Rapid chain tracing of polypeptide backbones in electron-density maps

Abstract

A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate C(alpha) positions at spacings of approximately 0.6 A along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C(alpha) positions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the process. The method was applied to 42 density-modified electron-density maps at resolutions from 1.5 to 3.8 A. A total of 21 428 residues in these maps were traced in 24 CPU min with an overall r.m.s.d. of 1.61 A for C(alpha) atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.

Figure 1

Finding potential C^α positions based on the density-modified electron-density map for S-hydrolase (see text). (a) Initial high-density points. (b) Points moved to the highest nearby location on the ridgeline. (c) Points in moderate density (in red) along lines connecting points in high density. (d) Potential C^α positions. These figures were created with PyMOL (DeLano, 2002 ▶).

Figure 2

Tracing chains using potential C^α positions from Fig. 1 ▶ (see text). (a) Scoring of potential C^α–C^α pairs. (b) Scoring of trimers. (c) Final connected chain (red) with refined C^α positions (green). These figures were created with PyMOL (DeLano, 2002 ▶).

Figure 3

Schematic of the message-passing technique. The blue lines represent nonamers and the dotted red lines indicate connections, so that nonamer A is connected on the right to nonamers B1, B2 and B3. In the first stage of message passing, each nonamer receives, from each nonamer connected to its right, the identity of that nonamer (e.g. nonamer C receives the identity ‘d’ from nonamer D). In subsequent iterations, each nonamer receives, from each nonamer to the right, the identity (if any) that it has been passed from its connection to the right (e.g. nonamer B1 receives from C the identity ‘d’ in the second cycle and nonamer A receives from B1 the identity ‘d’ in the third cycle). The process is complete when no further messages are received. If a nonamer receives its own identity then the connection is ignored (e.g. nonamer A receives from nonaner B3 the identity ‘a’ in the second cycle so this circular reference is ignored).

Figure 4

Backbone diagrams of chain tracings. (a) Mevalonate kinase (PDB entry 1kkh; Yang et al., 2002 ▶). (b) Structural genomics target 1038B (PDB entry 1lql; Choi et al., 2003 ▶). (c) Armadillo repeat region of murine β-catenin (PDB entry 3bct; Huber et al., 1997 ▶). Red tracings are from the present method; green tracings are from the deposited structures. These figures were created with Coot (Emsley & Cowtan, 2004 ▶).

Figure 5

Secondary structure identified in models compared with map quality (see text). Map quality is the correlation of the map with one based on the refined structure. Secondary structure is the percentage of residues in α-­helices or β-sheets in these models identified as described in the text.

Figure 6

Number of residues built as function of the target ratio of nonamers to atoms.