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Predicting the stability of homotrimeric and heterotrimeric collagen helices

Nature Chemistry volume 13, pages 260–269 (2021)Cite this article

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Abstract

Robust methods for predicting thermal stabilities of collagen triple helices are critical for understanding natural structure and stability in the collagen family of proteins and also for designing synthetic peptides mimicking these essential proteins. In this work, we determine the relative stability imparted on the collagen triple helix by single amino acids and interactions between amino acid pairs. Using this analysis, we create a comprehensive algorithm, SCEPTTr, for predicting melting temperatures of synthetic triple helices. Critically, our algorithm is compatible with every natural amino acid, can evaluate both homotrimers and heterotrimers, and accounts for all possible helix compositions and registers, including non-canonically staggered helices. We test and optimize our algorithm against 431 published collagen triple helices to demonstrate the quality of our predictive system. Finally, we use this algorithm to successfully guide the design of an ABC heterotrimer possessing high assembly specificity.

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Fig. 1: Organization of the collagen triple helix.
Fig. 2: Flow chart of the logical flow of SCEPTTr to predict melting temperatures of combinations of peptides in collagen-like triple helices.
Fig. 3: Performance of SCEPTTr for the library of triple helices available in the literature.
Fig. 4: Thermal characterization of the ABC heterotrimer.
Fig. 5: Structural characterization of the ABC heterotrimer.

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Data availability

The data that support the findings of this study are available within the paper, in the Supplementary Information and from the corresponding author. In particular, the NMR raw data are available on request due to the size of the files and the lack of appropriate public repositories for raw multi-dimensional NMR data.

Code availability

A compiled standalone Java application is available for download as Supplementary Software 1. The genetic algorithm used to optimize SCEPTTr requires human input to further optimize the values used. For this reason, it is available from the corresponding author upon reasonable request.

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Acknowledgements

This work was funded by the National Science Foundation (CHE 1709631) and the Robert A. Welch Foundation (C1557). I.-C.L. was supported by the Stauffer-Rothrock Fellowship. We thank the NMR and Drug Metabolism Core at Baylor College of Medicine for access to the 800 MHz NMR spectrometer and K. R. MacKenzie for assistance in acquiring NMR spectra.

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Authors and Affiliations

  1. Department of Chemistry, Rice University, Houston, TX, USA

    Douglas R. Walker, Sarah A. H. Hulgan, Caroline M. Peterson, I-Che Li, Kevin J. Gonzalez & Jeffrey D. Hartgerink

  2. Department of Bioengineering, Rice University, Houston, TX, USA

    Jeffrey D. Hartgerink

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Contributions

D.R.W., S.A.H.H., I.-C.L. and K.J.G. designed, synthesized and characterized deconvolution peptides. D.R.W. assembled the peptide library, designed, wrote and optimized SCEPTTr, performed and analysed NMR experiments, and co-wrote the manuscript. C.M.P. designed and synthesized the novel ABC system and characterized it using circular dichroism spectroscopy. J.D.H. supervised the research, evaluated all of the data and co-wrote the manuscript.

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Correspondence to Jeffrey D. Hartgerink.

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The authors declare no competing interests.

Additional information

Correspondence and requests for materials should be addressed to J.D.H.

Peer review information Nature Chemistry thanks the anonymous reviewers for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–76, Discussion and Tables 1–7.

Supplementary Video 1

Movie to show NMR correlations.

Supplementary Software 1

Java application for SCEPTTr.

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Walker, D.R., Hulgan, S.A.H., Peterson, C.M. et al. Predicting the stability of homotrimeric and heterotrimeric collagen helices. Nat. Chem. 13, 260–269 (2021). https://doi.org/10.1038/s41557-020-00626-6

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