Analysis of Fbox substrate adapter proteins using ProteoSync, a program for projection of evolutionary conservation onto protein atomic coordinates.

The projection of conservation onto the surface of a protein's 3D structure is a powerful way of inferring functionally important regions. For this reason, we created ProteoSync, a Python program that semi-automates the process. The program creates an annotated sequence alignment of orthologs from a diverse set of selectable species and enables the fast projection of amino acid conservation onto a predicted or known 3D model in PyMOL ¹. As a test case, we used ProteoSync to analyze a subset of 31 F-box proteins, which function as substrate recognition subunits for a large family of Cul1-based E3 ubiquitin ligases. We correctly identified known substrate interaction surfaces for 11 F-box members with previously solved structures. We also identified likely ligand binding sites for 16 other members, thus demonstrating ProteoSync's utility for discovering conserved, functionally relevant surfaces.