Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement
文献类型：期刊论文
| 作者 | Zhu, Jiang3; Cheng, Lingpeng1,2; Fang, Qin4; Zhou, Z. Hong1,2; Honig, Barry3 |
| 刊名 | Journal of molecular biology
 |
| 出版日期 | 2010-04-02 |
| 卷号 | 397期号:3页码:835-851 |
| 关键词 | Cryo-electron microscopy Density fitting Homology modeling Structure refinement Protein structure prediction |
| ISSN号 | 0022-2836 |
| DOI | 10.1016/j.jmb.2010.01.041 |
| 通讯作者 | Zhou, z. hong(hong.zhou@ucla.edu) |
| 英文摘要 | Automatic modeling methods using cryoelectron microscopy (cryoem) density maps as constraints are promising approaches to building atomic models of individual proteins or protein domains. however, their application to large macromolecular assemblies has not been possible largely due to computational limitations inherent to such unsupervised methods. here we describe a new method, em-imo (electron microscopy-iterative modular optimization), for building, modifying and refining local structures of protein models using cryoem maps as a constraint. as a supervised refinement method, em-imo allows users to specify parameters derived from inspections so as to guide, and as a consequence, significantly speed up the refinement. an em-imo-based refinement protocol is first benchmarked on a data set of 50 homology models using simulated density maps. a multiscale refinement strategy that combines em-imo-based and molecular dynamics-based refinement is then applied to build backbone models for the seven conformers of the five capsid proteins in our near-atomic-resolution cryoem map of the grass carp reovirus virion, a member of the aquareovirus genus of the reoviridae family. the refined models allow us to reconstruct a backbone model of the entire grass carp reovirus capsid and provide valuable functional insights that are described in the accompanying publication [cheng, l., zhu, j., hui, w. h., zhang, x., honig, b., fang, q. & zhou, z. h. (2010). backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. j. mol. biol. (this issue). doi:10.1016/j.jmb.2009.12.027.]. our study demonstrates that the integrated use of homology modeling and a multiscale refinement protocol that combines supervised and automated structure refinement offers a practical strategy for building atomic models based on medium- to high-resolution cryoem density maps. (c) 2010 elsevier ltd. all rights reserved. |
| WOS关键词 | REAL-SPACE REFINEMENT ; ELECTRON-MICROSCOPY ; LOW-RESOLUTION ; ATOMIC MODELS ; MACROMOLECULAR STRUCTURES ; MOLECULAR-DYNAMICS ; SEQUENCE PROFILES ; FOLD RECOGNITION ; CRYOEM DENSITY ; REOVIRUS CORE |
| WOS研究方向 | Biochemistry & Molecular Biology |
| WOS类目 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000276177300018 |
| 出版者 | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2375791 |
| 专题 | 武汉病毒研究所 |
| 通讯作者 | Zhou, Z. Hong |
| 作者单位 | 1.Univ Calif Los Angeles, Dept Microbiol Mol Genet & Immunol, Los Angeles, CA 90095 USA 2.Univ Calif Los Angeles, CNSI, Los Angeles, CA 90095 USA 3.Columbia Univ, Howard Hughes Med Inst, Dept Biochem & Mol Biophys, Ctr Computat Biol & Bioinformat, New York, NY 10032 USA 4.Chinese Acad Sci, State Key Lab Virol, Wuhan Inst Virol, Wuhan 430071, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhu, Jiang,Cheng, Lingpeng,Fang, Qin,et al. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement[J]. Journal of molecular biology,2010,397(3):835-851. |
| APA | Zhu, Jiang,Cheng, Lingpeng,Fang, Qin,Zhou, Z. Hong,&Honig, Barry.(2010).Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.Journal of molecular biology,397(3),835-851. |
| MLA | Zhu, Jiang,et al."Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement".Journal of molecular biology 397.3(2010):835-851. |
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来源：武汉病毒研究所
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