AlphaFun: Structural-Alignment-Based Proteome Annotation Reveals why the Functionally Unknown Proteins (uPE1) Are So Understudied.

With the rapid expansion of sequencing of genomes, the functional annotation of proteins becomes a bottleneck in understanding proteomes. The Chromosome-centric Human Proteome Project (C-HPP) aims to identify all proteins encoded by the human genome and find functional annotations for them. However, until now there are still 1137 identified human proteins without functional annotation, called uPE1 proteins. Sequence alignment was insufficient to predict their functions, and the crystal structures of most proteins were unavailable. In this study, we demonstrated a new functional annotation strategy, AlphaFun, based on structural alignment using deep-learning-predicted protein structures. Using this strategy, we functionally annotated 99% of the human proteome, including the uPE1 proteins and missing proteins, which have not been identified yet. The accuracy of the functional annotations was validated using the known-function proteins. The uPE1 proteins shared similar functions to the known-function PE1 proteins and tend to express only in very limited tissues. They are evolutionally young genes and thus should conduct functions only in specific tissues and conditions, limiting their occurrence in commonly studied biological models. Such functional annotations provide hints for functional investigations on the uPE1 proteins. This proteome-wide-scale functional annotation strategy is also applicable to any other species.