Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures.

ABSTRACT: Many proteins contain cleavable signal or transit peptides that direct them to their final subcellular locations. Such peptides are usually predicted from sequence alone using methods such as TargetP 2.0 and SignalP 6.0. While these methods are usually very accurate, we show here that an analysis of a protein's AlphaFold2-predicted structure can often be used to identify false positive predictions. We start by showing that when given a protein's full-length sequence, AlphaFold2 builds experimentally annotated signal and transit peptides in orientations that point away from the main body of the protein. This indicates that AlphaFold2 correctly identifies that a signal is not destined to be part of the mature protein's structure and suggests, as a corollary, that predicted signals that Alpha

SUBMITTER: Sanaboyana VR 

PROVIDER: S-EPMC10843742 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature