Peptide flexibility and calculations of an ensemble of molecules

Conformational averaging fast on the NMR time scale has been examined by computer simulations of multiple copies of the molecule and application of NOE and coupling constant restraints as an ensemble average. The calculation is illustrated for a model cyclic peptide, cyclo[-D-Pro-Ala²-Ala³-Ala⁴-Ala⁵-], for which conformational averaging is taking place. There is a well-defined type II'β-turn about the D-Pro-Ala², while no single conformation can be ascribed to the other half of the molecule which fulfills the NMR observables. From the ensemble calculations, four different conformations can be described for Ala⁴; γ- and γ’-turn and two conformations involving a rotation of one or the other amide bond so that both amide protons are oriented in the same direction, either above or below the plane of the β-turn. The NMR observables can only be described by averaging over the ensemble containing these four conformations.