Two major stable structures of amyloid-forming peptides: amorphous aggregates and amyloid fibrils

Abstract

A peptide -m, which is a fragment from residue 21 to residue 31 of -microgloblin, is experimentally known to self-assemble and form amyloid fibrils. In order to analyze the conformations of amyloid-forming peptides in the early stage of aggregation, we applied the replica-exchange molecular dynamics method to the system consisting of three fragments of -m. From the analyses concerned with the temperature dependence, we found that there is a clear transition temperature in which the peptides aggregate each other. Moreover, we found that there are two major stable states: One of them is like amyloid fibrils and the other is amorphous aggregates by the free energy analyses.

Keywords:

• -microgloblin
• amyloid fibrils
• self-assembly
• molecular dynamics simulation
• replica-exchange method
• free energy landscape

Notes

No potential conflict of interest was reported by the authors.

Additional information

Funding

Some of the computations were performed on the supercomputers at the Institute for Molecular Science and at the Information Technology Center, Nagoya University. N. N. was supported by the Grant-in-Aid for JSPS Research Fellow (DC2). This work was supported, in part, by the Grants-in-Aid for Scientific Research on Innovative Areas “Dynamical Ordering & Integrated Functions” [number JP25102009], for High Performance Computing Infrastructure, and by the Program for Leading Graduate Schools “Integrative Graduate Education and Research in Green Natural Sciences” from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.