A Structural Recognition Mechanism Study of MARCH and its Substrate

Abstract

Ubiquitination, used by all eukaryotic cells to tag proteins for proteasomal degradation, is also involved in membrane protein regulation. The process of ubiquitination is mediated by ubiquitin ligases, such as the MARCH ligases in this study. The MARCH ligases are membrane proteins and play a major immunoregulatory role in cells of the immune system. They recognize their (membrane protein) substrates via transmembrane (TM) interactions_a poorly understood phenomenon. In order to characterize these TM-induced MARCH-substrate interactions, we have performed replica exchange molecular dynamics (REX-MD) simulations in an implicit membrane to model TM structures of MARCH-1 and MARCH-9 based on their TM and loop sequences. Both MARCHs have two putative TM helices (TM1 and TM2) connected by an extracellular loop. The key TM1-TM2 interfacial residues and the relative orientation of the two TMs are identified and presented. We have also determined possible TM interaction modes of known MARCH-substrate by REX-MD simulations of the complex structure, and the results will be presented in terms of the molecular basis of the MARCH-substrate recognition mechanisms.