Unfolding proteins by external forces and temperature: The importance of topology and energetics

Unfolding of proteins by forced stretching with atomic force microscopy or laser tweezer experiments complements more classical techniques using chemi cal denaturants or temperature. Forced unfolding is of particular interest for proteins that are under mechanical stress in their biological function. For beta-sandwich proteins (a fibronectin type III and an immunoglobulin d omain), both of which appear in the muscle protein titin, the results of st retching simulations show important differences from temperature-induced un folding, but there are common features that point to the existence of foldi ng cores. Intermediates detected by comparing unfolding with a biasing pert urbation and a constant pulling force are not evident in temperature-induce d unfolding. For an alpha-helical domain (alpha-spectrin), which forms part of the cytoskeleton, there is little commonality in the pathways from unfo lding induced by stretching and temperature. Comparison of the forced unfol ding of the two beta-sandwich proteins and two alpha-helical proteins (the alpha-spectrin domain and an acyl-coenzyme A-binding protein) highlights im portant differences within and between protein classes that are related to the folding topologies and the relative stability of the various structural elements.