Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides

Xingqing Xiao; Alicia S Robang; Sudeep Sarma; Justin V Le; Michael E Helmicki; Matthew J Lambert; Ricardo Guerrero-Ferreira; Johana Arboleda-Echavarria; Anant K Paravastu; Carol K Hall

doi:10.1093/pnasnexus/pgac263

Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides

PNAS Nexus. 2022 Nov 25;1(5):pgac263. doi: 10.1093/pnasnexus/pgac263. eCollection 2022 Nov.

Affiliations

¹ Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
² Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
³ Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA.

Abstract

Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyloid-forming peptides. Discontinuous molecular dynamics (DMD) simulation with the PRIME20 force field combined with the FoldAmyloid tool is used to examine the fibrilization kinetics of PepAD-generated peptides. PepAD screening of ∼10,000 7-mer peptides resulted in twelve top-scoring peptides with two distinct hydration properties. Our studies revealed that eight of the twelve in silico discovered peptides spontaneously form amyloid fibrils in the DMD simulations and that all eight have at least five residues that the FoldAmyloid tool classifies as being aggregation-prone. Based on these observations, we re-examined the PepAD-generated peptides in the sequence pool returned by PepAD and extracted five sequence patterns as well as associated sequence signatures for the 7-mer amyloid-forming peptides. Experimental results from Fourier transform infrared spectroscopy (FTIR), thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. This is the first attempt to use a computational approach to search for amyloid-forming peptides based on customized settings. Our efforts facilitate the identification of β-sheet-based self-assembling peptides, and contribute insights towards answering a fundamental scientific question: "What does it take, sequence-wise, for a peptide to self-assemble?".

Keywords: amyloid-forming peptides; discontinuous molecular dynamics; fourier-transform infrared spectroscopy; peptide assembly design; transmission electron microscopy.