Deciphering the mechanisms of binding induced folding at nearly atomic resolution: The Φ value analysis applied to IDPs

Abstract

The Φ value analysis is a method to analyze the structure of metastable states in reaction pathways. Such a methodology is based on the quantitative analysis of the effect of point mutations on the kinetics and thermodynamics of the probed reaction. The Φ value analysis is routinely used in protein folding studies and is potentially an extremely powerful tool to analyze the mechanism of binding induced folding of intrinsically disordered proteins. In this review we recapitulate the key equations and experimental advices to perform the Φ value analysis in the perspective of the possible caveats arising in intrinsically disordered systems. Finally, we briefly discuss some few examples already available in the literature.

Mg2+ Shifts Ligand-Mediated Folding of a Riboswitch from Induced-Fit to Conformational Selection

“…30 For example, TSA recently has been applied to probe the coupled binding and folding mechanisms of intrinsically disordered proteins (IDPs), protein oligomerization and aggregation. 31–33 In these studies, mutations were introduced into one of the binding partners and their effects on the nature of the folding transition state were probed.…”

“…This approach gives information on the structure of the initial “encounter complex”, thereby providing insights into the mechanism of folding. 30 We here use a similar approach, albeit the external ligand in our case is a small molecule to which we introduce subtle conservative “mutations”.…”

“…21 Notably, our use of average rate constants from single-exponential fits then yields insights into the nature of the overall folding mechanism that can be related with those obtained from classical, ensemble-averaging kinetic measurements. 30 …”

Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins

“…Changes in temperature as a driving force for LCST or UCST phase transition, while eminently useful in the application of such polymers in an abiotic and technological context, are less relevant to natural biological conditions. In the largely isothermal environment of life, nature frequently uses other variables to drive phase behavior within cells such as changes in protein concentration 98 , post-translation modifications of key proteins 82 , or ligand binding induced coacervation 99 . What unites these myriad and seemingly disparate manifestations of aqueous phase behavior is the concept of the miscibility, specifically the miscibility of a two component solution consisting of polymer chains and solvent molecules 100 .…”

Deciphering the dark proteome of Chikungunya virus

“…A globular structure attained by the ordered proteins that typically prevent the formation of aggregate or misfolding because of the frustrations in amino acid sequence compositions 26 . IDPs/IDPRs are promiscuous binders that can be involved in numerous interactions with many partners, thereby acting as an important hub in protein-protein interaction networks to regulate multiple signaling pathways at a time 27 – 29 . Many IDPs/IDPRs show disorder to order transition after binding to their partners 30 – 32 .…”