Dabrowski-Tumanski, P.; Stasiak, A. AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology. Molecules2023, 28, 7462.
Dabrowski-Tumanski, P.; Stasiak, A. AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology. Molecules 2023, 28, 7462.
Dabrowski-Tumanski, P.; Stasiak, A. AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology. Molecules2023, 28, 7462.
Dabrowski-Tumanski, P.; Stasiak, A. AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology. Molecules 2023, 28, 7462.
Abstract
AlphaFold is a groundbreaking Deep Learning tool for protein structure prediction. It achieved remarkable accuracy in modeling the many 3D structures while taking as the input only the known amino acid sequence of proteins in question. Intriguingly though, in the early steps of each individual structure prediction procedure, AlphaFold is not respecting topological barriers that in real proteins result from the reciprocals impermeability of polypeptide chains. This study aims to investigate how this non-respecting of topological barriers affects AlphaFold predictions with respect to the topology of protein chains. We focus on such classes of proteins that during their natural folding form reproducibly the same knot type on their linear polypeptide chain as revealed by their crystallographic analysis. We use partially artificial test constructs in which the mutual non-permeability of polypeptide chains should not permit the formation of such knots during natural protein folding. We find that despite the formal impossibility that the protein folding process could produce such knots, AlphaFold predicts these proteins to be knotted. Our study underscores the necessity for cautious interpretation and further validation of topological features in protein structures predicted by AlphaFold.
Keywords
AlphaFold; protein structure prediction; topological barriers; knotted proteins; topology validation; residue gas model; overlapping residues
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
