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

Abstract

A method for detecting structural homologs of components in an intermediate resolution cryo-EM map and their spatial configuration is presented. 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 Å 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 Å resolution.

Authors:
;  [1];  [2];  [3];  [1]
  1. School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel)
  2. Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978 (Israel)
  3. (United States)
Publication Date:
OSTI Identifier:
22348012
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 63; Journal Issue: Pt 1; Other Information: PMCID: PMC2483490; PUBLISHER-ID: ba5093; PMID: 17164525; OAI: oai:pubmedcentral.nih.gov:2483490; Copyright (c) International Union of Crystallography 2007; This is an open-access article distributed under the terms described at http://journals.iucr.org/services/termsofuse.html.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; CONFIGURATION; ELECTRON MICROSCOPY; ELECTRONS; INSTABILITY; PROTEINS; RESOLUTION

Citation Formats

Dror, Oranit, E-mail: oranit@post.tau.ac.il, Lasker, Keren, Nussinov, Ruth, E-mail: oranit@post.tau.ac.il, Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Building 469, Room 151, Frederick, MD 21702, and Wolfson, Haim. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. Denmark: N. p., 2007. Web. doi:10.1107/S0907444906041059.
Dror, Oranit, E-mail: oranit@post.tau.ac.il, Lasker, Keren, Nussinov, Ruth, E-mail: oranit@post.tau.ac.il, Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Building 469, Room 151, Frederick, MD 21702, & Wolfson, Haim. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. Denmark. doi:10.1107/S0907444906041059.
Dror, Oranit, E-mail: oranit@post.tau.ac.il, Lasker, Keren, Nussinov, Ruth, E-mail: oranit@post.tau.ac.il, Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Building 469, Room 151, Frederick, MD 21702, and Wolfson, Haim. Mon . "EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies". Denmark. doi:10.1107/S0907444906041059.
@article{osti_22348012,
title = {EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies},
author = {Dror, Oranit, E-mail: oranit@post.tau.ac.il and Lasker, Keren and Nussinov, Ruth, E-mail: oranit@post.tau.ac.il and Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Building 469, Room 151, Frederick, MD 21702 and Wolfson, Haim},
abstractNote = {A method for detecting structural homologs of components in an intermediate resolution cryo-EM map and their spatial configuration is presented. 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 Å 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 Å resolution.},
doi = {10.1107/S0907444906041059},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 1,
volume = 63,
place = {Denmark},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}