Conformational Locking and Unlocking in the Ubiquitin Family of Proteins

Abstract

Ubiquitin fold modifier 1 (UFM1) is an ubiquitin‐like protein (UBL) found in eukaryotic organisms which plays a crucial role in cell cycle regulation, signal transduction, and more. A three step enzymatic pathway composed of enzymes E1, E2, and E3 is utilized to attach UFM1 to its target protein. This conjugation pathway is common to Ubiquitin and other UBL proteins such as UFM1, ATG8, and SUMO. The crystal structure of UFM1 and its E1 (UBA5) in complex shows that UFM1 binds to the adenylation domain of UBA5 and interacts with a separate ubiquitin interacting sequence (UIS) in the C‐terminus of UBA5. The UIS interacts with UFM1 on the opposite side of the UBL protein from the adenylation domain. The reason for this second interaction site is unclear. Through molecular dynamics simulations paired with ConSurf and STRESS analysis, we analyzed UFM1 bound to the UIS sequence in the absence of the UBA5 adenylation domain. The residues in the adenylation interaction site of UFM1 have less movement when the UIS peptide was bound to UFM1 and formed a structure that aligns well UFM1 bound to the UBA5 adenylation domain. These data suggest the UIS induces formation of the proper structure for interacting with UBA5 and may enhance the affinity by locking the conformation of UFM1. The “locked” conformation of UFM1 is observed in the absence of the peptide, but less frequently. Through additional simulations on Ubiquitin and Ubiquitin‐like proteins, we show that similar allosteric trends exist for ATG8 which like UFM1 uses a non‐canonical E1 enzyme while Ubiquitin and SUMO do not show this behavior. Ubiquitin and SUMO, instead show increased motion (“unlocking”) upon binding to known interacting partners. Non‐canonical E1 enzymes lack of some substrate binding domains found in the canonical E1 enzymes suggesting this locking mechanism may compensate for the lack of these domains.Support or Funding InformationNSF REU (CHE‐1461175)US Israel Binational Science Foundation