Normal modes as refinement parameters for the F-actin model.
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.
Tirion
M M
MM
Department of Physics, Clarkson University, Potsdam, New York 13699-5820.
ben-Avraham
D
D
Lorenz
M
M
Holmes
K C
KC
D000199:Actins / Q000737:chemistry*; D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D013237:Stereoisomerism; D014961:X-Ray Diffraction
D000199:Actins