Determining protein structures using deep mutagenesis

Abstract

Determining the three-dimensional structures of macromolecules is a major goal of biological research, because of the close relationship between structure and function; however, thousands of protein domains still have unknown structures. Structure determination usually relies on physical techniques including X-ray crystallography, NMR spectroscopy and cryo-electron microscopy. Here we present a method that allows the high-resolution three-dimensional backbone structure of a biological macromolecule to be determined only from measurements of the activity of mutant variants of the molecule. This genetic approach to structure determination relies on the quantification of genetic interactions (epistasis) between mutations and the discrimination of direct from indirect interactions. This provides an alternative experimental strategy for structure determination, with the potential to reveal functional and in vivo structures.

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Fig. 1: Extracting epistatic mutational effects from DMS of a protein domain.
Fig. 2: Likelihood of epistatic interactions and correlated interaction profiles predict tertiary structure contacts.
Fig. 3: Secondary and tertiary structure prediction from DMS data.
Fig. 4: Deep mutagenesis identifies protein-interaction contacts.
Fig. 5: Generality and data requirements for successful protein structure prediction from DMS data.
Fig. 6: Deep learning improves contact prediction and structural models from deep mutagenesis data.

Data availability

No primary data were generated in this study. Data sources are listed in the Methods at appropriate places. Processed interaction scores for all datasets are included in Supplementary Table 1. All intermediate steps of data processing can be recapitulated with the scripts provided at https://github.com/lehner-lab/DMS2structure.

Code availability

Paired-end sequencing reads were merged with USearch v.10.0.240. Data were analyzed with custom scripts written and executed in the R programming language, v.3.4.3. Structural simulations were performed with Xplor-NIH modeling suite v.2.46. TM-Score72 (update 23 March 2016) was used to evaluate accuracy of structural models. PSIPRED v.3.3 was used to predict secondary structure elements from amino acid sequences. PyMOL v.1.8.6.073 was used to visualize protein structures. All custom scripts needed to repeat the analyses are available at https://github.com/lehner-lab/DMS2structure.

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Acknowledgements

We thank Y. Liu and J. Peng for making their DeepContact code available and for their advice; members of the Lehner laboratory, T. Gross, G. Mönke, M. Bolognesi and C. Camilloni for discussions and feedback. This work was supported by a European Research Council (ERC) Consolidator grant (616434), the Spanish Ministry of Economy, Industry and Competitiveness (MEIC; BFU2017-89488-P), the AXA Research Fund, the Bettencourt Schueller Foundation, Agencia de Gestio d’Ajuts Universitaris i de Recerca (AGAUR, 2017 SGR 1322), the EMBL-CRG Systems Biology Program and the CERCA Program/Generalitat de Catalunya. J.M.S. was supported by an EMBO Long-Term Fellowship (ALTF 857-2016). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement 752809 (J.M.S.). We acknowledge support from the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership and the Centro de Excelencia Severo Ochoa.

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J.M.S. and B.L. conceptualized the study; J.M.S. developed the methods and carried out the study; J.M.S. and B.L. wrote the paper; B.L. supervised the study.

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Correspondence to Ben Lehner.

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Schmiedel, J.M., Lehner, B. Determining protein structures using deep mutagenesis. Nat Genet 51, 1177–1186 (2019). https://doi.org/10.1038/s41588-019-0431-x

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