A Decoy Folding Nucleus can Modulate Protein Folding Kinetics

Abstract

The ability to modulate the folding kinetics of a specific protein in a milieu can be an important tool for chemical biology and pharmacology. Kinetics and thermodynamics of folding are routinely modulated by changing solvent conditions, but such changes are not protein specific. Here we demonstrate a general principle by which specific kinetic modulation can be achieved for any protein whose folding route is known. Our strategy is to design a pre-stabilized folding nucleus of a protein. We show that the β1- β2 part (residues 1 to 17) of ubiquitin, which is the segment known to fold first (into a β-hairpin shape)[1], can make folding faster when introduced as a separate conformationally constrained peptide at excess concentrations. A weaker but still significant effect is observed when this ‘decoy nucleus’ peptide is not conformationally constrained, or is in an unfolding buffer to start with. Interestingly, the thermodynamic stability of the protein remains unchanged, as the unfolding rate also becomes faster. We simulate the system for both a weakly constrained and a strongly constrained decoy nucleus, and observe that the decoy interacts strongly with the protein only when it is conformationally constrained. Together, our results suggest that the folding of almost any protein which possesses a well-defined folding nucleus can be modulated, by introducing a nucleus-mimicking molecule with a stabilized structure. It also implies that in vivo, fragments of proteins which are naturally present as degradation by-products can in principle affect the folding of the full length proteins. [1] Atomic-level description of ubiquitin folding. Piana et al., PNAS, 2013, 110 (15), 5915-5920