Download MendeleyPredicting multiple conformations via sequence clustering and AlphaFold2.
Wayment-Steele, H.K., Ojoawo, A., Otten, R., Apitz, J.M., Pitsawong, W., Homberger, M., Ovchinnikov, S., Colwell, L., Kern, D.(2024) Nature 625: 832-839
- PubMed: 37956700
- DOI: https://doi.org/10.1038/s41586-023-06832-9
- Primary Citation of Related Structures:
8UBH - PubMed Abstract:
AlphaFold2 (ref. 1 ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates 2 , and disease-causing point mutations often cause population changes within these substates 3,4 . We demonstrate that clustering a multiple-sequence alignment by sequence similarity enables AlphaFold2 to sample alternative states of known metamorphic proteins with high confidence. Using this method, named AF-Cluster, we investigated the evolutionary distribution of predicted structures for the metamorphic protein KaiB 5 and found that predictions of both conformations were distributed in clusters across the KaiB family. We used nuclear magnetic resonance spectroscopy to confirm an AF-Cluster prediction: a cyanobacteria KaiB variant is stabilized in the opposite state compared with the more widely studied variant. To test AF-Cluster's sensitivity to point mutations, we designed and experimentally verified a set of three mutations predicted to flip KaiB from Rhodobacter sphaeroides from the ground to the fold-switched state. Finally, screening for alternative states in protein families without known fold switching identified a putative alternative state for the oxidoreductase Mpt53 in Mycobacterium tuberculosis. Further development of such bioinformatic methods in tandem with experiments will probably have a considerable impact on predicting protein energy landscapes, essential for illuminating biological function.
Organizational Affiliation:
Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
