Normal modes as refinement parameters for the F-actin model

Abstract

The slow normal modes of G-actin were used as structural parameters to refine the F-actin model against 8-A resolution x-ray fiber diffraction data. The slowest frequency normal modes of G-actin pertain to collective rearrangements of domains, motions that are characterized by correlation lengths on the order of the resolution of the fiber diffraction data. Using a small number of normal mode degrees of freedom (< or = 12) improved the fit to the data significantly. The refined model of F-actin shows that the nucleotide binding cleft has narrowed and that the DNase I binding loop has twisted to a lower radius, consistent with other refinement techniques and electron microscopy data. The methodology of a normal mode refinement is described, and the results, as applied to actin, are detailed.