How well do SMFS experiments reflect protein mechanics in vivo? For the case of extension machines like the sarcomere, SMFS seems to adequately mimic the pulling geometry since proteins are pulled apart from both ends of the polypeptide chain. Ms may also be the case for other cytoskeletal machineries, the adhesion machinery, and some mechanosensitive ion channels. Furthermore, it has been suggested that some chaperonins may pull, in a similar way, their protein substrates apart prior to their refolding (Shtilerman et al. 1999). However, the case of other unfoldase machines is not so clear-cut. tte accepted model for the case of protein translocases (from the mitochondrion, chloroplast, and endoplasmic reticulum) and compartmental proteases such as the proteasome is also a mechanical one. Nevertheless, rather than a linear pulling geometry with two attachment points, the evidence here favors a different geometry that involves a single attachment point from which the pulling would be done by threading the protein towards the entrance of a narrow channel present in these nanomachines (Sect. 8.2.3, Fig. 8.2). ttis model is mainly based on the fact that the susceptibility of substrate proteins to be unfolded by these nanomachines (in vivo) correlates more closely with the mechanical stability obtained by mechanical unfolding (using SMFS) than with thermodynamic or kinetic stability (measured in vitro by bulk chemical or heat denaturation). In the case of compartmental proteases, the AAA+ ATPase motor involved in the pulling process seems to unfold the structure adjacent to the degradation tag by trapping local unfolding fluctuations. Global unfolding then occurs immediately, driven by the cooperativity of the protein unfolding process (Matouschek 2003; Prakash and Ma-touschek 2004; Sauer et al. 2004). In this "local stability" model, like in SMFS findings, the structure and pulling geometry at the attachment point (i.e., local stability) are more important than their global counterparts, ttis highlights the importance of the existence of Achilles heels in proteins. As a result, mechanical unfoldases may have evolved specific pulling mechanisms to take advantage of the presence of weak spots in their protein substrates in order to unfold them more economically. For instance, since polyubiquitins may act as handles for mechanical pulling (Carrion-Vazquez et al. 2003; Pickart and Cohen 2004), it is tempting to suggest that pro-teasomal substrates may have placed lysine residues for ubiquitination at specific locations in order to minimize the forces required for their unfolding. It is also conceivable that the cell's metabolism may on occasion generate some protein structures (misfolded proteins or aggregates) with very high mechanical stability that may jam the proteasomal motor, leading to pathological situations. It therefore seems critical in the future to develop experimental systems to mechanically analyze unfoldase protein substrates in a way that closely mimics the physiological configuration.
In the case of mechanical proteins, the mechanical design of their structures probably reflects precise solutions to adapt their function to specific mechanical challenges (e.g., mechanical elasticity or resistance) organisms have encountered though evolution. In fact, as a result of eons of evolution, most modern bionanoma-chines are probably perfect or near-perfect solutions to the variety of challenges organisms have encountered (some of which must certainly have been mechanical), ttese bionanomachines are truly amazing devices from the engineering point of view. For instance, the ATP synthase achieves near 100% efficiency (Wang and Oster 1998), while artificial machines do not surpass 40%. Evolution therefore remains the best engineer and a constant source of ideas for the development of biologically inspired materials.
Was this article helpful?