A significant fraction of the human proteins are intrinsically disordered (IDP - intrinsically disordered proteins) and lack a well-defined 3D structure. These proteins typically fold only after recognition of a physiological partner. Although the role of disordered proteins is still to be clarified, it is hypothesized that protein disorder plays a crucial role by expanding the repertoire of protein-protein interactions taking place in the living cells. The present research project aims at clarifying the mechanisms of folding upon binding of a key experimental systems using chemical kinetics approach in synergy with protein engineering. We will therefore study the binding-induced-folding reaction of different intrinsically disordered systems, with the specific aim of clarifying the role of disorder in protein function. Moreover, we will also address the role of protein dynamics in the allosteric regulation of different protein systems.
Our major goal is therefore to unveil the role of disorder in protein recognition and to elucidate the involvement of protein frustration, in terms of energetically unfavourable interactions, in controlling allostery.
The classical view on proteins is deeply affected by the belief that a well-defined three dimensional structure is a pre-requisite for their function. Consequently, the past ten decades have witnessed a continuous advance of structural biology, with the aim of depicting the structure of very complex protein architectures. Notably, one of the most important finding in recent biology has not been represented by the description of a beautiful fold, but rather by the observation that many proteins, or portions of them, lack a well-defined structure and appear highly dynamic. While disordered, these proteins may mediate many critical cellular functions, such as intracellular signaling, transcription and replication. Often, these intrinsically unstructured systems fold upon binding to their target ligand, thereby undergoing a binding induced folding reaction.
The concept of functional disorder is slowly percolating in the scientific community and many untested hypotheses have been put forward to explain its role in the living systems. The most relevant theories are: i) It is a way of decoupling affinity and specificity; ii) It increases the association rate with the ligand; iii) It allows for increased plasticity with regard to the ligand; iv) A large interaction surface area is provided in a short amino acid sequence as the protein folds around its ligand; v) Rapid turnover in the cell. Despite all these hypotheses are intriguing and would corroborate a potential value for protein disorder, there is a paucity of experimental data on the mechanisms by which intrinsically denatured systems recognize their partners. Consequently, the role of disorder in proteins is still shrouded in mystery.