A Hooke׳s law-based approach to protein folding rate.

Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke׳s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons among structural classes and folding mechanisms were carried out showing the good performance of our model with proteins of different types. The present model constitutes a simple rationale for the structural and energetic factors involved in protein folding kinetics.

Global stability of protein folding from an empirical free energy function.

The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded and unfolded states and electrostatic interactions between residues. The parameters of the model were fixed from a protein data set whose unfolding free energy has been measured at the "standard" experimental conditions proposed by Maxwell et al. (2005) and a large data set of 1151 monomeric proteins obtained from the PDB. A blind test with proteins taken from ProTherm database, at similar experimental conditions, was carried out. We found a good correlation with the test data set, proving the effectiveness of our model for predicting protein folding free energies in considered standard conditions. Such a prediction compares favorably against estimations made with FoldX's function and the force field GROMOS96. This model constitutes a valuable tool for the fast evaluation of protein structure stability in 3D structure prediction methods.

Optical and mechanical properties of nanofibrillated cellulose: Toward a robust platform for next-generation green technologies.

Nanofibrillated cellulose, a polymer that can be obtained from one of the most abundant biopolymers in nature, is being increasingly explored due to its outstanding properties for packaging and device applications. Still, open challenges in engineering its intrinsic properties remain to address. To elucidate the optical and mechanical stability of nanofibrillated cellulose as a standalone platform, herein we report on three main findings: (i) for the first time an experimental determination of the optical bandgap of nanofibrillated cellulose, important for future modeling purposes, based on the onset of the optical bandgap of the nanofibrillated cellulose film at Eg≈275 nm (4.5 eV), obtained using absorption and cathodoluminescence measurements. In addition, comparing this result with ab-initio calculations of the electronic structure the exciton binding energy is estimated to be Eex≈800 meV; (ii) hydrostatic pressure experiments revealed that nanofibrillated cellulose is structurally stable at least up to 1.2 GPa; and (iii) surface elastic properties with repeatability better than 5% were observed under moisture cycles with changes of the Young modulus as large as 65%. The results obtained show the precise determination of significant properties as elastic properties and interactions that are compared with similar works and, moreover, demonstrate that nanofibrillated cellulose properties can be reversibly controlled, supporting the extended potential of nanofibrillated cellulose as a robust platform for green-technology applications.