Simulation of the β‐ to α‐sheet transition results in a twisted sheet for antiparallel and an α‐nanotube for parallel strands: Implications for amyloid formation

Abstractα‐sheet has been proposed to be the main constituent of the toxic amyloid intermediate. Molecular dynamics simulations on proteins known to be involved in amyloid diseases have demonstrated that β‐sheet can, under certain conditions, spontaneously convert to α‐sheet via ββ→αRαL peptide‐plane flipping. Using torsion‐angle driving to simulate this flip the transition has been investigated for parallel and antiparallel sheets. Concerted and sequential flipping processes were simulated, the former allowing direct calculation of helical parameters. For antiparallel sheet, the strands tend to splay apart during the transition. This can be understood by consideration of the geometry of repeating dipeptide conformations. At the end of the transition antiparallel α‐sheet is slightly twisted, comprising gently curving strands. In parallel sheet, the strands maintain identical conformations and stay hydrogen bonded during the transition as they curl up to suggest a hitherto unseen structure, the multi‐helix α‐nanotube. Intriguingly, the α‐nanotube has some of the characteristics of the parallel β‐helix, a single‐helix structure also implicated in amyloid. Unlike the β‐helix, α‐nanotube formation could involve identical strands aligning with each other in register as in most amyloids. Proteins 2011;. © 2011 Wiley‐Liss, Inc.