Probing the infraed behavior of the ghost-gluon vertex in quantum chromodynamics

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Clinical and microbiological changes after minimally invasive therapeutic approaches in intrabony defects: a 12-month follow-up

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

Investigation of DMSO-Induced Conformational Transitions in Human Serum Albumin Using Two-Dimensional Raman Optical Activity Spectroscopy

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

Microbiological changes after periodontal therapy in diabetic patients with inadequate metabolic control

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Probing the Enamel Topography After Acid Erosion by Scanning Electrochemical Microscopy

In this work, we present an investigation on the thickness of the eroded enamel layer in tooth samples after exposure to citric and hydrochloric acid by using Scanning Electrochemical Microscopy (SECM). Approaching curves with typical negative feedback behavior were obtained in enamel samples for evaluation of topographic changes. In a control experiment, SECM images showed no significant difference in the current monitored during the scan, implying that enamel demineralization did not occur in mineral water medium. Topographic SECM images obtained after contact with citric and hydrochloric acid for different periods of time showed a significant increase in the current relative to a previously protected surface, indicating the structural loss of enamel. The thickness of the enamel layer eroded after contact with hydrochloric acid was significantly higher when compared to the one obtained with citric acid. Hence, our results showed that the enamel acid erosion is a relatively fast process, which is strongly dependent on parameters such as pH, time, acid strength and acid concentration.

Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

The peroxisome proliferator-activated receptors (PPARs) regulate genes involved in lipid and carbohydrate metabolism, and are targets of drugs approved for human use. Whereas the crystallographic structure of the complex of full length PPAR gamma and RXR alpha is known, structural alterations induced by heterodimer formation and DNA contacts are not well understood. Herein, we report a small-angle X-ray scattering analysis of the oligomeric state of hPPAR gamma alone and in the presence of retinoid X receptor (RXR). The results reveal that, in contrast with other studied nuclear receptors, which predominantly form dimers in solution, hPPAR gamma remains in the monomeric form by itself but forms heterodimers with hRXR alpha. The low-resolution models of hPPAR gamma/RXR alpha complexes predict significant changes in opening angle between heterodimerization partners (LBD) and extended and asymmetric shape of the dimer (LBD-DBD) as compared with X-ray structure of the full-length receptor bound to DNA. These differences between our SAXS models and the high-resolution crystallographic structure might suggest that there are different conformations of functional heterodimer complex in solution. Accordingly, hydrogen/deuterium exchange experiments reveal that the heterodimer binding to DNA promotes more compact and less solvent-accessible conformation of the receptor complex.

Probing the interaction of brain fatty acid binding protein (B-FABP) with model membranes

Brain fatty acid-binding protein (B-FABP) interacts with biological membranes and delivers polyunsaturated fatty acids (FAs) via a collisional mechanism. The binding of FAs in the protein and the interaction with membranes involve a motif called "portal region", formed by two small α-helices, A1 and A2, connected by a loop. We used a combination of site-directed mutagenesis and electron spin resonance to probe the changes in the protein and in the membrane model induced by their interaction. Spin labeled B-FABP mutants and lipidic spin probes incorporated into a membrane model confirmed that BFABP interacts with micelles through the portal region and led to structural changes in the protein as well in the micelles. These changes were greater in the presence of LPG when compared to the LPC models. ESR spectra of B-FABP labeled mutants showed the presence of two groups of residues that responded to the presence of micelles in opposite ways. In the presence of lysophospholipids, group I of residues, whose side chains point outwards from the contact region between the helices, had their mobility decreased in an environment of lower polarity when compared to the same residues in solution. The second group, composed by residues with side chains situated at the interface between the α-helices, experienced an increase in mobility in the presence of the model membranes. These modifications in the ESR spectra of B-FABP mutants are compatible with a less ordered structure of the portal region inner residues (group II) that is likely to facilitate the delivery of FAs to target membranes. On the other hand, residues in group I and micelle components have their mobilities decreased probably as a result of the formation of a collisional complex. Our results bring new insights for the understanding of the gating and delivery mechanisms of FABPs.

Probing unoccupied electronic states in aqueous solutions

Water is one of the most common compounds on earth and is essential for all biological activities. Water has, however, been a mystery for many years due to the large number of unusual chemical and physical properties, e.g. decreased volume during melting and maximum density at 4 °C. The origin of the anomalies behavior is the nature of the hydrogen bond. This thesis will presented an x-ray absorption spectroscopy (XAS) study to reveal the hydrogen bond structure in liquid water. The x-ray absorption process is faster than a femtosecond and thereby reflects the molecular orbital structure in a frozen geometry locally around the probed water molecules. The results indicate that the electronic structure of liquid water is significantly different from that of the solid and gaseous forms. The molecular arrangement in the first coordination shell of liquid water is actually very similar as the two-hydrogen-bonded configurations at the surface of ice. This discovery suggests that most molecules in liquid water have two-hydrogen-bonded configurations with one donor and one acceptor hydrogen bond compared to the four-hydrogen-bonded tetrahedral structure in ice. This result is controversial since the general picture is that the structure of liquid water is very similar to the structure of ice. The results are, however, consistent with x-ray and neutron diffraction data but reveals serious discrepancies with structures based on current molecular dynamics simulations. The two-hydrogen-bond configuration in liquid water is rigid and heating from 25 °C to 90 °C introduce a minor change in the hydrogen-bonded configurations. Furthermore, XAS studies of water in aqueous solutions show that ion hydration does not affect the hydrogen bond configuration of the bulk. Only water molecules in the close vicinity to the ions show changes in the hydrogen bond formation. XAS data obtained with fluorescence yield are sensitive enough to resolved electronic structure of water molecules in the first hydration sphere and to distinguish between different protonated species. Hence, XAS is a useful tool to provide insight into the local electronic structure of a hydrogen-bonded liquid and it is applied for the first time on water revealing unique information of high importance.

Contribution of Non-Covalent Interactions and Electronic Effects on the Conformational Landscape and Tautomeric Equilibria of Molecules and Molecular Complexes: Structural and Dynamical Data from Rotational Spectroscopy

This thesis concerns the study of complex conformational surfaces and tautomeric equilibria of molecules and molecular complexes by quantum chemical methods and rotational spectroscopy techniques. In particular, the focus of this research is on the effects of substitution and noncovalent interactions in determining the energies and geometries of different conformers, tautomers or molecular complexes. The Free-Jet Absorption Millimeter Wave spectroscopy and the Pulsed-Jet Fourier Transform Microwave spectroscopy have been applied to perform these studies and the obtained results showcase the suitability of these techniques for the study of conformational surfaces and intermolecular interactions. The series of investigations of selected medium-size molecules and complexes have shown how different instrumental setups can be used to obtain a variety of results on molecular properties. The systems studied, include molecules of biological interest such as anethole and molecules of astrophysical interest such as N-methylaminoethanol. Moreover halogenation effects have been investigated on halogen substituted tautomeric systems (5-chlorohydroxypyridine and 6-chlorohydroxypyridine), where it has shown that the position of the inserted halogen atom affects the prototropic equilibrium. As for fluorination effects, interesting results have been achieved investigating some small complexes where a molecule of water is used as a probe to reveal the changes on the electrostatic potential of different fluorinated compounds: 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine. While in the case of the molecular complex between water and 2-fluoropyridine and 3-fluoropyridine the geometry of the complex with one water molecule is analogous to that of pyridine with the water molecule linked to the pyridine nitrogen, the case of pentafluoropyridine reveals the effect of perfluorination and the water oxygen points towards the positive center of the pyridine ring. Additional molecular adducts with a molecule of water have been analyzed (benzylamine-water and acrylic acid-water) in order to reveal the stabilizing driving forces that characterize these complexes.

Microscopic and Spectroscopic Methods for Probing the Clay Water Interface

Clay minerals have a fundamental importance in many processes in soils and sediments such as the bioavailability of nutrients, water retention, the adsorption of common pollutants, and the formation of an impermeable barrier upon swelling. Many of the properties of clay minerals are due to the unique environment present at the clay mineral/water interface. Traditional techniques such as X-ray diffraction (XRD) and absorption isotherms have provided a wealth of information about this interface but have suffered from limitations. The methods and results presented herein are designed to yield new experimental information about the clay mineral/water interface.A new method of studying the swelling dynamics of clay minerals was developed using in situ atomic force microscopy (AFM). The preliminary results presented here demonstrate that this technique allows one to study individual clay mineral unit layers, explore the natural heterogeneities of samples, and monitor swelling dynamics of clay minerals in real time. Cation exchange experiments were conducted monitoring the swelling change of individual nontronite quasi-crystals as the chemical composition of the surrounding environment was manipulated several times. A proof of concept study has shown that the changes in swelling are from the exchange of interlayer cations and not from the mechanical force of replacing the solution in the fluid cell. A series of attenuated total internal reflection Fourier transform infrared spectroscopy (ATR-FTIR) experiments were performed to gain a better understanding of the organization of water within the interlayer region of two Fe-bearing clay minerals. These experiments made use of the Subtractive Kramers-Kronig (SKK) Transform and the calculation of difference spectra to obtain information about interfacial water hidden within the absorption bands of bulk water. The results indicate that the reduction of structural iron disrupts the organization of water around a strongly hydrated cation such as sodium as the cation transitions from an outer-sphere complex with the mineral surface to an inner-sphere complex. In the case of a less strongly hydrated cation such as potassium, reduction of structural iron actually increases the ordering of water molecules at the mineral surface. These effects were only noticed with the reduction of iron in the tetrahedral sheet close to the basal surface where the increased charge density is localized closer to the cations in the interlayer.

[Impact of tobacco use on the periodontium--an update. Part 2: Clinical and radiographic changes in the periodontium and effects on periodontal and implant therapy]

This third part of a series of publications from the Swiss task force "Smoking--Intervention in the private dental office" on the topic "tobacco use and dental medicine" describes the clinical and radiographic changes of the periodontium within smokers as well as the consequences of tobacco use on periodontal and implant therapy. With increased use of tobacco, patients show higher periodontal probing depths, increased clinical attachment loss, more alveolar bone resorption, a higher prevalence of gingival recessions, and a higher risk for tooth loss. In contrast to this, with smokers, the clinical characteristics of gingival inflammation or bleeding on periodontal probing are less established. Smokers show less positive results after conventional, surgical and regenerative periodontal therapy. The benefits of mucogingval surgery are reduced and less successful in smokers. Moreover, smoking impairs the osseointegration of oral implants and is at least partly responsible for a majority of biological complications in implant dentistry, such as periimplantitis. Based on the present understanding of periodontal diseases, the clinical findings, and the specific therapeutic outcomes with smokers, it appears to be reasonable, next to the current classification of periodontal diseases, to use the term "smokers periodontitis".

Changes of periodontal parameters following apical surgery: a prospective clinical study of three incision techniques

AIM: To evaluate periodontal changes following apical surgery, and to relate changes to the type of incision and to the type of restoration present at the gingival margin (GM). METHODOLOGY: Periodontal parameters [probing depth (PD), level of GM and clinical attachment, plaque and bleeding indices] were recorded at baseline and 1 year following apical surgery. The periodontal changes were calculated and assessed with respect to the incision technique (intrasulcular incision, papilla base incision and submarginal incision), as well as to the presence and type of a restoration margin in contact with the gingiva. RESULTS: One hundred and eighty-four teeth could be evaluated. No significant differences between the three incision techniques were found regarding changes in PDs and plaque index over time. However, significant differences between the intrasulcular and submarginal incisions were found for changes in levels of GM and clinical attachment. For example, with the intrasulcular incision, there was a mean recession of 0.42 mm at buccal sites, whereas using the submarginal incision there was a gain of 0.05 mm. No statistically significant influence could be demonstrated for the presence and type of restoration margins, or the smoking habit of the patient. CONCLUSION: The type of incision was found to affect changes significantly in periodontal parameters within an observation period of 1 year following apical surgery, whereas the restoration margin and smoking habit did not prove to have any significant effect.

Radiographic bone level changes of implant-supported restorations in edentulous and partially dentate patients: 5-year results.

PURPOSE To evaluate and compare crestal bone level changes and peri-implant status of implant-supported reconstructions in edentulous and partially dentate patients after a minimum of 5 years of loading. MATERIALS AND METHODS All patients who received a self-tapping implant with a microstructured surface during the years 2003 and 2004 at the Department of Prosthodontics, University of Bern, were included in this study. The implant restorations comprised fixed and removable prostheses for partially and completely edentulous patients. Radiographs were taken immediately after surgery, at impression making, and 1 and 5 years after loading. Crestal bone level (BIC) was measured from the implant shoulder to the first bone contact, and changes were calculated over time (ΔBIC). The associations between pocket depth, bleeding on probing (BOP), and ΔBIC were assessed. RESULTS Sixty-one implants were placed in 20 patients (mean age, 62 ± 7 years). At the 5-year follow-up, 19 patients with 58 implants were available. Implant survival was 98.4% (one early failure; one patient died). The average ΔBIC between surgery and 5-year follow-up was 1.5 ± 0.9 mm and 1.1 ± 0.6 mm for edentulous and partially dentate patients, respectively. Most bone resorption (50%, 0.7 mm) occurred during the first 3 months (osseointegration) and within the first year of loading (21%, 0.3 mm). Mean annual bone loss during the 5 years of loading was < 0.12 mm. Mean pocket depth was 2.6 ± 0.7 mm. Seventeen percent of the implant sites displayed BOP; the frequency was significantly higher in women. None of the variables were significantly associated with crestal bone loss. CONCLUSION Crestal bone loss after 5 years was within the normal range, without a significant difference between edentulous and partially dentate patients. In the short term, this implant system can be used successfully for various prosthetic indications.

Probing the Electrocatalytic Oxygen Reduction Reaction Reactivity of Immobilized Multicopper Oxidase CueO

The bioelectrocatalytic (oxygen reduction reaction, ORR) properties of the multicopper oxidase CueO immobilized on gold electrodes were investigated. Macroscopic electrochemical techniques were combined with in situ scanning tunneling microscopy (STM) and surface-enhanced Raman spectroscopy at the ensemble and at the single-molecule level. Self-assembled monolayer of mercaptopropionic acid, cysteamine, and p-aminothiophenol were chosen as redox mediators. The highest ORR activity was observed for the protein attached to amino-terminated adlayers. In situ STM experiments revealed that the presence of oxygen causes distinct structure and electronic changes in the metallic centers of the enzyme, which determine the rate of intramolecular electron transfer and, consequently, affect the rate of electron tunneling through the protein. Complementary Raman spectroscopy experiments provided access for monitoring structural changes in the redox state of the type 1 copper center of the immobilized enzyme during the CueO-catalyzed oxygen reduction cycle. These results unequivocally demonstrate the existence of a direct electronic communication between the electrode substrate and the type 1 copper center.