Accurate protein stability predictions from homology models

Audrone Valanciute, Lasse Nygaard, Henrike Zschach, Michael Maglegaard Jepsen, Kresten Lindorff-Larsen*, Amelie Stein

*Corresponding author af dette arbejde

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Abstract

Calculating changes in protein stability (ΔΔG) has been shown to be central for predicting the consequences of single amino acid substitutions in protein engineering as well as interpretation of genomic variants for disease risk. Structure-based calculations are considered most accurate, however the tools used to calculate ΔΔGs have been developed on experimentally resolved structures. Extending those calculations to homology models based on related proteins would greatly extend their applicability as large parts of e.g. the human proteome are not structurally resolved. In this study we aim to investigate the accuracy of ΔΔG values predicted on homology models compared to crystal structures. Specifically, we identified four proteins with a large number of experimentally tested ΔΔGs and templates for homology modeling across a broad range of sequence identities, and selected three methods for ΔΔG calculations to test. We find that ΔΔG-values predicted from homology models compare equally well to experimental ΔΔGs as those predicted on experimentally established crystal structures, as long as the sequence identity of the model template to the target protein is at least 40%. In particular, the Rosetta cartesian_ddg protocol is robust against the small perturbations in the structure which homology modeling introduces. In an independent assessment, we observe a similar trend when using ΔΔGs to categorize variants as low or wild-type-like abundance. Overall, our results show that stability calculations performed on homology models can substitute for those on crystal structures with acceptable accuracy as long as the model is built on a template with sequence identity of at least 40% to the target protein.
OriginalsprogEngelsk
TidsskriftComputational and Structural Biotechnology Journal
Vol/bind21
Sider (fra-til)66-73
Antal sider8
ISSN2001-0370
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
We thank members of the Lindorff-Larsen and Stein labs for helpful discussions and comments. This work is supported by a Novo Nordisk Foundation , Denmark, Challenge Grant ( PRISM, NNF18OC0033950 to K.L.-L., A.S.) and the Lundbeck Foundation , Denmark ( R272-2017-4528 to A.S.).

Publisher Copyright:
© 2022

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