The electrostatic properties of a molecule are often essential in determining its behavior; as such, the ability to approximate these electrostatic potentials computationally is often essential to obtaining a full understanding of how these molecules function. An approximate, analytical solution to the (linearized) Poisson-Boltzmann equation is proposed that is suitable for realistic biomolecules of virtually any size. A comparison with accepted numerical approaches on a large test set of biomolecular structures shows that the proposed method is considerably less expensive computationally, yet accurate enough to be considered as a possible alternative. The utility of the approach is demonstrated by computing and analyzing the electrostatic potential generated by full capsid of the tobacco ringspot virus (half a million atoms) at atomic resolution. The details of the potential distribution on the molecular surface sheds light on the mechanism behind the high selectivity of the capsid to the viral RNA. These results are generated with the modest computational power of a desktop PC. The applicability of the analytical approximation as an initial guess for traditional numerical methods as a means of improving the convergence of iterative solutions is investigated and found to be quite promising. / Master of Science

In recent years the nitrated polycyclic aromatic hydrocarbons (nitroPAH's) have been recognized as powerful mutagens in the Ames Salmonella test. Most nitroPAH’s are direct-acting mutagens in the Ames test i.e. they induce mutation in the absence of S9, and appear to be activated through nitroreduction by bacterial enzymes. Others, however, such as 3-nitroperylene, are indirect-acting mutagens and show maximum activity only when S9 is present. Studies using the Ames test have indicated that the cytochrome P-450-dependent mixed function oxidase system of S9 is responsible for the activation of 3-nitroperylene to mutagenic species. However, the pattern of P-450 isozymes involved in this process appears to be different from that involved in the conversion of most PAH's, such as the standard indirect-acting mutagen benzo(a)pyrene (B(a)P), to proximate mutagens. 6-NitroB(a)P, in contrast, behaves in an analogous manner to its parent hydrocarbon. Using appropriate Salmonella mutants, the activation of 3-nitroperylene was found to require bacterial involvement, although the nature of the bacterial contribution has yet to be determined. Studies with other mutants have indicated that nitroreduction, at least as a primary activation step, does not appear to be important. Incubation of 3-nitroperylene with high concentrations of S9 led to the formation of a number of metabolites, of which phenolic derivatives were prominent. In addition, S9-derived microsomes were able to catalyse the conversion of 3-nitroperylene to species which were able to bind to protein and DNA. Under the conditions employed in these binding studies, 3-nitroperylene appears to be acting like a simple PAH, and such experiments with very high concentrations of liver protein may be unrepresentative of the processes responsible for the mutagenesis of the compound. / Thesis / Master of Science (MSc)

O estudo de macrointeraçães na matriz extracelular (ECM) foi abordado em três modelos; a interação colágeno/colagenase, a interação colágeno/fibronectina e finalmente, a evolução da família enzimática das metaloproteinases de matriz (MMP). As MMP se caracterizam por sua notável especificidade contra componentes da ECM. As colagenases intersticiais, os membros mais estudados, clivam os colágenos intersticiais em um único ponto da molécula produzindo dois fragmentos característicos. Usando a hipótese da hidropaticidade complementar, a qual estipula que peptídeos codificados por sequências nucleotídicas complementares podem interagir entre si, foi possível caracterizar a sequência SQNPVQP em colagenase de fibroblasto ou SSNPIQP em colagenase de neutrófilo como importantes na interação das respectivas enzimas com o colágeno nativo. O fato da fibronectina, outro componente da ECM, ligar-se no mesmo domínio do colágeno clivado pelas colagenases possibilitou a utilização da mesma abordagem acima (hidropaticidade complementar) no estudo da interação colágeno/fibronectina. Sendo assim, foi possível caracterizar a sequência TNEGVMY da fibronectina como importante na interação com o colágeno. Adjacente a este sítio na fibronectina, existe uma sequência (AAHEEIC) que é homóloga ao sítio de ligação ao zinco presente nas MMP. Isto originou a possibilidade de que zinco pudesse modular a interação colágeno/fibronectina. De fato, zinco aumentou especificamente a ligação entre colágeno e fibronectina. Finalmente, abordou-se alguns aspectos filogenéticos da família das MMP. Foi caracterizada uma relação filogenética entre o núcleo enzimático das MMP e o domínio correspondente tanto na protease de Serratia como na protease B de Erwinia chrysanthemi, membros da mesma família de metaloproteinases bacterianas. Sendo assim, a atividade catalítica das MMP pode ter sido herdada das metaloproteinases bacterianas, enquanto a especificidade ao substrato talvez se constitua em uma aquisição das MMP eucarióticas. / The study of extracellular matrix (ECM) macrointeractions was approached in three models: the collagen/collagenase interaction, the collagen/fibronectin interaction and the molecular evolution of the matrix metalloproteinase (MMP) family of enzymes. MMP is characterized by its remarkable specificity against ECM components. Interstitial collagenases, the best studied members, attack interstitial collagens at a unique site producing two fragments. Using the complementary hydropathy hypothesis that states that peptides encoded by complementary nucleotide sequence can interact one to another, it was possible to characterize the sequence SQNPVQP (in fibroblast collagenase) or SSNPIQP (in neutrophil collagenase) as important in the interaction of the respective enzymes with collagen. The fact that fibronectin, another ECM component, binds at the same domain on collagen that is cleaved by collagenases arose the possibility of using the same approach (complementary hydropathy) in the study of collagen/fibronectin interaction. It was possible to characterize the fibronectin sequence TNEGVMY as important in the interaction with collagen. Adjacent to this site, there is a sequence (AAHEEIC) that shows an homology to the zinc-binding site present in several MMP. Therefore, zinc could be a modulator the collagen/fibronectin interaction. Finnaly, some phylogenetic aspects of the MMP family were studied. It was characterized a phylogenetic relationship between the catalytic core of MMP and the corresponding domain in Serratia protease and protease B from E. chrysanthemi, members of the same family of bacterial metalloproteinases. The catalytic activity of MMP can have evolved from the bacterial metaloproteinases whereas the substrate specificity is an acquisition of eukaryotic MMP

Obesity is a metabolic disorder that results in elevated levels of free fatty acids and triglycerides in the blood circulation, which further leads to accumulation of lipids within various tissues. Like in other similar metabolic disorders, obesity is thought to be originated from structural and regulatory changes in macromolecular assemblies. This current study aims to investigate the effects of obesity on macromolecular alterations in order to characterize Berlin fat mouse inbred (BFMI) lines which arenew models for the obesity research that may contribute to understanding of spontaneous obesity without induction of a high fat diet. Attenuated Total Reflectance - Fourier Transform Infrared (ATR-FTIR) spectroscopy was used to characterize content and structure of macromolecules in male and female control (DBA/2J) and BFMI lines / namely BFMI856, BFMI860 and BFMI861, in two different adipose tissues / inguinal fat (IF) which is subcutaneous adipose tissue (SAT), gonadal fat (GF) which is visceral adipose tissue (VAT). Structural and compositional alterations in proteins, lipids, saturated and unsaturated lipid contents, nucleic acid, collagen and glycogen contents and variations in the lipid chain length were determined. BFMI860 and BFMI861 lines were found to be the most affected lines since they showed the indications of lipid peroxidation and insulin resistance more severely as they had lower glycogen content in all tissues and lower unsaturated lipid content especially in IF adipose tissues. Moreover, structural changes in lipids were observed especially in male GF adipose tissues of BFMI856 and BFMI861 lines. Protein content decreased significantly specifically in female IF adipose tissues but no change was observed in the structure. Furthermore, BFMI852 line was found to be affected different than other lines and had an effect on especially female IF. To conclude, obesity induced changes differ in BFMI lines according to the gender, adipose tissue type and distinctness in the strains.

Delivery of macromolecules into mammalian cells in vitro and in vivo has enabled new areas of research and offers the potential for powerful new treatment options. Recent research has generated many delivery platforms but these solutions remain limited by scope, potency and safety. We have reported a superpositively charged green fluorescent protein (+36 GFP) with the ability to deliver nucleic acids into a variety of mammalian cell lines in vitro and to potently deliver protein in vitro and in vivo without toxicity. These results have directed us to identify a subset of naturally occurring human proteins with similar but previously unknown cell-penetrating and protein delivery properties. Preliminary efforts have been made towards establishing the therapeutic potential for supercharged proteins replacement of the cytosolic enzyme, argininosuccinate synthase. Preliminary efforts have also been made towards enhancing endosomal escape with \(His_{39} GFP\).

X-ray absorption is not only element specific, but atom specific: two atoms of the same element in different states or in different neighbourhoods will have slightly different absorption characteristics. These energy dependent atomic form factors are carried over to the diffraction intensities. The atomic form factors are sensitive not only to the the energy of the X-ray but also the diffraction criteria; providing individual local physical data at different ratios in various diffractions. This process is referred to as site selectivity, it is unique to Diffraction Spectroscopy, and is achieved only when the sample is in crystal form. Through this work, a technique has been devised to site-separate two atoms of iron from within a protein, that builds on prior small unit cell Diffraction Anomalous Fine Structure experiments and harnesses the collection and processing software commonly used in large unit cell crystallography. A technique (dev + PCA) has been developed to retrieve the small signals from individual atom-labels out of the large and noisy background of real diffraction taken across a spectrum. The intensity of the diffractions are calculated by integrating over multiple images, profiling spots, merging datasets, and scaling across the whole spectrum. This thesis explores how Diffraction Spectroscopy can be used effectively on large unit cells, namely those of proteins. Site-selective absorption experiments were conducted on large unit cell crystals at a 3rd generation beamline, exclusively using existing equipment. The spectra generated were limited in scope but are an adequate proof of concept.

O estudo de macrointeraçães na matriz extracelular (ECM) foi abordado em três modelos; a interação colágeno/colagenase, a interação colágeno/fibronectina e finalmente, a evolução da família enzimática das metaloproteinases de matriz (MMP). As MMP se caracterizam por sua notável especificidade contra componentes da ECM. As colagenases intersticiais, os membros mais estudados, clivam os colágenos intersticiais em um único ponto da molécula produzindo dois fragmentos característicos. Usando a hipótese da hidropaticidade complementar, a qual estipula que peptídeos codificados por sequências nucleotídicas complementares podem interagir entre si, foi possível caracterizar a sequência SQNPVQP em colagenase de fibroblasto ou SSNPIQP em colagenase de neutrófilo como importantes na interação das respectivas enzimas com o colágeno nativo. O fato da fibronectina, outro componente da ECM, ligar-se no mesmo domínio do colágeno clivado pelas colagenases possibilitou a utilização da mesma abordagem acima (hidropaticidade complementar) no estudo da interação colágeno/fibronectina. Sendo assim, foi possível caracterizar a sequência TNEGVMY da fibronectina como importante na interação com o colágeno. Adjacente a este sítio na fibronectina, existe uma sequência (AAHEEIC) que é homóloga ao sítio de ligação ao zinco presente nas MMP. Isto originou a possibilidade de que zinco pudesse modular a interação colágeno/fibronectina. De fato, zinco aumentou especificamente a ligação entre colágeno e fibronectina. Finalmente, abordou-se alguns aspectos filogenéticos da família das MMP. Foi caracterizada uma relação filogenética entre o núcleo enzimático das MMP e o domínio correspondente tanto na protease de Serratia como na protease B de Erwinia chrysanthemi, membros da mesma família de metaloproteinases bacterianas. Sendo assim, a atividade catalítica das MMP pode ter sido herdada das metaloproteinases bacterianas, enquanto a especificidade ao substrato talvez se constitua em uma aquisição das MMP eucarióticas. / The study of extracellular matrix (ECM) macrointeractions was approached in three models: the collagen/collagenase interaction, the collagen/fibronectin interaction and the molecular evolution of the matrix metalloproteinase (MMP) family of enzymes. MMP is characterized by its remarkable specificity against ECM components. Interstitial collagenases, the best studied members, attack interstitial collagens at a unique site producing two fragments. Using the complementary hydropathy hypothesis that states that peptides encoded by complementary nucleotide sequence can interact one to another, it was possible to characterize the sequence SQNPVQP (in fibroblast collagenase) or SSNPIQP (in neutrophil collagenase) as important in the interaction of the respective enzymes with collagen. The fact that fibronectin, another ECM component, binds at the same domain on collagen that is cleaved by collagenases arose the possibility of using the same approach (complementary hydropathy) in the study of collagen/fibronectin interaction. It was possible to characterize the fibronectin sequence TNEGVMY as important in the interaction with collagen. Adjacent to this site, there is a sequence (AAHEEIC) that shows an homology to the zinc-binding site present in several MMP. Therefore, zinc could be a modulator the collagen/fibronectin interaction. Finnaly, some phylogenetic aspects of the MMP family were studied. It was characterized a phylogenetic relationship between the catalytic core of MMP and the corresponding domain in Serratia protease and protease B from E. chrysanthemi, members of the same family of bacterial metalloproteinases. The catalytic activity of MMP can have evolved from the bacterial metaloproteinases whereas the substrate specificity is an acquisition of eukaryotic MMP

The majority of state-of-the-art polymeric membranes for industrial or medical applications are fabricated by phase inversion. Complexation induced phase separation (CIPS)—a surprising variation of this well-known process—allows direct fabrication of hybrid membranes in existing facilities. In the CIPS process, a first step forms the thin metal-rich selective layer of the membrane, and a succeeding step the porous support. Precipitation of the selective layer takes place in the same solvent used to dissolve the polymer and is induced by a small concentration of metal ions. These ions form metal-coordination-based crosslinks leading to the formation of a solid skin floating on top of the liquid polymer film. A subsequent precipitation in a nonsolvent bath leads to the formation of the porous support structure. Forming the dense layer and porous support by different mechanisms while maintaining the simplicity of a phase inversion process, results in unprecedented control over the final structure of the membrane. The thickness and morphology of the dense layer as well as the porosity of the support can be controlled over a wide range by manipulating simple process parameters. CIPS facilitates control over (i) the thickness of the dense layer throughout several orders of magnitude—from less than 15 nm to more than 6 μm, (ii) the type and amount of metal ions loaded in the dense layer, (iii) the morphology of the membrane surface, and (iv) the porosity and structure of the support. The nature of the CIPS process facilitates a precise loading of a high concentration of metal ions that are located in only the top layer of the membrane. Moreover, these metal ions can be converted—during the membrane fabrication process—to nanoparticles or crystals. This simple method opens up fascinating possibilities for the fabrication of metal-rich polymeric membranes with a new set of properties. This dissertation describes the process in depth and explores promising applications: (i) catalytic membranes containing palladium nanoparticles (PdNPs), (ii) antibiofouling tight-UF membranes containing silver chloride (AgCl) crystals, and (iii) palladiumrich PBI hollow fibers for H2 recovery.

This article presents current aspects of transvascular exchange for solutes and water in the microcirculation. Also discussed are various concepts concerning the modulation of the barrier in inflammatory-like states, as well as information describing the receptor-operated channels in endothelial cells and their processing.

No description available.