Diffusion-collision of foldons elucidates the kinetic effects of point mutations and suggests control strategies of the folding process of helical proteins.
In this article we use mutation studies as a benchmark for a minimal model of the folding process of helical proteins. The model ascribes a pivotal role to the collisional dynamics of a few crucial residues (foldons) and predicts the folding rates by exploiting information drawn from the protein sequence. We show that our model rationalizes the effects of point mutations on the kinetics of folding. The folding times of two proteins and their mutants are predicted. Stability and location of foldons have a critical role as the determinants of protein folding. This allows us to elucidate two main mechanisms for the kinetic effects of mutations. First, it turns out that the mutations eliciting the most notable effects alter protein stability through stabilization or destabilization of the foldons. Secondly, the folding rate is affected via a modification of the foldon topology by those mutations that lead to the birth or death of foldons. The few mispredicted folding rates of some mutants hint at the limits of the current version of the folding model proposed in the present article. The performance of our folding model declines in case the mutated residues are subject to strong long-range forces. That foldons are the critical targets of mutation studies has notable implications for design strategies and is of particular interest to address the issue of the kinetic regulation of single proteins in the general context of the overall dynamics of the interactome.
Capriotti
Emidio
E
Laboratory of Biocomputing, University of Bologna, Bologna, Italy.
Compiani
Mario
M
D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D004058:Diffusion; D007700:Kinetics; D008958:Models, Molecular; D017354:Point Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism*; D054334:Viral Regulatory and Accessory Proteins
D004268:DNA-Binding Proteins; D011994:Recombinant Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins