@Article{C5CP04601G,
author ="Castaneda, Carlos A. and Chaturvedi, Apurva and Camara, Christina M. and Curtis, Joseph E. and Krueger, Susan and Fushman, David",
title  ="Linkage-specific conformational ensembles of non-canonical polyubiquitin chains",
journal  ="Phys. Chem. Chem. Phys.",
year  ="2016",
volume  ="18",
issue  ="8",
pages  ="5771-5788",
publisher  ="The Royal Society of Chemistry",
doi  ="10.1039/C5CP04601G",
url  ="http://dx.doi.org/10.1039/C5CP04601G",
abstract  ="Polyubiquitination is a critical protein post-translational modification involved in a variety of processes in eukaryotic cells. The molecular basis for selective recognition of the polyubiquitin signals by cellular receptors is determined by the conformations polyubiquitin chains adopt; this has been demonstrated for K48- and K63-linked chains. Recent studies of the so-called non-canonical chains (linked via K6{,} K11{,} K27{,} K29{,} or K33) suggest they play important regulatory roles in growth{,} development{,} and immune system pathways{,} but biophysical studies are needed to elucidate the physical/structural basis of their interactions with receptors. A first step towards this goal is characterization of the conformations these chains adopt in solution. We assembled diubiquitins (Ub2) comprised of every lysine linkage. Using solution NMR measurements{,} small-angle neutron scattering (SANS){,} and in silico ensemble generation{,} we determined population-weighted conformational ensembles that shed light on the structure and dynamics of the non-canonical polyubiquitin chains. We found that polyubiquitin is conformationally heterogeneous{,} and each chain type exhibits unique conformational ensembles. For example{,} K6-Ub2 and K11-Ub2 (at physiological salt concentration) are in dynamic equilibrium between at least two conformers{,} where one exhibits a unique Ub/Ub interface{,} distinct from that observed in K48-Ub2 but similar to crystal structures of these chains. Conformers for K29-Ub2 and K33-Ub2 resemble recent crystal structures in the ligand-bound state. Remarkably{,} a number of diubiquitins adopt conformers similar to K48-Ub2 or K63-Ub2{,} suggesting potential overlap of biological function among different lysine linkages. These studies highlight the potential power of determining function from elucidation of conformational states."}