Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy Journal Article

Authors: Topf, M.; Baker, M. L.; John, B.; Chiu, W.; Sali, A.
Article Title: Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy
Abstract: We explore structural characterization of protein assemblies by a combination of electron cryo-microscopy (cryoEM) and comparative protein structure modeling. Specifically, our method finds an optimal atomic model of a given assembly subunit and its position within an assembly by fitting alternative comparative models into a cryoEM map. The alternative models are calculated by MODELLER [J. Mol. Biol. 234 (1993) 313] from different sequence alignments between the modeled protein and its template structures. The fitting of these models into a cryoEM density map is performed either by FOLDHUNTER [J. Mol. Biol. 308 (2001) 1033] or by a new density fitting module of MODELLER (Mod-EM). Identification of the most accurate model is based on the correlation between the model accuracy and the quality of fit into the cryoEM density map. To quantify this correlation, we created a benchmark consisting of eight proteins of different structural folds with corresponding density maps simulated at five resolutions from 5 to 15 Å, with three noise levels each. Each of the proteins in the set was modeled based on 300 different alignments to their remotely related templates (12-32% sequence identity), spanning the range from entirely inaccurate to essentially accurate alignments. The benchmark revealed that one of the most accurate models can usually be identified by the quality of its fit into the cryoEM density map, even for noisy maps at 15 Å resolution. Therefore, a cryoEM density map can be helpful in improving the accuracy of a comparative model. Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs. © 2004 Elsevier Inc. All rights reserved.
Keywords: sequence analysis; comparative study; protein conformation; accuracy; protein analysis; quality control; protein assembly; analytic method; protein; simulation; correlation analysis; amino acid sequence; sequence alignment; models, molecular; protein subunit; protein structure; density; structure analysis; model; calculation; qualitative analysis; cryoelectron microscopy; noise; atom; comparative modeling; electron cryo-microscopy; fitting; protein structure prediction
Journal Title: Journal of Structural Biology
Volume: 149
Issue: 2
ISSN: 1047-8477
Publisher: Academic Press, Elsevier Inc  
Date Published: 2005-02-01
Start Page: 191
End Page: 203
Language: English
DOI: 10.1016/j.jsb.2004.11.004
PUBMED: 15681235
PROVIDER: scopus
Notes: --- - "Cited By (since 1996): 46" - "Export Date: 24 October 2012" - "CODEN: JSBIE" - "Source: Scopus"
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  1. Bino John
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