Protein Collapse is Encoded in the Folded State Architecture

TL;DR

This paper presents a universal theory linking protein fold architecture to the compactness of unfolded states, revealing that contact maps encode folding propensity and that beta-sheet rich proteins tend to be more compact.

Contribution

It introduces a novel theoretical framework connecting folded state architecture to unfolded state compactness, supported by analysis of over 2000 proteins and RNA molecules.

Findings

Unfolded state compactness is encoded in the folded contact map.

Beta-sheet rich proteins are more likely to be compact in unfolded states.

The theory explains small protein sizes and the evolution of multi-domain proteins.

Abstract

Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The dependence of the radii of gyration on protein size in the folded and unfolded states obeys the same scaling laws as synthetic polymers. Thus, one might surmise that the mechanism of collapse in proteins and polymers ought to be similar. However, because the number of amino acids in single domain proteins is not significantly greater than about two hundred, it has not been resolved if the unfolded states of proteins are compact under conditions that favor the folded states - a problem at the heart of how proteins fold. By adopting a theory used to derive polymer-scaling laws, we find that the propensity for the unfolded state of a protein to be compact is universal and is encoded in the contact map of the folded state. Remarkably, analysis of over 2000 proteins shows that proteins rich in $\beta$-sheets have greater tendency to be compact than $\alpha$-helical proteins. The theory provides insights into the reasons for the small size of single domain proteins and the physical basis for the origin of multi-domain proteins. Application to non-coding RNA molecules show that they have evolved to collapse sharing similarities to $\beta$-sheet proteins. An implication of our theory is that the evolution of natural foldable sequences is guided by the requirement that for efficient folding they should populate minimum energy compact states under folding conditions. This concept also supports the compaction selection hypothesis used to rationalize the unusually condensed states of viral RNA molecules.