Rapid model building of alpha-helices in electron-density maps

Abstract

A method for the identification of alpha-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where alpha-helices appear as tubes of density. The positioning and direction of the alpha-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. An average of 63% of the alpha-helical residues in these proteins were built and an average of 76% of the residues built matched helical residues in the refined models of the proteins. The overall average r.m.s.d. between main-chain atoms in the modeled alpha-helices and the nearest atom with the same name in the refined models of the proteins was 1.3 A.

Figure 1

Model α-helix density and interpretation. (a) Model α-helix at a resolution of 3 Å. (b) Model α-helix at a resolution of 7 Å. (c) Points along the axis of a tube of density at a resolution of 7 Å. (d) Positioning an α-helix in model density. The dark blue mesh is a contour of model electron density at a resolution of 3 Å. The gray helix is fitted to the main-chain atoms of the model α-helix and has a radius of 2 Å and a pitch of 5.4 Å. The red and yellow helices are offset by ±1 Å along the helix axis from the gray main-chain helix and have radii of 4 Å. (e) Model α-helix (in green), model density (in blue) and fitted α-helix (in red). This figure was created using PyMOL (DeLano, 2002 ▶).

Figure 2

SAD-phased density-modified electron-density map of a calcium pump (Sorensen et al., 2004 ▶) recalculated using the PHENIX AutoSol wizard at a resolution of 3.1 Å. (a) Section of map truncated at a resolution of 7 Å. (b) The same section as in (a) but calculated at a resolution of 3.1 Å, showing the helices found with the present procedure in yellow and those from the refined structure (PDB entry 1t5s; Sorensen et al., 2004 ▶) in red. This figure was created using Coot (Emsley & Cowtan, 2004 ▶)

Figure 3

Accuracy of α-helical models. The r.m.s.d. between the α-helical models obtained using the present method and the corresponding refined models from Table 1 ▶ is plotted. (a) R.m.s.d. as a function of map quality. (b) R.m.s.d. as a function of resolution. (c) R.m.s.d. as a function of map–helical model correlation.

Figure 4

Accuracy and residues built versus cutoff for accepting helices. (a) The overall r.m.s.d. as in Fig. 3 ▶ is plotted as a function of the parameter cc_helix_min which defines the minimum correlation of density between a helix and the electron-density map. The default is 0.5. (b) The overall number of residues built for the 42 structures in Table 1 ▶ is plotted as a function of cc_helix_min.