Analyzing the effect of homogeneous frustration in protein folding

The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins. © 2013 Wiley Periodicals, Inc.

Aplicação do copolímero PLA/PGA adicionado ao fosfato de cálcio ao redor de implantes osseointegráveis instalados sem estabilidade primária em tíbia de coelhos: estudo biomecânico, histométrico e imunoistoquímico

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Avaliação da interface osso/implante após o uso do copolímero de PLA/PGA associado a osso autógeno em coelhos: estudo biomecânico e imunohistoquímico

Pós-graduação em Odontologia - FOA

Desenvolvimento de nanopartículas de PLA e PLA-PEG para administração intranasal de zidovudina

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo da influência de argilas organofílicas no processo de biodegradação do PLA

In this study nanocomposites of PLA and organoclays Cloisite 20A and Cloisite 30B were prepared by melt intercalation. The influence from the organoclays on the biodegradation of PLA was evaluated based on the respirometry method. The incorporation of clay Cloisite 20A did not change the mineralization curve of PLA. The nanocomposite with Cloisite 30B, on the other hand, presented a different behavior, indicating a delay in the polymer biodegradation. The materials were characterized by X-ray Diffraction, Thermogravimetric Analysis and Differential Scanning Calorimetry. The materials characterization indicated nanocomposites with an intercalated structure as well as reduced thermal stability and a slight increase in the degree of crystallinity compared to the pure polymer.

Identification of folding intermediates of streblin, the most stable serine protease: biophysical analysis

Streblin, a serine proteinase from plant Streblus asper, has been used to investigate the conformational changes induced by pH, temperature, and chaotropes. The near/far UV circular dichroism activities under fluorescence emission spectroscopy and 8-aniline-1-naphthalene sulfonate (ANS) binding have been carried out to understand the unfolding of the protein in the presence of denaturants. Spectroscopic studies reveal that streblin belongs to the alpha+beta class of proteins and exhibits stability towards chemical denaturants, guanidine hydrochloride (GuHCl). The pH-induced transition of this protein is noncooperative for transition phases between pH 0.5 and 2.5 (midpoint, 1.5) and pH 2.5 and 10.0 (midpoint, 6.5). At pH 1.0 or lower, the protein unfolds to form acid-unfolded state, and for pH 7.5 and above, protein turns into an alkaline denatured state characterized by the absence of ANS binding. At pH 2.0 (1M GuHCl), streblin exists in a partially unfolded state with characteristics of amolten globule state. The protein is found to exhibit strong and predominant ANS binding. In total, six different intermediate states has been identified to show protein folding pathways.

Visualization of Protein Folding Funnels in Lattice Models

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

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

PLA/PGA copolymer as a bone substitute in maxillary sinus augmentation: histological, histometric and immunohistochemistry study in rabbits

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Uso do copolímero de PLA/PGA no processo de reparo de defeitos ósseos em tíbia de coelhos: análise histomorfométrica

Pós-graduação em Odontologia - FOA

Regeneração óssea guiada com o uso de membrana de copolímero PLA/PGA em levantamento da membrana do seio maxilar: estudo experimental com análises histomorfométrica e imunoistoquímica

Pós-graduação em Odontologia - FOA

Development and characterization of cefoxitin loaded D,L-PLA nanoparticles

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

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence of the peptide behavior on temperature was tested with the commonly employed thermostat scheme consisting of one thermostat for the protein and another for the solvent. The thermostat coupling time of the protein was increased to infinity, when the protein is not in direct contact with the thermal bath, a situation known as minimally invasive thermostat. In agreement with other works, it was observed that only in the last situation the instantaneous temperature of the model protein obeys a canonical distribution. As for the folding studies, it was shown that, in the applications of the commonly utilized thermostat schemes, the systems are trapped in local minima regions from which it has difficulty escaping. With the minimally invasive thermostat the time that the protein needs to fold was reduced by two to three times. These results show that the obstacles to the evolution of the extended peptide to the folded structure can be overcome when the temperature of the peptide is not directly controlled.