Ab initio folding of a trefoil‐fold motif reveals structural similarity with a β‐propeller blade motif

• Published in: Protein science 2020-05, Vol.29 (5), p.1172-1185
• Main Authors: Tenorio, Connie A., Longo, Liam M., Parker, Joseph B., Lee, Jihun, Blaber, Michael
• Format: Article
• Language: English
• Subjects: Amino Acid Motifs; Architecture; Assembly; Buried structures; Circularity; Density Functional Theory; domain swapping; Domains; Folding; folding pathway; Gene duplication; Homology; Humans; Hydrophobic and Hydrophilic Interactions; Hydrophobicity; Models, Molecular; Monomers; Permutations; Polypeptides; Propeller blades; Protein Conformation; protein evolution; Protein Folding; protein symmetry; Proteins; Symmetry; Trefoil Factors - chemistry; Trefoil Factors - genetics; Trefoil Factors - isolation & purification
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1002/pro.3850

Many protein architectures exhibit evidence of internal rotational symmetry postulated to be the result of gene duplication/fusion events involving a primordial polypeptide motif. A common feature of such structures is a domain‐swapped arrangement at the interface of the N‐ and C‐termini motifs and postulated to provide cooperative interactions that promote folding and stability. De novo designed symmetric protein architectures have demonstrated an ability to accommodate circular permutation of the N‐ and C‐termini in the overall architecture; however, the folding requirement of the primordial motif is poorly understood, and tolerance to circular permutation is essentially unknown. The β‐trefoil protein fold is a threefold‐symmetric architecture where the repeating ~42‐mer “trefoil‐fold” motif assembles via a domain‐swapped arrangement. The trefoil‐fold structure in isolation exposes considerable hydrophobic area that is otherwise buried in the intact β‐trefoil trimeric assembly. The trefoil‐fold sequence is not predicted to adopt the trefoil‐fold architecture in ab initio folding studies; rather, the predicted fold is closely related to a compact “blade” motif from the β‐propeller architecture. Expression of a trefoil‐fold sequence and circular permutants shows that only the wild‐type N‐terminal motif definition yields an intact β‐trefoil trimeric assembly, while permutants yield monomers. The results elucidate the folding requirements of the primordial trefoil‐fold motif, and also suggest that this motif may sample a compact conformation that limits hydrophobic residue exposure, contains key trefoil‐fold structural features, but is more structurally homologous to a β‐propeller blade motif.