Research Article: Rapid model building of β-sheets in electron-density maps

Date Published: March 01, 2010

Publisher: International Union of Crystallography

Author(s): Thomas C. Terwilliger.


A method for rapid model building of β-sheets at moderate resolution is presented.

Partial Text

Many methods for the automatic interpretation of macromolecular electron-density maps and model building have recently been developed. These methods address the critical problem of building an atomic model that is consistent with the known sequence of the macromolecule and the expected geometrical features of the polymer. Automated map-interpretation methods are a natural extension of the powerful tools for interactive model building of models into maps [e.g. O (Jones et al., 1991 ▶), MAIN (Turk, 1992 ▶), XtalView (McRee, 1999 ▶) and Coot (Emsley & Cowtan, 2004 ▶)], which include semi-automated procedures for the generation of models after the user specifies some information about the chain location or geometry (Oldfield, 1994 ▶; Jones & Kjeldgaard, 1997 ▶; McRee, 1999 ▶). Recently developed highly automated methods for model building of proteins and nucleic acids include procedures that first identify Cα-atom positions and then extend these to create a model (Oldfield, 2002 ▶, 2003 ▶; Ioerger & Sacchettini, 2003 ▶; Cowtan, 2006 ▶) as well as methods that first find regular secondary structure followed by extension to build loops and other structures (Levitt, 2001 ▶; Terwilliger, 2003 ▶). Other methods begin with the identification of atomic positions and their interpretation in terms of a polypeptide chain (Perrakis et al., 1999 ▶) or begin with some information about the location of the chain and extensive conformational sampling to identify the conformation of the polymer (DePristo et al., 2005 ▶). Recently, probabilistic methods based on the recognition of density patterns in electron-density maps have been developed that extend automated model building to lower resolution ranges than were previously accessible (DiMaio et al., 2007 ▶; Baker et al., 2007 ▶) and methods for building nucleic acids into electron-density maps have been demonstrated (Pavelcik & Schneider, 2008 ▶).

Our approach for modeling the β-sheets in an electron-density map of a protein focuses on speed by examining the map for characteristic features of these structures. The method consists of three steps.(i) Identification of the location of sheets based on the presence of nearly parallel tubes of density.(ii) Identification of β-strand alignment and direction using the pattern of high density corresponding to carbonyl and Cβ atoms along the strand averaged over all repeats present in the strand.(iii) Assembly of β-strands into a single model.The result of this process is a model of the β-sheet portions of the structure. It can be used as a starting point for further model building and map interpretation in combination with a model of the α-helical portions of the structure. The steps carried out are described in detail below.

We tested our approach for modeling β-strands using a set of 42 density-modified electron-density maps from the PHENIX structure library previously solved by MAD, SAD, MIR and a combination of SAD and SIR procedures with data extending to high resolutions ranging from 1.5 to 3.8 Å. Maps were calculated with the PHENIX AutoSol wizard (Adams et al., 2002 ▶; Terwilliger et al., 2009 ▶) using the data that had previously led to refined models for each of the structures considered. Each map was examined for β-strands using the procedure described above.

The procedure that we have developed for modelling β-sheets is quite rapid and reasonably accurate. It identifies most of the β-­sheets in the tests we have carried out. The method does show some overprediction and can accidentally build β-­structure into helical or side-chain density in some cases (Fig. 2 ▶b), but in general it builds β-sheets very well (Fig. 2 ▶c).