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Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density.
Haiyun Ma1, Phillip Pham2, Bingnan Luo1
1The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
Methods in Molecular Biology (Clifton, N.J.)
|October 13, 2022
Summary
This study introduces auto-DRRAFTER, a Rosetta-based method for building RNA models into cryo-electron microscopy (cryo-EM) maps. This protocol automates RNA modeling, aiding the study of RNA structure-function relationships.
Area of Science:
- Structural Biology
- Biochemistry
- Computational Biology
Background:
- RNA three-dimensional structures are crucial for understanding biological functions.
- Cryogenic electron microscopy (cryo-EM) enables the determination of RNA and ribonucleoprotein (RNP) complex structures.
- Challenges exist in tracing RNA coordinates within moderate-resolution cryo-EM maps.
Purpose of the Study:
- To present a detailed protocol for the Rosetta-based auto-DRRAFTER method.
- To demonstrate automated RNA modeling into cryo-EM density maps.
- To facilitate the study of RNA structure-function relationships.
Main Methods:
- Utilized the Rosetta-based auto-DRRAFTER method within the Ribosolve pipeline.
- Developed a step-by-step protocol for applying auto-DRRAFTER.
- Applied the protocol to a glycine riboswitch from Fusobacterium nucleatum.
Main Results:
- Successful automated RNA modeling into moderate-resolution cryo-EM density was achieved.
- The protocol enables efficient construction of RNA models from cryo-EM data.
- Input and output files are publicly available for reproducibility.
Conclusions:
- The auto-DRRAFTER protocol streamlines the process of RNA modeling from cryo-EM data.
- Automated modeling accelerates the investigation of RNA structure and function.
- This method enhances the utility of cryo-EM for RNA structural biology.
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