Bojan Zagrovic, Guha Jayachandran, Ian S. Millett, Sebastian Doniach and Vijay S. Pande.
Journal of Molecular Biology (2005)
SUMMARY: Direct comparisons are made between Folding@home simulations and experimental measurements (SAXS) to determine molecular size of helical peptides of varying length, revealing the compact nature of such helical peptides.
TECHNICAL ABSTRACT: Using synchrotron radiation and the small-angle X-ray scattering technique we have measured the radii of gyration of a series of alaninebased a-helix-forming peptides of the composition Ace-(AAKAA)n-GYNH2, nZ2-7, in aqueous solvent at 10C. In contrast to other techniques typically used to study a-helices in isolation (such as nuclear magnetic resonance and circular dichroism), small-angle X-ray scattering reports on the global structure of a molecule and, as such, provides complementary information to these other, more sequence-local measuring techniques. The radii of gyration that we measure are, except for the 12-mer, lower than the radii of gyration of ideal a-helices or helices with frayed ends of the equivalent sequence-length. For example, the measured radius of gyration of the 37-mer is 14.2 A , which is to be compared with the radius of gyration of an ideal 37-mer a-helix of 17.6 A . Attempts are made to analyze the origin of this discrepancy in terms of the analytical Zimm-Bragg-Nagai (ZBN) theory, as well as distributed computing explicit solvent molecular dynamics simulations using two variants of the AMBER force-field. The ZBN theory, which treats helices as cylinders connected by random walk segments, predicts markedly larger radii of gyration than those measured. This is true even when the persistence length of the random walk parts is taken to be extremely short (about one residue). Similarly, the molecular dynamics simulations, at the level of sampling available to us, give inaccurate values of the radii of gyration of the molecules (by overestimating them by around 25% for longer peptides) and/or their helical content. We conclude that even at the short sequences examined here (%37 amino acid residues), these a-helical peptides behave as fluctuating semi-broken rods rather than straight cylinders with frayed ends.