RT Journal Article
SR Electronic
T1 Milieu-Initiated Inversion of the Aqueous Polyproline II/Beta Propensity in the Alanine Tripeptide: Energetics Origin of the Onset of Amyloid Formation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 238006
DO 10.1101/238006
A1 Noemi G. Mirkin
A1 Samuel Krimm
YR 2017
UL http://biorxiv.org/content/early/2017/12/22/238006.abstract
AB Extending our earlier analogous study of the alanine dipeptide (ADP), we have now analyzed the effect of the external environment on the polyproline II (P) and β relative energies, the P/β propensity, of the alanine tripeptide (ATP). Ab initio calculations of ATP(H2O)19 and ATP(H2O)19(HCl) exhibit the same propensity inversion as in ADP: in the pure-water case the PP conformation is favored while the addition of the HCl molecule results in the ββ conformation being of lower energy. A comparison, following an intermediate insertion and departure of an HCl molecule, shows that the energy of a hydrogen-bonded (H2O)19βATP::βATP(H2O)19 structure is lower than that of the sum of two separate PP systems, i.e., that the aggregated state of the peptide is favored. This arises from the basic physical response to their total environmental influences. Questions about quantitative results from molecular dynamics simulations, obviously needed to analyze longer chains and other side chains, are addressed via rigid-water calculations. The desirability of basing studies of amyloid formation on our proposed alternative milieufolding paradigm is discussed.