@article {18694,
	title = {Affinity Makes the Difference: Nonselective Interaction of the UBA Domain of Ubiquilin-1 with Monomeric Ubiquitin and Polyubiquitin Chains},
	journal = {Journal of Molecular Biology},
	volume = {377},
	year = {2008},
	month = {2008/03/14/},
	pages = {162 - 180},
	abstract = {Ubiquilin/PLIC proteins belong to the family of UBL{\textendash}UBA proteins implicated in the regulation of the ubiquitin-dependent proteasomal degradation of cellular proteins. A human presenilin-interacting protein, ubiquilin-1, has been suggested as potential therapeutic target for treating Huntington{\textquoteright}s disease. Ubiquilin{\textquoteright}s interactions with mono- and polyubiquitins are mediated by its UBA domain, which is one of the tightest ubiquitin binders among known ubiquitin-binding domains. Here we report the three-dimensional structure of the UBA domain of ubiquilin-1 (UQ1-UBA) free in solution and in complex with ubiquitin. UQ1-UBA forms a compact three-helix bundle structurally similar to other known UBAs, and binds to the hydrophobic patch on ubiquitin with a Kd of 20~μM. To gain structural insights into UQ1-UBA{\textquoteright}s interactions with polyubiquitin chains, we have mapped the binding interface between UQ1-UBA and Lys48- and Lys63-linked di-ubiquitins and characterized the strength of UQ1-UBA binding to these chains. Our NMR data show that UQ1-UBA interacts with the individual ubiquitin units in both chains in a mode similar to its interaction with mono-ubiquitin, although with an improved binding affinity for the chains. Our results indicate that, in contrast to UBA2 of hHR23A that has strong binding preference for Lys48-linked chains, UQ1-UBA shows little or no binding selectivity toward a particular chain linkage or between the two ubiquitin moieties in the same chain. The structural data obtained in this study provide insights into the possible structural reasons for the diversity of polyubiquitin chain recognition by UBA domains.},
	keywords = {polyubiquitin, protein{\textendash}protein interaction, UBA domain, ubiquilin, ubiquitin},
	isbn = {0022-2836},
	doi = {10.1016/j.jmb.2007.12.029},
	url = {http://www.sciencedirect.com/science/article/pii/S0022283607016452},
	author = {Zhang,Daoning and Raasi,Shahri and Fushman, David}
}
@article {18700,
	title = {Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin},
	journal = {Protein Science},
	volume = {16},
	year = {2007},
	month = {2007///},
	pages = {369 - 378},
	abstract = {In solution, Lys48-linked di-ubiquitin exists in dynamic equilibrium between closed and open conformations. To understand the effect of interdomain motion in polyubiquitin chains on their ability to bind ligands, we cyclized di-ubiquitin by cross-linking the free C terminus of the proximal ubiquitin with the side chain of residue 48 in the distal ubiquitin, using a chemical cross-linker, 1,6-Hexane-bis-vinylsulfone. Our NMR studies confirm that the cyclization affects conformational dynamics in di-ubiquitin by restricting opening of the interface and shifting the conformational equilibrium toward closed conformations. The cyclization, however, did not rigidly lock di-ubiquitin in a single closed conformation: The chain undergoes slow exchange between at least two closed conformations, characterized by interdomain contacts involving the same hydrophobic patch residues (Leu8-Ile44-Val70) as in the uncyclized di-ubiquitin. Lowering the pH changes the relative populations of these conformations, but in contrast with the uncyclized di-ubiquitin, does not lead to opening of the interface. This restriction of domain motions inhibits direct access of protein molecules to the hydrophobic patch residues located at the very center of the interdomain interface in di-ubiquitin, although the residual motions are sufficient to allow access of small molecules to the interface. This renders di-ubiquitin unable to bind protein molecules (e.g., UBA2 domain) in the normal manner, and thus could interfere with Ub2 recognition by various downstream effectors. These results emphasize the importance of the opening/closing domain motions for the recognition and function of di-ubiquitin and possibly longer polyubiquitin chains.},
	keywords = {cyclization, di-ubiquitin, interdomain dynamics, Lys48-linked ubiquitin chain, UBA domain},
	isbn = {1469-896X},
	doi = {10.1110/ps.062508007},
	url = {http://onlinelibrary.wiley.com/doi/10.1110/ps.062508007/abstract},
	author = {Dickinson,Bryan C. and Varadan,Ranjani and Fushman, David}
}
