Knotted Proteins: Tie Etiquette in Structural Biology

TL;DR

This review discusses the study of knotted proteins, focusing on insights gained from lattice Gō models and their role in understanding protein folding and structure in comparison to experimental and other computational methods.

Contribution

It synthesizes the role of lattice Gō models in understanding knotted proteins, highlighting their contributions relative to experimental and more complex computational approaches.

Findings

Lattice Gō models provide valuable insights into protein knot formation.

Knotted proteins are rare but structurally significant.

Computational models complement experimental data in protein folding studies.

Abstract

A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past decade with different approaches, such as structural characterization, in vitro experiments, and simulations of protein models with varying levels of complexity. The simplest among these are the lattice G\=o models, which belong to the class of structure-based models, i.e., models that are biased to the native structure by explicitly including structural data. In this review we highlight the contributions to the field made in the scope of lattice G\=o models, putting them into perspective in the context of the main experimental and theoretical results and of other, more realistic, computational approaches.