The equilibrium structural ensemble of a 20-residue polyglutamic acid peptide (E-20) was studied with FRET, circular dichroism, and molecular dynamics (MD) simulations. A FRET donor, o-aminobenzamide, and acceptor, 3-nitrotyrosine, were introduced at the N- and C-termini, respectively. circular dichroisrn, steady state FRET, and time-resolved FRET measurements were employed to characterize the fraction helix and end-to-end distance under different pH conditions: pH 4 (60% alpha -helix), pH 6 (0% alpha-helix), and pH 9 (0% a -helix). At pH 4, the end-to-end distance was measured at 24 angstrom and determined to be considerably less than the 31 angstrom predicted for an alpha-helix of the same length. At pH 6 and 91 the end-to-end distance was measured at > 31 and 39 A respectively, both which are determined to be considerably greater than the 27 A predicted for a freely jointed random coil of the same length. To better understand the physical forces underlying the unusual helix-coil transition in this peptide, three theoretical MD models of E-20 were constructed: (1) a pure alpha-helix, (2) an alpha-helix with equivalent attractive intramolecular contacts, and (3) a weak alpha-helix with termini-weighted intramolecular contacts ("sticky ends"). Using MD simulations, the bent helix structure calculated from Model 3 was found to be the closest in agreement with the experimental data.
Available at: http://works.bepress.com/john_finke/1/