Role of bulk and of interface contacts in the behaviour of model dimeric proteins

TL;DR

This paper investigates how bulk and interface contacts influence the folding mechanisms of dimeric proteins using a minimal lattice model, revealing distinct roles and evolutionary implications for different dimer types.

Contribution

It distinguishes between three-state and two-state dimer folding mechanisms based on contact energy partitioning and contact topology, providing insights into their folding pathways and evolution.

Findings

Three-state dimers fold via hierarchical pathways controlled by local structures.

Two-state dimers stabilize through interface assembly, leading to chain folding.

Three-state dimers' properties are more evolutionarily robust, impacting viral protein studies.

Abstract

Some dimeric proteins first fold and then dimerize (three--state dimers) while others first dimerize and then fold (two--state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences obeying to one or to the other mechanism on the basis of the partition of the ground state energy between bulk than for interface contacts. The topology of contacts is very different for the bulk than for the interface: while the bulk displays a rich network of interactions, the dimer interface is built up a set of essentially independent contacts. Consequently, the two sets of interactions play very different roles both in the the folding and in the evolutionary history of the protein. Three--state dimers, where a large fraction of the energy is concentrated in few contacts buried in the bulk, and where the relative contact energy of interface contacts is considerably smaller than that associated with bulk contacts, fold according to a hierarchycal pathway controlled by local elementary structures, as also happens in the folding of single--domain monomeric proteins. On the other hand, two--state dimers display a relative contact energy of interface contacts which is larger than the corresponding quantity associated with the bulk. In this case, the assembly of the interface stabilizes the system and lead the two chains to fold. The specific properties of three--state dimers acquired through evolution are expected to be more robust than those of two--state dimers, a fact which has consequences on proteins connected with viral diseases.