Sequence/Temperature Dependence of Properties of Unfolded/Disordered Proteins

The unfolded/denatured state of peptides and proteins has attracted prominent interest for decades, for better understanding of protein folding problem, aggregation/misfolding and collapse transitions. Moreover intrinsically disordered proteins (IDPs), which have lack of well-defined tertiary structures yet still have biologically relevant function in the cell, enlarges the interest. In this work, we simulated five different unfolded/disordered peptide chains in aqueous solution for the systematic investigation of their characteristic polymer properties. We used all-atom protein model and explicit solvent which naturally captures temperature-dependent solvation effects. We found that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. We also were able to regenerate temperature-induced collapse of polypeptide chains. Change of hydration of individual residues as a function of temperature provides an explanation on the origin of collapse. As a result of the chain collapse, some of the proteins switch from an excluded-volume towards a Flory-type random walk scaling as temperature is increased. Furthermore, we find that unfolded ensembles of peptides at different temperatures are remarkably similar.