Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0:a quantitative molecular docking study

Background: HLA-DPs are class II MHC proteins mediating immune responses to many diseases. Peptides bind MHC class II proteins in the acidic environment within endosomes. Acidic pH markedly elevates association rate constants but dissociation rates are almost unchanged in the pH range 5.0 - 7.0. This pH-driven effect can be explained by the protonation/deprotonation states of Histidine, whose imidazole has a pKa of 6.0. At pH 5.0, imidazole ring is protonated, making Histidine positively charged and very hydrophilic, while at pH 7.0 imidazole is unprotonated, making Histidine less hydrophilic. We develop here a method to predict peptide binding to the four most frequent HLA-DP proteins: DP1, DP41, DP42 and DP5, using a molecular docking protocol. Dockings to virtual combinatorial peptide libraries were performed at pH 5.0 and pH 7.0. Results: The X-ray structure of the peptide - HLA-DP2 protein complex was used as a starting template to model by homology the structure of the four DP proteins. The resulting models were used to produce virtual combinatorial peptide libraries constructed using the single amino acid substitution (SAAS) principle. Peptides were docked into the DP binding site using AutoDock at pH 5.0 and pH 7.0. The resulting scores were normalized and used to generate Docking Score-based Quantitative Matrices (DS-QMs). The predictive ability of these QMs was tested using an external test set of 484 known DP binders. They were also compared to existing servers for DP binding prediction. The models derived at pH 5.0 predict better than those derived at pH 7.0 and showed significantly improved predictions for three of the four DP proteins, when compared to the existing servers. They are able to recognize 50% of the known binders in the top 5% of predicted peptides. Conclusions: The higher predictive ability of DS-QMs derived at pH 5.0 may be rationalised by the additional hydrogen bond formed between the backbone carbonyl oxygen belonging to the peptide position before p1 (p-1) and the protonated ε-nitrogen of His 79β. Additionally, protonated His residues are well accepted at most of the peptide binding core positions which is in a good agreement with the overall negatively charged peptide binding site of most MHC proteins. © 2012 Patronov et al.; licensee BioMed Central Ltd.

Characterization of Juvenile Hormone Biosynthetic Enzymes in the Mosquito, Aedes aegypti

The juvenile hormones (JHs) are sesquiterpenoid compounds that play a central role in insect reproduction, development and behavior. They are synthesized and secreted by a pair of small endocrine glands, the corpora allata (CA), which are intimately connected to the brain. The enzymes involved in the biosynthesis of JH are attractive targets for the control of mosquito populations. This dissertation is a comprehensive functional study of five Aedes aegypti CA enzymes, HMG-CoA synthase (AaHMGS), mevalonate kinase (AaMK), phosphomevalonate kinase (AaPMK), farnesyl diphosphate synthase (AaFPPS) and farnesyl pyrophosphate phosphatase (AaFPPase). The enzyme AaHMGS catalyzes the condensation of acetoacetyl-CoA and acetyl-CoA to produce HMG-CoA. The enzyme does not require any co-factor, although its activity is enhanced by addition of Mg2+. The enzyme AaMK is a class I mevalonate kinase that catalyzes the ATP-dependent phosphorylation of mevalonic acid to form mevalonate 5-phosphate. Activity of AaMK is inhibited by isoprenoids. The enzyme AaPMK catalyzes the cation-dependent reversible reaction of phosphomevalonate and ATP to form diphosphate mevalonate and ADP. The enzyme AaFPPS catalyzes the condensation of isopentenyl diphosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) to form geranyl diphosphate (GPP) and farnesyl pyrophosphate (FPP). The enzyme AaFPPS shows an unusual product regulation mechanism, with chain length final product of 10 or 15 C depending on the metal cofactor present. The enzymes AaFPPase-1 and AaFPPase-2 efficiently hydrolyze FPP into farnesol, although RNAi experiments demonstrate that only AaFPPase-1 is involved in the catalysis of FPP into FOL in the CA of A. aegypti. This dissertation also explored the inhibition of the activity of some of the JH biosynthesis enzymes as tools for insect control. We described the effect of N-acetyl-S-geranylgeranyl-L-cysteine as a potent inhibitor of AaFPPase 1 and AaFPPase-2. In addition, inhibitors of AaMK and AaHMGS were also investigated using purified recombinant proteins. The present study provides an important contribution to the characterization of recombinant proteins, the analysis of enzyme kinetics and inhibition constants, as well as the understanding of the importance of these five enzymes in the control of JH biosynthesis rates.

Tratamento de cascalho de perfuração utilizando sistemas microemulsionados

The oil industry is one of the activities that generates more waste to the environment. The drill cuttings is a waste generated in large quantities in the drilling process and that may cause environmental damage such as soil contamination and consequently the contamination of groundwater if disposed of without prior treatment. Arises the need to develop scientific activities and research ways to adapt these wastes the current environmental standards. In the case of solid wastes, the NBR 10004: 2004 of the Brazilian Association of Technical Standards (ABNT) classifies them into class I waste (hazardous) and class II (not dangerous), which determines which wastes may or may not be discarded in the environment without causing environmental impact. This study presents a novel alternative for treating drill cuttings, where this waste was classified as class I (Abreu & Souza, 2005), mainly by removing the n-paraffin present in it, since this arises when using drilling fluids base oil. Using microemulsion systems promotes the removal of this contaminant drill cuttings samples from wells located in Alto do Rodrigues - RN. Initially, we determined the concentration of paraffin using infrared method in samples were extracted with ultrasound, we obtained a paraffin concentration in the range from 36.59 to 43.52 g of paraffin per kilogram of cuttings. Used two microemulsion systems containing two nonionic surfactants from different classes, one is an alcohol ethoxylated (UNTL-90) and the other an nonylphenol ethoxylated (RNX 110). The results indicated that the system UNTL-90 surfactant has better efficiency than the system with RNX 110. The study of the influence of contact time at the extraction showed that for times greater than 25 minutes has a tendency to increase the percentage extraction with increasing contact time. It was also observed that the extraction is fast because at 1 minute contact has 22.7% extraction. The reuse of the microemulsion system without removing the paraffin extracted in previous steps, showed reduction of 29.32 in percentage of extraction by comparing the first and third extraction, but by comparing the first and second extractions reduction is 8.5 in percentage extraction, so the systems reuse optimization can be an option for economically viable removing paraffin from cuttings. The extraction with shaking is more effective in the treatment of cuttings, reaching the extraction percentage of 87.04%, that is, obtaining a drill cuttings with 0.551% paraffin. Using the percentage of paraffin employed in non-aqueous drilling fluids and fluid maximum limit on cuttings for disposal established by the Environmental Protection Agency of the United States (US EPA), one arrives at the conclusion that the level of paraffin on gravel cannot exceed 3.93%. Conclude that the amount of paraffin in the treated cuttings with the microemulsion system with shaking is below the established by US EPA, showing that the system used was efficient in removing the paraffin from the drill cuttings.

Ethics in the provision of removable partial dentures

Aim: To investigate the construction of cobalt-chromium removable partial dentures by commercial private dental laboratories. Methods: Ninety master casts for fabrication of cobalt-chromium removable partial dentures were obtained from three commercial laboratories randomly selected. Casts were assessed for dental arch treated, Kennedy classification, cast surveying, denture design information provided by the dentist, and mouth preparation (rest seat, guiding plane and retentive area). Dental technicians answered a questionnaire regarding qualification of assisted dentists, monthly number of framework castings, and use of dental surveyor. Mouth preparation was compared among laboratories using Kruskal-Wallis test (α=0.05). Results: The percentage of Kennedy class I was 16%, class II 19%, class III 56%, and class IV 9%. The majority of master cats (51%) examined was sent to dental laboratories without any design information and did not comply with ethical guidelines in the provision of RPD. Approximately half of the casts were considered “inappropriate” for guiding planes and retentive areas. One of the laboratories presented all casts “inappropriate” for rest seat distribution (p<0.001). Conclusions: Mouth preparation frequently failed for guiding planes, retentive areas and distribution of rest seats. It is necessary to provide students with adequate clinical experience at the dental school environment, which will actually be carried into the practice of dentistry.

Ethics in the provision of removable partial dentures

Aim: To investigate the construction of cobalt-chromium removable partial dentures by commercial private dental laboratories. Methods: Ninety master casts for fabrication of cobalt-chromium removable partial dentures were obtained from three commercial laboratories randomly selected. Casts were assessed for dental arch treated, Kennedy classification, cast surveying, denture design information provided by the dentist, and mouth preparation (rest seat, guiding plane and retentive area). Dental technicians answered a questionnaire regarding qualification of assisted dentists, monthly number of framework castings, and use of dental surveyor. Mouth preparation was compared among laboratories using Kruskal-Wallis test (α=0.05). Results: The percentage of Kennedy class I was 16%, class II 19%, class III 56%, and class IV 9%. The majority of master cats (51%) examined was sent to dental laboratories without any design information and did not comply with ethical guidelines in the provision of RPD. Approximately half of the casts were considered “inappropriate” for guiding planes and retentive areas. One of the laboratories presented all casts “inappropriate” for rest seat distribution (p<0.001). Conclusions: Mouth preparation frequently failed for guiding planes, retentive areas and distribution of rest seats. It is necessary to provide students with adequate clinical experience at the dental school environment, which will actually be carried into the practice of dentistry.

Inter-relação entre lesão cervical não cariosa e comprometimento periodontal: diagnóstico, tratamento e previsibilidade - estudo clínico prospectivo e laboratorial

The coexistence of gingival recession (GR) with root coverage indication and non-carious cervical lesions (LCNC) generates the need for a protocol that respects and promotes health of dental and periodontal tissues and allows treatment predictability. The main objectives of this theses were: (1) verify, through clinical evaluations, the connective tissue graft for root coverage on direct and indirect restorations made of ceramic resin; (2) analyze the influence of the battery level of the LED curing unit in the composite resin characteristics; (3) assess the influence of restorative materials, composite resin and ceramics, on the viability of gingival fibroblasts from primary culture. Nine patients with good oral hygiene and occlusal stability diagnosed with LCNCs the anterior teeth including premolars associated with gingival recession (class I and II of Miller) and only gingival recession were selected. After initial clinical examination, occlusal adjustment was performed and the patients had their teeth randomized allocated on direct composite resin restoration of LCNC, polishing and GR treatment with connective tissue graft and advanced coronally flap CR group (n = 15); and indirect ceramic restoration of the LCNC's and GR treatment (CTG+CAF) Group C (n = 15). The GR presented teeth with no clinically formed LCNCs cavity were treated using (CTG+CAF) being the control group (n = 15). Sorption and solubility tests, analysis of the degree of conversion and diametral tensile strength were performed in composite resin samples (n = 10) photoactivated by 100, 50 and 10% battery charge LED unit. The viability of fibroblasts on composite resin, ceramics and dentin disks (n = 3) was examined. Clinical follow-up was performed for three months. The data obtained at different stages were tabulated and subjected to analysis for detection of normal distribution and homogeneity. The results showed that: the LED unit with 10% battery affects the characteristics of the composite resin; restorative materials present biocompatibility with gingival fibroblasts; and the association of surgical and restorative treatment of teeth affected by NCCL and GR presents successful results at 3-month follow-up.

Difficult Labor: Troublesome Company at the New Birth of Freedom

Extended contribution to a roundtable on Mark A. Lause's Free Labor: The Civil War and the Making of an American Working Class, emphasizing the wartime labor movement's great difficulty in responding to rapid industrialization brought on by the war, and to the increasing diversity of the labor force brought about by mass immigration.