Steric constraints as folding coadjuvant

Through the analyses of the Miyazawa-Jernigan matrix it has been shown that the hydrophobic effect generates the dominant driving force for protein folding. By using both lattice and off-lattice models, it is shown that hydrophobic-type potentials are indeed efficient in inducing the chain through nativelike configurations, but they fail to provide sufficient stability so as to keep the chain in the native state. However, through comparative Monte Carlo simulations, it is shown that hydrophobic potentials and steric constraints are two basic ingredients for the folding process. Specifically, it is shown that suitable pairwise steric constraints introduce strong changes on the configurational activity, whose main consequence is a huge increase in the overall stability condition of the native state; detailed analysis of the effects of steric constraints on the heat capacity and configurational activity are provided. The present results support the view that the folding problem of globular proteins can be approached as a process in which the mechanism to reach the native conformation and the requirements for the globule stability are uncoupled.

Zidovudine-Loaded PLA and PLA-PEG Blend Nanoparticles: Influence of Polymer Type on Phagocytic Uptake by Polymorphonuclear Cells

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

The X-ray crystallographic structure of Escherichia coli branching enzyme

Branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch. We report the 2.3-Angstrom crystal structure of glycogen branching enzyme from Escherichia coli. The enzyme consists of three major domains, an NH2-terminal seven-stranded beta-sandwich domain, a COOH-terminal domain, and a central alpha/beta-barrel domain containing the enzyme active site. While the central domain is similar to that of all the other amylase family enzymes, branching enzyme shares the structure of all three domains only with isoamylase. Oligosaccharide binding was modeled or branching enzyme using the enzyme-oligosaccharide complex structures of various alpha-amylases and cyclodextrin glucanotransferase and residues were implicated in oligosaccharide binding. While most of the oligosaccharides modeled well in the branching enzyme structure, an approximate 50degrees rotation between two of the glucose units was required to avoid steric clashes with Trp(298) of branching enzyme. A similar rotation was observed in the mammalian alpha-amylase structure caused by an equivalent tryptophan residue in this structure. It appears that there are two binding modes for oligosaccharides in these structures depending on the identity and location of this aromatic residue.

Interfacial surface charge and free accessibility to the PLA(2)-active site-like region are essential requirements for the activity of Lys49 PLA(2) homologues

Lys49 phospholipase A(2) homologues are highly myotoxic and cause extensive tissue damage but do not display hydrolytic activity towards natural phospholipids. The binding of heparin, heparin derivatives and polyanionic compounds such as suramin result in partial inhibition (up to 60%) of the myotoxic effects due to a change in the overall charge of the interfacial surface. In vivo experiments demonstrate that polyethylene glycol inhibits more than 90% of the myotoxic effects without exhibiting secondary toxic effects. The crystal structure of bothropstoxin-I complexed with polyethylene glycol reveals that this inhibition is due to steric hindrance of the access to the PLA(2)-active site-like region. These two inhibitory pathways indicate the roles of the overall surface charge and free accessibility to the PLA2-active site-like region in the functioning of Lys49 phospholipases A(2) homologues. Molecular dynamics simulations, small angle X-ray scattering and structural analysis indicate that the oligomeric states both in solution and in the crystalline states of Lys49 phospholipases A2 are principally mediated by hydrophobic contacts formed between the interfacial surfaces. These results provide the framework for the potential application of both clinically approved drugs for the treatment of Viperidae snakebites. (c) 2006 Elsevier Ltd. All rights reserved.

The water factor in the protein-folding problem

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

Hydrodechlorination of 1,2-dichloroethane by rhodium catalysts under water gas shift reaction conditions

Homogeneous catalysts prepared from rhodium trichloride in aqueous aromatic amines have been shown to reduce C-CI bonds under mild water gas shift conditions (T=100 degrees C, P-CO = 1.0 atm). In a 4-picoline/water solvent mixture, 1,2-dichloroethane is reduced to ethylene and ethane in yields compatible with the consumption of the reducing agent CO and with the formation of CO2. Variation of the catalyst solutions by using different substituted pyridines shows a pattern of catalytic activity parallel to that reported previously for H-2 production from the shift reaction, There is a moderate dependence of activity on the basicity of the aromatic amine, but a methyl group at the alpha-position exercises a strong negative steric effect. Long term studies show decrease of the activity with the time perhaps due to the build up of chloride in the medium. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Structural modifications in silica sonogels prepared with additions of poly(vinyl alcohol)

Silica wet gels were prepared from acid sonohydrolysis of tetraethoxysilane (TEOS) and additions of poly(vinyl alcohol) (PVA)-water solution. Aerogels were obtained from supercritical CO(2) extraction. The samples were studied by thermal gravimetric (TG) analysis, small-angle X-ray scattering (SAXS), and nitrogen adsorption. The structure of wet gels can be described as a mass fractal with dimension D equal to 2.0 on the whole length scale experimentally probed by SAXS, from similar to 0.3 to similar to 15 nm. Pure and low-PVA-addition wet gels exhibit an upper cutoff accounting for a finite characteristic length xi of the mass fractal structure. Additions , of PVA increase without modifying D, which was attributed to a steric effect of the polymer in the structure. The pore volume fraction of the aerogels diminishes typically about 11% with respect to that of the wet gels, although nitrogen adsorption could be underestimating some porosity. The pore size distribution of the aerogels is shifted toward the mesopore region with the additions of PVA, in a straight relationship with the increase of xi in the wet gels. The thermal stability of the pore size distribution of the aerogels was studied up to 1000 degrees C.

Influência do pH sobre a estabilidade de suspensões de alumina estabilizadas eletroestericamente

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Efeitos estéricos e eletrônicos de substituintes alquilas em catalisadores titanocênicos solúveis na polimerização sindioespecífica de estireno

Titanocenos são catalisadores solúveis conhecidos para a polimerisação estereoespecífica de olefinas pró-quirais como o estireno. Nesse trabalho descrevemos as relações entre as características do poliestireno e a estrutura do precursor do catalisador, de fato aqueles da família (RCp)2TiCl2 (R = H, etila, iso-propila, n-propila, sec-butila, n-butila, iso-amila e ciclohexila). Todos os catalisadores são ativos para a produção de poliestireno acima de zero graus centígrados. A sindiotaticidade dos polímeros são dependentes da cadeia lateral dos anéis aromáticos do titanoceno e da temperatura da polimerização. A relação entre os fatores estéricos e eletrônicos do precursor do catalisador e os produtos de polimerização são apresentados e discutidos.

The use of classification methods for modeling the antioxidant activity of flavonoid compounds

A study using two classification methods (SDA and SIMCA) was carried out in this work with the aim of investigating the relationship between the structure of flavonoid compounds and their free-radical-scavenging ability. In this work, we report the use of chemometric methods (SDA and SIMCA) able to select the most relevant variables (steric, electronic, and topological) responsible for this ability. The results obtained with the SDA and SIMCA methods agree perfectly with our previous model, in which we used other chemometric methods (PCA, HCA and KNN) and are also corroborated with experimental results from the literature. This is a strong indication of how reliable the selection of variables is.

Interactions between the non-ionic surfactant C(12)E(5) and poly(ethylene oxide) studied using dynamic light scattering and fluorescence quenching

Dynamic light scattering measurements have been made to elucidate changes in the coil conformation of a high molecular weight poly(ethylene oxide) (PEG) fraction when the non-ionic surfactant C(12)E(5) is present in dilute solutions. The measurements were made at 20 degrees C as functions of(a) the C(12)E(5) concentration at constant PEO concentration, (b) the PEO concentration at constant C(12)E(5) concentration, and (c) the C(12)E(5)/PEO concentration ratio. The influence of temperature on the interactions in terms of the relaxation time distributions was also examined up to the cloud point. It was found that when the C(12)E(5)/PEO weight ratio was >2 and when the temperature was >14 degrees C, the correlation functions became bimodal with well-separated components. The fast mode derives fi om individual surfactant micelles which are present in the solution at high number density. The appearance of the slow mode, which dominates the scattering, is interpreted as resulting from the formation of micellar clusters due to an excluded-volume effect when the high molar mass (M = 6 x 10(5)) PEO is added to the surfactant solution. It is shown that the micellar clusters form within the PEO coils and lead to a progressive swelling of the latter for steric reasons. The dimensions of the PEO/C(12)E(5) complex increase with increasing surfactant concentration to a value of R(H) approximate to 94 nm (R(g) approximate to 208 nm) at C-C12E5 = 3.5%. Fluorescence quenching measurements show that the average aggregation number of C(12)E(5) increases significantly on addition of the high molar mass PEG. With increasing temperature toward the cloud point the clusters increase in number density and/or become larger. The cloud point is substantially lower than that for C12E5 in water solution and is strongly dependent on the PEO concentration.

AN ISOCOUMARIN DERIVATIVE FROM PAEPALANTHUS BROMELIOIDES

The structure of 5,7,9,10-tetramethoxy-3-methyl-1 H-naphtho[2,3-c]pyran-1-one, C18H18O6, a derivative of a natural isocoumarin isolated from Paepalanthus bromelioides, was determined by X-ray analysis, which unequivocally confirmed the previously assigned structure. Small deviations from the standard angles, resulting from steric hindrance between the methoxyl and carbonyl groups, were observed.

Direct electron paramagnetic resonance monitoring of the peptide synthesis coupling reaction in polymeric support

This work demonstrates, for the first time. a time-resolved electron paramagnetic resonance (EPR) monitoring of a chemical reaction occurring in a polymeric structure. The progress of the coupling of a N-alpha-tert-butyloxycarbonyl-2.2.6.6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (Boc-TOAC) spin probe to a model peptide-resin was followed through EPR spectra. Progressive line broadening of EPR peaks was observed, indicative of an increased population of immobilized spin probe molecules attached to the solid support. The time for spectral stabilization of this process coincided with that determined in a previous Coupling study. thereby validating this in situ quantitative monitoring of the reaction. In addition, the influence of polymer swelling degree and solvent viscosity, as well as of the steric hindrance within beads. on the rate of coupling reaction was also addressed. A deeper evaluation of the latter effect was possible by determining unusual polymer parameters such as the average site-site distance and site-concentration within resin beads in each solvent system. (c) 2006 Elsevier Ltd. All rights reserved.

Synthesis and functionalization of magnetite nanoparticles with different amino-functional alkoxysilanes

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Sensitive Affimer and Antibody Based Impedimetric Label-Free Assays for C-Reactive Protein

C-reactive protein (CRP) is an acute phase protein whose levels are increased in many disorders. Levels greater than 3 mu g/mL serum have hitherto been considered to indicate pathology, but there is increasing interest in assessments between 0.1 and 10 mu g/mL, which have been found to correlate with severity of risk for cardiovascular disease. We report herein the generation of both antibody and Affimer based impedance immunoassays for CRP that are substantially more sensitive than clinically utilized immunonephelometry and immunoturbidity assessments. Significant in this study is not only the use of a constrained peptide to detect a clinically important target but also that derived electrochemical impedance assays can be highly sensitive even with probes whose relatively weak (mu M) affinities are not amenable to target detection by surface plasmon resonance (SPR). Key to this finding is acknowledging that receptive surfaces of comparatively low initial steric bulk and charge transfer resistance are especially primed to be highly responsive to target binding in electroanalytical assays of this type.