EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.

Keren Lasker,Ruth Nussinov,Haim Wolfson,Oranit Dror

doi:10.1107/s0907444906041059

Abstract

Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 A resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 A resolution.

Highlights

Key cellular mechanisms are carried out through the formation of large macromolecular assemblies
Owing to their large size and instability, the structures of only a small number of macromolecular complexes have successfully been determined at atomic resolution, comprising a tiny portion of the PDB (Dutta & Berman, 2005; Krogan et al, 2006)
Cryo-electron microscopy is a term referring to several different approaches to freezing a sample and reconstructing its three-dimensional structure from a set of twodimensional projections

Summary

Introduction

Key cellular mechanisms are carried out through the formation of large macromolecular assemblies. Understanding the three-dimensional structure of these biological machines is essential for comprehension of their function (Alberts, 1998). Owing to their large size and instability, the structures of only a small number of macromolecular complexes have successfully been determined at atomic resolution, comprising a tiny portion of the PDB (Dutta & Berman, 2005; Krogan et al, 2006). Cryo-EM has emerged as a principal tool for structural analysis of macromolecular assemblies that are too large and flexible to be solved at atomic (high) resolution by NMR or X-ray crystallography (Baumeister & Steven, 2000; Frank, 2002; Chiu et al, 2005). At 6–10 Ait is possible to reveal secondary-structure elements (helices or -sheets)

Objectives

Methods

Results