Molecular recycling during fibrillization observed in a coarse-grained model

A molecular recycling mechanism has been observed by a combination of NMR spectroscopy and mass spectroscopy for an amyloid fibril formed from an SH3 domain. Details are given in the publication accompanying this movie (see page 40 of the Supplemental Materials). Initially, those monomers that are part of fibrillar aggregates are colored in red. Conversely, monomers that are dissociated or engaged in nonfibrillar assembly processes are colored in blue. This coloring is adjusted dynamically and unilaterally to highlight the recycling process. Specifically, a monomer detaching from the fibril turns blue but a monomer newly incorporated into a fibril does not turn red. At the end of this movie, all monomers are colored blue, which means that they have all been recycled at least once with respect to the monomer pool.