The Role of Non-native Interactions in the Folding of Knotted Proteins

TL;DR

This study uses simulations to explore how non-native interactions influence the early folding stages and knot formation in homologous proteins, revealing that such interactions significantly affect knotting propensity.

Contribution

It demonstrates that non-native interactions are crucial in promoting or preventing knot formation during early protein folding stages, especially in natively-knotted proteins.

Findings

Non-native interactions increase knotting in AOTCase but not in OTCase.

Knotting propensity depends on the orientation of the C-terminal during folding.

Natively-knotted proteins can spontaneously form knots early in folding.

Abstract

Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein show a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavoring early knotting events.