Family-wide analysis of integrin structures predicted by AlphaFold2

Abstract

Recent advances in highly accurate protein structure prediction by AlphaFold have opened new avenues for analyzing all structures within a single protein family. In this study, we evaluated the capacity of the newly developed AlphaFold2-multimer for predicting integrin heterodimers. Integrins are heterodimeric cell surface receptors made up of a combination of 18 α and 8 β subunits, forming a family of 24 different members. Both α and β subunits contain a large extracellular domain, a short transmembrane domain, and usually a short cytoplasmic domain. Integrins play a wide range of cellular functions by recognizing diverse ligands. Structural studies in recent decades have greatly advanced our understanding of integrin biology, but high-resolution structures have only been determined for a few members of the integrin family. We studied the single-chain atomic structures of 18 α and 8 β integrins in the AlphaFold2 protein structure database. We then applied the AlphaFold2-multimer program to predict the α/β heterodimer structures of all 24 human integrins. The results show a high level of accuracy in the predicted structures for the subdomains of both α and β subunits and provide high-resolution structure information of all integrin heterodimers. Our structural analysis of the entire integrin family reveals a potentially diverse range of conformations among the 24 members and provides a useful structure database for guiding functional studies. However, our results also suggest the limitations of AlphaFold2 structure prediction and thus caution is required in the interpretation and usage of the AlphaFold2 structures.