期刊
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
卷 72, 期 -, 页码 1137-1148出版社
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S2059798316013541
关键词
multimolecular protein complexes; modelling protein assemblies; PRISM-EM; three-dimensional electron microscopy; protein structure prediction
资金
- TUBITAK (The Scientific and Technological Research Council of Turkey) fellowship
- TUBITAK Research Grant [114M196]
- National Cancer Institute, National Institutes of Health [HHSN261200800001E]
- Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research
The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 angstrom. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.
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