Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Structure and Dynamics of Polyubiquitin Chains in Solution

Signaling via the ubiquitin-mediated pathways is modulated by the length and topology of polyubiquitin chains. Therefore, knowledge of the physiological conformations of these chains should provide insight into mechanisms of specific recognition events in the pathways. Here we use NMR methods to characterize the solution conformation of K48-linked Ub2 and Ub4.

Our chemical shift perturbation data indicate the presence of a well-defined ?closed? conformation of Ub2 at neutral and alkaline pH that switches to ?open? conformation(s) under acidic conditions (1). Characterization of these conformations using 15N relaxation data and residual dipolar couplings indicates that the closed conformation is related to, but distinguishable from that observed in the Ub2 crystal structure. Our solvent accessibility studies suggest that this interface is dynamic in solution, allowing important hydrophobic residues sequestered at the interface in the closed conformation to be accessible for recognition by other factors of Ub-mediated pathways. We also present data that suggest that the closed conformation of Ub2 might be physiologically relevant in the context of the distal end of Ub4 chains. Results from binding studies of Ub4 with its potential binding partners will be presented.

Finally, we also discuss results from our characterization of alternatively linked Ub chains using similar methods.

Supported by NIH grants GM65334 (D.F.) and DK46984 (C.P.). A.H. acknowledges HHMI Undergraduate Research Fellowship.

Ranjani Varadan1
Aydin Haririnia1
Michael Assfalg1
Olivier Walker1
Cecile Pickart2
David Fushman1,*

1Department of Chemistry and Biochemistry
Center of Biomolecular Structure and Organization
University of Maryland
College Park, MD 20742
2Department of Biochemistry and Molecular Biology
Bloomberg School of Public Health
Johns Hopkins University
Baltimore, MD 21205

References and Footnotes
  1. Varadan et al., J. Mol. Biol. 324, 637 (2002).