Biophysical prediction of protein–peptide interactions and signaling networks using machine learning

Abstract

In mammalian cells, much of signal transduction is mediated by weak protein–protein interactions between globular peptide-binding domains (PBDs) and unstructured peptidic motifs in partner proteins. The number and diversity of these PBDs (over 1,800 are known), their low binding affinities and the sensitivity of binding properties to minor sequence variation represent a substantial challenge to experimental and computational analysis of PBD specificity and the networks PBDs create. Here, we introduce a bespoke machine-learning approach, hierarchical statistical mechanical modeling (HSM), capable of accurately predicting the affinities of PBD–peptide interactions across multiple protein families. By synthesizing biophysical priors within a modern machine-learning framework, HSM outperforms existing computational methods and high-throughput experimental assays. HSM models are interpretable in familiar biophysical terms at three spatial scales: the energetics of protein–peptide binding, the multidentate organization of protein–protein interactions and the global architecture of signaling networks.

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Fig. 1: PBDs and modeling frameworks.
Fig. 2: Model performance and newly predicted PPIs.
Fig. 3: Predicted mechanisms for newly predicted interactions.
Fig. 4: Mechanistic analysis of SH3 domain binding.
Fig. 5: Energy surface of SH3–peptide cocomplex.
Fig. 6: Hierarchical organization of the human PBD-mediated PPI network.

Data availability

The domain–peptide and PPI predictions are made available through a custom website (https://ProteinPeptide.io). The protein–peptide interaction data are also made available in figshare with the identifiers https://doi.org/10.6084/m9.figshare.10084745. Data used in training the model are available as Supplementary Dataset 2.

Code availability

All code and data used for training and testing HSM are available in a public repository at https://github.com/aqlaboratory/hsm.

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Acknowledgements

This work was funded by NIH grants (nos. U54-CA225088 and P50-GM107618) and by DARPA/DOD (grant no. W911NF-14-1-0397) to P.K.S.

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Affiliations

Authors

Contributions

J.M.C., P.K.S. and M.A. conceived and designed the model, analysis and computational experiments. J.M.C. implemented the model and carried out the analysis and experiments. G.K. collected and processed binding and structural data and contributed to the analysis. All authors wrote and reviewed the manuscript.

Corresponding authors

Correspondence to Peter K. Sorger or Mohammed AlQuraishi.

Ethics declarations

Competing interests

P.K.S. is a member of the SAB or Board of Directors of Merrimack Pharmaceutical, Glencoe Software, Applied Biomath and RareCyte Inc. and has equity in these companies. P.K.S. declares that none of these relationships are directly or indirectly related to the content of this manuscript.

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Peer review information Rita Strack was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–7, Tables 1–5 and Notes 1 and 2.

Reporting Summary

Supplementary Dataset 1

Domain sequences and multiple sequence alignments used in both HSM/D and HSM/P.

Supplementary Dataset 2

Raw domain-peptide training data used for training HSM/D.

Supplementary Dataset 3

Potential peptidic sites used in predictions generated with HSM/P.

Supplementary Dataset 4

Assessment of HSM/D relative to other domain models. Contains source data for Fig. 2a and Supplementary Fig. 3.

Supplementary Dataset 5

PyMOL structural data associated with analysing HSM/D inferred energy profiles. Includes source data for Figs. 4 and 5 and Supplementary Figs. 5 and 6.

Supplementary Dataset 6

Assessment of HSM/P. Contains source data for Figs. 2b, 3 and 6 and Supplementary Fig. 7.

Source data

Source Data Fig. 2

Source Data

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Cunningham, J.M., Koytiger, G., Sorger, P.K. et al. Biophysical prediction of protein–peptide interactions and signaling networks using machine learning. Nat Methods 17, 175–183 (2020). https://doi.org/10.1038/s41592-019-0687-1

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