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Structural insights into peptide self‐assembly using photo‐induced crosslinking experiments and discontinuous molecular dynamics
Author(s) -
Bunce Samuel J.,
Wang Yiming,
Radford Sheena E.,
Wilson Andrew J.,
Hall Carol K.
Publication year - 2021
Publication title -
aiche journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.958
H-Index - 167
eISSN - 1547-5905
pISSN - 0001-1541
DOI - 10.1002/aic.17101
Subject(s) - chemistry , quenching (fluorescence) , molecular dynamics , mass spectrometry , monomer , peptide , nucleation , fluorescence , self assembly , electrospray ionization , molecule , fibril , ion mobility spectrometry , combinatorial chemistry , biophysics , computational chemistry , polymer , organic chemistry , chromatography , biochemistry , physics , biology , quantum mechanics
Determining the structure of the (oligomeric) intermediates that form during the self‐assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the underlying molecular structure of these transient species. In this work, a combination of fluorescence quenching, photo‐induced crosslinking (PIC) and molecular dynamics simulation was used to study the assembly of a synthetic amyloid‐forming peptide, Aβ 16‐22 . A PIC amino acid containing a trifluormethyldiazirine (TFMD) group—Fmoc(TFMD)Phe—was incorporated into the sequence (Aβ* 16–22 ). Electrospray ionization ion‐mobility spectrometry mass‐spectrometry (ESI‐IMS‐MS) analysis of the PIC products confirmed that Aβ* 16–22 forms assemblies with the monomers arranged as anti‐parallel, in‐register β‐strands at all time points during the aggregation assay. The assembly process was also monitored separately using fluorescence quenching to profile the fibril assembly reaction. The molecular picture resulting from discontinuous molecule dynamics simulations showed that Aβ 16‐22 assembles through a single‐step nucleation into a β‐sheet fibril in agreement with these experimental observations. This study provides detailed structural insights into the Aβ 16‐22 self‐assembly processes, paving the way to explore the self‐assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease.