. 341 cells/μl) at initiation of second-line ART. The adjusted hazard ratio comparing tenofovir with zidovudine was 1.00 (95% confidence interval 0.59-1.68) for virologic failure and 1.40 (0.57-3.41) for death. CONCLUSIONS We did not find any difference in treatment outcomes between patients on tenofovir or zidovudine; however, the precision of our estimates was limited. There is an urgent need for randomized trials to inform second-line ART strategies in resource-limited settings.

Age models of sediment cores from the Southern Ocean

Recent geochemical models invoke ocean alkalinity changes, particularly in the surface Southern Ocean, to explain glacial age pCO2 reduction. In such models, alkalinity increases in glacial periods are driven by reductions in North Atlantic Deep Water (NADW) supply, which lead to increases in deep-water nutrients and dissolution of carbonate sediments, and to increased alkalinity of Circumpolar Deep Water upwelling in the surface Southern Ocean. We use cores from the Southeast Indian Ridge and from the deep Cape Basin in the South Atlantic to show that carbonate dissolution was enhanced during glacial stages in areas now bathed by Circumpolar Deep Water. This suggests that deep Southern Ocean carbonate ion concentrations were lower in glacial stages than in interglacials, rather than higher as suggested by the polar alkalinity model [Broecker and Peng, 1989, doi:10.1029/GB001i001p00015]. Our observations show that changes in Southern Ocean CaCO3 preservation are coherent with changes in the relative flux of NADW, suggesting that Southern Ocean carbonate chemistry is closely linked to changes in deepwater circulation. The pattern of enhanced dissolution in glacials is consistent with a reduction in the supply of nutrient-depleted water (NADW) to the Southern Ocean and with an increase of nutrients in deep water masses. Carbonate mass accumulation rates on the Southeast Indian Ridge (3200-3800 m), and in relatively shallow cores (<3000 m) from the Kerguelen Plateau and the South Pacific were significantly reduced during glacial stages, by about 50%. The reduced carbonate mass accumulation rates and enhanced dissolution during glacials may be partly due to decreases in CaCO3:Corg flux ratios, acting as another mechanism which would raise the alkalinity of Southern Ocean surface waters. The polar alkalinity model assumes that the ratio of organic carbon to carbonate production on surface alkalinity is constant. Even if overall productivity in the Southern Ocean were held constant, a decrease in the CaCO3:Corg ratio would result in increased alkalinity and reduced pCO2 in Southern Ocean surface waters during glacials. This ecologically driven surface alkalinity change may enhance deepwater-mediated changes in alkalinity, and amplify rapid changes in pCO2.

Structural origins of the exonuclease resistance of a zwitterionic RNA

Nuclease resistance and RNA affinity are key criteria in the search for optimal antisense nucleic acid modifications, but the origins of the various levels of resistance to nuclease degradation conferred by chemical modification of DNA and RNA are currently not understood. The 2′-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1°C per modified residue. We found that oligodeoxynucleotides containing AP-RNA residues at their 3′ ends competitively inhibit the degradation of single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3′-5′ exonuclease and snake venom phosphodiesterase. To shed light on the origins of nuclease resistance brought about by the AP modification, we determined the crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-Å resolution. In addition, the crystal structures of complexes between short DNA fragments carrying AP-RNA modifications and wild-type KF were determined at resolutions between 2.2 and 3.0 Å and compared with the structure of the complex between oligo(dT) and the D355A/E357A KF mutant. The structural models suggest that interference of the positively charged 2′-O-substituent with the metal ion binding site B of the exonuclease allows AP-RNA to effectively slow down degradation.

Key residues revealed in a major conformational epitope of the U1-70K protein

Epitopes depending on three-dimensional folding of proteins have during recent years been acknowledged to be main targets for many autoantibodies. However, a detailed resolution of conformation-dependent epitopes has to date not been achieved in spite of its importance for understanding the complex interaction between an autoantigen and the immune system. In analysis of immunodominant epitopes of the U1-70K protein, the major autoantigen recognized by human ribonucleoprotein (RNP)-positive sera, we have used diversely mutated recombinant Drosophila melanogaster 70K proteins as antigens in assays for human anti-RNP antibodies. Thus, the contribution of individual amino acids to antigenicity could be assayed with the overall structure of the major antigenic domain preserved, and analysis of how antigenicity can be reconstituted rather than obliterated was enabled. Our results reveal that amino acid residue 125 is situated at a crucial position for recognition by human anti-RNP autoantibodies and that flanking residues at positions 119–126 also appear to be of utmost importance for recognition. These results are discussed in relation to structural models of RNA-binding domains, and tertiary structure modeling indicates that the residues 119–126 are situated at easily accessible positions in the end of an α-helix in the RNA binding region. This study identifies a major conformation-dependent epitope of the U1-70K protein and demonstrates the significance of individual amino acids in conformational epitopes. Using this model, we believe it will be possible to analyze other immunodominant regions in which protein conformation has a strong impact.

Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest.

RNA polymerases encounter specific DNA sites at which RNA chain elongation takes place in the absence of enzyme translocation in a process called discontinuous elongation. For RNA polymerase II, at least some of these sequences also provoke transcriptional arrest where renewed RNA polymerization requires elongation factor SII. Recent elongation models suggest the occupancy of a site within RNA polymerase that accommodates nascent RNA during discontinuous elongation. Here we have probed the extent of nascent RNA extruded from RNA polymerase II as it approaches, encounters, and departs an arrest site. Just upstream of an arrest site, 17-19 nucleotides of the RNA 3'-end are protected from exhaustive digestion by exogenous ribonuclease probes. As RNA is elongated to the arrest site, the enzyme does not translocate and the protected RNA becomes correspondingly larger, up to 27 nucleotides in length. After the enzyme passes the arrest site, the protected RNA is again the 18-nucleotide species typical of an elongation-competent complex. These findings identify an extended RNA product groove in arrested RNA polymerase II that is probably identical to that emptied during SII-activated RNA cleavage, a process required for the resumption of elongation. Unlike Escherichia coli RNA polymerase at a terminator, arrested RNA polymerase II does not release its RNA but can reestablish the normal elongation mode downstream of an arrest site. Discontinuous elongation probably represents a structural change that precedes, but may not be sufficient for, arrest by RNA polymerase II.