Design of parallel 𝛽‐sheet nanofibrils using Monte Carlo search, coarse‐grained simulations, and experimental testing

Abstract

Peptide self‐assembly into amyloid fibrils provides numerous applications in drug delivery and biomedical engineering applications. We augment our previously‐established computational screening technique along with experimental biophysical characterization to discover 7‐mer peptides that self‐assemble into “parallel β‐sheets”, that is, β‐sheets with N‐terminus‐to‐C‐terminus 𝛽‐strand vectors oriented in parallel. To accomplish the desired β‐strand organization, we applied the PepAD amino acid sequence design software to the Class‐1 cross‐β spine defined by Sawaya et al. This molecular configuration includes two layers of parallel β‐sheets stacked such that N‐terminus‐to‐C‐terminus vectors are oriented antiparallel for molecules on adjacent β‐sheets. The first cohort of PepAD identified peptides were examined for their fibrillation behavior in DMD/PRIME20 simulations, and the top performing sequence was selected as a prototype for a subsequent round of sequence refinement. The two rounds of design resulted in a library of eight 7‐mer peptides. In DMD/PRIME20 simulations, five of these peptides spontaneously formed fibril‐like structures with a predominantly parallel 𝛽‐sheet arrangement, two formed fibril‐like structure with <50% in parallel 𝛽‐sheet arrangement and one remained a random coil. Among the eight candidate peptides produced by PepAD and DMD/PRIME20, five were synthesized and purified. All five assembled into amyloid fibrils composed of parallel β‐sheets based on Fourier transform infrared spectroscopy, circular dichroism, electron microscopy, and thioflavin‐T fluorescence spectroscopy measurements.