Structural entanglements in protein complexes

TL;DR

This paper introduces a criterion to identify entanglement in multi-chain protein structures, analyzes their stability and functions, and studies their folding and stretching behaviors, including in knotted dimers.

Contribution

It proposes a novel criterion for detecting entanglement in protein complexes and provides detailed analysis of entangled systems and their properties.

Findings

Approximately 900 entangled systems identified in PDB.

Entanglement may enhance thermodynamic stability and facilitate functional roles.

Stretching experiments reveal separation mechanisms and direction-dependent forces in dimers.

Abstract

We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface, and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.