How Accurate Must Potentials Be for Successful Modeling of Protein Folding?

TL;DR

This paper investigates how inaccuracies in interaction energy potentials affect the ability of designed heteropolymers to correctly fold into their target structures, finding that stable designed sequences tolerate significant errors.

Contribution

It introduces a theoretical framework using replica mean field theory to assess the impact of interaction energy errors on protein folding predictions.

Findings

Designed heteropolymers' ground states are stable despite energy errors.

Folding success depends on correlation between design and renaturation interaction matrices.

Even with substantial energy inaccuracies, correct folding can still occur.

Abstract

Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,'' or ``optimal energy'' of the desirable target conformation over all possible sequences, such that the ``design'' of the sequence is governed by the interactions between monomers. With replica mean field theory, we examine the possibility to reconstruct the renaturation, or freezing transition, of the ``designed'' heteropolymer given the inevitable errors in the determination of interaction energies, that is, the difference between sets (matrices) of interactions governing chain design and conformations, respectively. We find that the possibility of folding to the designed conformation is controlled by the correlations of the elements of the design and renaturation interaction matrices; unlike random heteropolymers, the ground state of designed heteropolymers is sufficiently stable, such that even a substantial error in the interaction energy should still yield correct renaturation.