Conformational States and Protein Stability in a Proteomic Perspective

Protein structure and stability rely on the interplay of a large number of weak molecular interactions working in concert to assure a stable and unique native fold. Throughout evolution, different strategies have been devised to modulate protein conformational stability and enhance function and survival of proteins, even under adverse conditions. The increasing number of characterized genomes and proteomes, especially those from thermophiles, provides a unique resource to study protein conformations at a wider scale. An integrated, proteome-level perspective of protein conformational states in different cellular contexts is likely to contribute to a better understanding of functioning and control of biological systems. This review will address recent proteomic approaches, which allow screening and profiling proteins according to particular conformational features. We will discuss emerging methodologies that allow screening proteomes for unstructured or conformationally altered proteins, and novel approaches that profile and identify proteins within complete proteomes, on the basis of their differential resistances to temperature, chemicals, or proteolysis. In particular, the profiling of proteins from thermophiles according to their thermostability will be highlighted, as these studies may contribute to elicit general strategies accounting for protein stability and thermostable cellular processes.