Succinct Amyloid and Non-Amyloid Patterns in Hexapeptides

TL;DR

This paper uses an AI-based classifier to identify succinct amyloidogenic and non-amyloidogenic hexapeptide patterns with high accuracy, providing new rules for understanding peptide amyloid states.

Contribution

It introduces novel, succinct amyloid pattern rules derived from AI predictions, enhancing understanding of peptide amyloidogenicity beyond prior methods.

Findings

Achieved 80-84% accuracy in pattern prediction.

Identified specific amyloidogenic patterns like CxFLWx and FxFLFx.

Discovered non-amyloidogenic patterns such as PxDxxx and xxKxEx.

Abstract

Hexapeptides are widely applied as a model system for studying amyloid-forming properties of polypeptides, including proteins. Recently, large experimental databases have become publicly available with amyloidogenic labels. Using these datasets for training and testing purposes, one may build artificial intelligence (AI)-based classifiers for predicting the amyloid state of peptides. In our previous work (Biomolecules, 11(4) 500, (2021)) we described the Support Vector Machine (SVM)-based Budapest Amyloid Predictor (\url{https://pitgroup.org/bap}). Here we apply the Budapest Amyloid Predictor for discovering numerous amyloidogenic and non-amyloidogenic hexapeptide patterns with accuracy between 80\% and 84\%, as surprising and succinct novel rules for further understanding the amyloid state of peptides. For example, we have shown that for any independently mutated residue (position marked by ``x''), the patterns CxFLWx, FxFLFx, or xxIVIV are predicted to be amyloidogenic, while those of PxDxxx, xxKxEx, and xxPQxx non-amyloidogenic at all. We note that each amyloidogenic pattern with two x's (e.g.,CxFLWx) describes succinctly $20^2=400$ hexapeptides, while the non-amyloidogenic patterns comprising four point mutations (e.g.,PxDxxx) gives $20^4=160,000$ hexapeptides in total. To our knowledge, no similar applications of artificial intelligence tools or succinct amyloid patterns were described before the present work.