The ability of mutations to change the fold of a protein provides evolutionary pathways to new structures. To study hypothetical pathways for protein fold evolution, we designed intermediate sequences between Xfaso1 and Pfl6, two homologous Cro proteins that have 40% sequence identity but adopt all–α and α+β folds, respectively. The designed hybrid sequences XPH1 and XPH2 have 70% sequence identity to each other. XPH1 is more similar in sequence to Xfaso1 (86% sequence identity) while XPH2 is more similar to Pfl6 (80% sequence identity). NMR solution ensembles show that XPH1 and XPH2 have structures intermediate between Xfaso1 and Pfl6. Specifically, XPH1 loses α-helices 5 and 6 of Xfaso1 and incorporates a small amount of β-sheet structure; XPH2 preserves most of the β-sheet of Pfl6 but gains a structure comparable to helix 6 of Xfaso1. These findings illustrate that the sequence space between two natural protein folds may encode a range of topologies, which may allow a protein to change its fold extensively through gradual, multistep mechanisms. Evolving a new fold may have consequences, such as a strained conformation. Here we show that Pfl6 represents an early, strained form of the α+β Cro fold resulting from an ancestral remnant of the all-α Cro proteins retained after the fold switch. This nascent fold can be stabilized through deletion mutations in evolution, which can relieve the strain but may also negatively affect DNA-binding function. Compensatory mutations that increase dimerization appear to offset these effects to maintain function. These findings suggest that new folds can undergo mutational editing through evolution, which may occur in parallel pathways with slightly different outcomes.
| Identifer | oai:union.ndltd.org:arizona.edu/oai:arizona.openrepository.com:10150/605218 |
| Date | January 2016 |
| Creators | Kumirov, Vlad K. |
| Contributors | Cordes, Matthew, Cordes, Matthew, Ghosh, Indraneel, Hruby, Victor, McEvoy, Megan, Montfort, William |
| Publisher | The University of Arizona. |
| Source Sets | University of Arizona |
| Language | en_US |
| Detected Language | English |
| Type | text, Electronic Dissertation |
| Rights | Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. |
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