Deciphering the role of the thermodynamic and kinetic stabilities of SH3 domains on their aggregation inside bacteria

Abstract

The formation of insoluble deposits by globular proteins underlies the onset of many human diseases. Recent studies suggest a relationship between the thermodynamic stability of proteins and their in vivo aggregation. However, it has been argued that, in the cell, the occurrence of irreversible aggregation might shift the system from equilibrium, in such a way that it could be the rate of unfolding and associated kinetic stability instead of the conformational stability that controls protein deposition. This is an important but difficult to decipher question, because kinetic and thermodynamic stabilities appear usually correlated. Here we address this issue by comparing the in vitro folding kinetics and stability features of a set of non-natural SH3 domains with their aggregation properties when expressed in bacteria. In addition, we compare the in vitro stability of the isolated domains with their effective stability in conditions that mimic the cytosolic environment. Overall, the data argue in favor of a thermodynamic rather than a kinetic control of the intracellular aggregation propensities of small globular proteins in which folding and unfolding velocities largely exceed aggregation rates. These results have implications regarding the evolution of proteins.

Sequence-Based Prediction of Protein Solubility

“…1a) is provided by considering the correlation that was recently reported between protein aggregation rates and mRNA expression levels, which arises as a consequence of the stringent requirement for proteins to remain soluble in order to function at the concentrations at which they are expressed in the cell. 17,[29][30][31][32][33] On the basis of this observation, we demonstrated that it is possible to estimate the solubility of recombinant human proteins in E. coli from the corresponding maximal mRNA expression levels. 20 Here, we used this approach to provide an alternative prediction of the solubility scores provided by Niwa et al 19 finding a very high correlation (Fig.…”

Contribution of Disulfide Bonds to Stability, Folding, and Amyloid Fibril Formation: The PI3-SH3 Domain Case

“…Because protein aggregation requires at least local backbone fluctuations and in many cases partial unfolding (12,14), the deposition propensity of globular proteins appears to be linked to their thermodynamic and/or kinetic stability (10), in such a way that mutations or environmental conditions that destabilize the native structure or increase unfolding rates are associated to pathological phenotypes in several protein models (6,24). This could be one of the underlying reasons why proteins that function in harsh environments, such as the extracellular space, have evolved disulfide bonds (48).…”

Protein aggregation profile of the human kinome

“…This has allowed the development of a set of algorithms able to predict aggregation-prone regions in protein sequences as well as the overall aggregation propensity of polypeptides (Castillo et al, 2010; Hamodrakas, 2011). Several of these programs are well suited for the analysis of large protein sets, among them AGGRESCAN, an algorithm previously developed by our group (Conchillo-Sole et al, 2007; de Groot et al, 2012), which displays a high power to predict in vivo protein aggregation (Belli et al, 2011).…”