title: Cullin neddylation may allosterically tune polyubiquitin chain length and topology.
abstract: Conjugation of Nedd8 (neddylation) to Cullins (Cul) in Cul-RING E3 ligases (CRLs) stimulates ubiquitination and polyubiquitination of protein substrates. CRL is made up of two Cul-flanked arms: one consists of the substrate-binding and adaptor proteins and the other consists of E2 and Ring-box protein (Rbx). Polyubiquitin chain length and topology determine the substrate fate. Here, we ask how polyubiquitin chains are accommodated in the limited space available between the two arms and what determines the polyubiquitin linkage topology. We focus on Cul5 and Rbx1 in three states: before Cul5 neddylation (closed state), after neddylation (open state), and after deneddylation, exploiting molecular dynamics simulations and the Gaussian Network Model. We observe that regulation of substrate ubiquitination and polyubiquitination takes place through Rbx1 rotations, which are controlled by Nedd8-Rbx1 allosteric communication. Allosteric propagation proceeds from Nedd8 via Cul5 dynamic hinges and hydrogen bonds between the C-terminal domain of Cul5 (Cul5CTD) and Rbx1 (Cul5CTDresidues R538/R569 and Rbx1 residue E67, or Cul5CTDE474/E478/N491 and Rbx1 K105). Importantly, at each ubiquitination step (homogeneous or heterogeneous, linear or branched), the polyubiquitin linkages fit into the distances between the two arms, and these match the inherent CRL conformational tendencies. Hinge sites may constitute drug targets.
authors.affiliation: Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey.
authors.forename: Melis
authors.initials: M
authors.lastname: Onel
authors.affiliation: Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey.
authors.forename: Fidan
authors.initials: F
authors.lastname: Sumbul
authors.affiliation: Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, U.S.A.
authors.forename: Jin
authors.initials: J
authors.lastname: Liu
authors.affiliation: Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, U.S.A. nussinor@helix.nih.gov halilogt@boun.edu.tr.|Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.affiliation: Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey nussinor@helix.nih.gov halilogt@boun.edu.tr.
authors.forename: Turkan
authors.initials: T
authors.lastname: Haliloglu
mesh_terms: D000494:Allosteric Regulation; D000495:Allosteric Site; D002352:Carrier Proteins / Q000737:chemistry / Q000378:metabolism*; D044842:Cullin Proteins / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D006860:Hydrogen Bonding; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D000075687:NEDD8 Protein; D025821:Polyubiquitin; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary; D013379:Substrate Specificity; D054875:Ubiquitination; D014452:Ubiquitins / Q000737:chemistry / Q000378:metabolism*
chemical_list: C496871:CUL5 protein, human; D002352:Carrier Proteins; D044842:Cullin Proteins; D000075687:NEDD8 Protein; C082860:NEDD8 protein, human; C479529:RBX1 protein, human; D014452:Ubiquitins; D025821:Polyubiquitin
keywords: Nedd8; allosteric regulation; polyubiquitination; ubiquitin ligases