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

Oranit Dror; Keren Lasker; Ruth Nussinov; Haim Wolfson

doi:10.1107/s0907444906041059

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

Oranit Dror·Keren Lasker·Ruth Nussinov·Haim Wolfson

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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.

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Algorithms Chaperonin 60 Cryoelectron Microscopy Data Interpretation, Statistical Macromolecular Substances Models, Molecular Molecular Conformation Protein Conformation Protein Folding Protein Structure, Secondary Protein Structure, Tertiary Software Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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Oranit Dror, Keren Lasker, Ruth Nussinov, Haim Wolfson. 2006-12-13. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.. https://doi.org/10.1107/s0907444906041059

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