The stability and dynamics of the human calcitonin amyloid peptide DFNKF

Biophysical Journal
Hui-Hsu TsaiRuth Nussinov

Abstract

The stability and dynamics of the human calcitonin-derived peptide DFNKF (hCT(15-19)) are studied using molecular dynamics (MD) simulations. Experimentally, this peptide is highly amyloidogenic and forms fibrils similar to the full length calcitonin. Previous comparative MD studies have found that the parallel beta-stranded sheet is a stable organization of the DFNKF protofibril. Here, we probe the stability and dynamics of the small parallel DFNKF oligomers. The results show that even small DFNKF oligomers, such as trimers and tetramers, are stable for a sufficient time in the MD simulations, indicating that the crucial nucleus seed size for amyloid formation can be quite small. The simulations also show that the stability of DFNKF oligomers increases with their sizes. The small but stable seed may reflect the experimental rapid formation of the DFNKF fibrils. Further, a noncooperative process of parallel beta-sheet formation from the out-of-register trimer is observed in the simulations. In general, the residues of DFNKF peptides near the N-/C-termini are more flexible, whereas the interior residues are more stable. Simulations of mutants and capped peptides show that both interstrand hydrophobic and electrostatic interaction...Continue Reading

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Citations

Oct 25, 2011·Journal of Chemical Information and Modeling·Alok Jain, Ramasubbu Sankararamakrishnan
May 19, 2010·Journal of Biomolecular Structure & Dynamics·Liang-Kai ChangYih Ho
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Nov 3, 2016·Chemistry : a European Journal·Arianna BertolaniPierangelo Metrangolo

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