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Evolution and Functional Advantages of Protein Metamorphosis

2020; Elsevier BV; Volume: 118; Issue: 3 Linguagem: Inglês

10.1016/j.bpj.2019.11.310

1542-0086

Acacia F. Dishman, Robert T. Tyler, J.E.B. Fox, Michelle Lee, Jaime de Anda, Ernest Y. Lee, G. C. L. Wong, Brian F. Volkman,

Machine Learning in Bioinformatics

Metamorphic proteins adopt two or more different native folds, expanding the protein folding paradigm. Initially viewed as an anomaly, numerous analyses suggest that metamorphic proteins may be more common than expected. The chemokine XCL1 is a metamorphic protein that spontaneously, reversibly interconverts between two distinct structures (an all β-sheet dimer and the α-β chemokine structure) and exhibits antibacterial activity. Here, we investigate the emergence of XCL1's metamorphosis using ancestral reconstruction, biophysical characterization, and bioinformatic analysis. We show that XCL1 likely underwent an evolutionary transition from occupying a single, stable structure to two distinct folds. Further, we demonstrate that over time, XCL1 has likely optimized its folding landscape to occupy its two native states in approximately equal proportion. We use bioinformatic analyses to calculate intra- and intermolecular contacts in XCL1 and one of its ancestors to identify changes likely to be involved in the introduction of metamorphosis, providing ideas for the design of fold-switching proteins. Additionally, we investigate the functional implications of metamorphic folding. Specifically, we characterize membrane permeation capacities of different native structures of XCL1. We use small angle X-ray scattering (SAXS), to measure the induction of negative Gaussian curvature (NGC), a topological requirement for membrane disruption, in model membrane systems by XCL1 and engineered XCL1 structural variants. We find that XCL1's β-sheet structure and unfolded state, but not its chemokine structure, selectively induce NGC in model bacterial and fungal membranes, but not mammalian membranes. This structure-function relationship correlates directly with in vitro bacterial killing. Because membrane remodeling activity is present in only one of XCL1's structures, there is potential for control over activity via shifts in metamorphic equilibrium, providing a foundational basis for engineering antibiotics with context-dependent functions. Together, this work yields insight into the relationship between metamorphic protein structure and function.