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                                           BIOINFORMATICS COLLOQUIUM
					       College of Science
                                            George Mason University
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		Characterization of the structure and conformational dynamics in multi-domain proteins. 
					  Applications to polyUbiquitin.
 
					       David Fushman, Ph.D.
                                                    Professor 
                                             University of Maryland 

Abstract:
Many proteins in the cell have modular architecture, i.e. they are composed of several well-folded regions 
(domains). Structural organization and interdomain dynamics often play a key role in molecular recognition 
events and functional regulation. Specifically, numerous cellular processes are regulated by 
(poly)ubiquitin-mediated signaling events, and knowledge of the conformational properties of polyubiquitin 
chains is essential for understanding of the structural determinants of functional diversity of polyubiquitin. 
Characterization of these systems, however, presents a significant challenge, because the existing methods for 
structure determination, X-ray crystallography and NMR, rest on the assumption of a unique conformation and, 
therefore, could be inadequate when applied to inherently flexible systems. Domain motions, naturally occurring 
in solution, are completely restricted in crystals, and packing forces could result in a positioning of protein 
domains in a crystal structure that might not represent the physiologically relevant conformation. The challenges 
for conventional NMR characterization of multidomain systems are due to (1) insufficient information on the relative 
interdomian positioning/contacts and orientation and (2) the absence of adequate models for interdomain mobility 
in these systems. I will discuss some recently developed approaches based on spin-relaxation measurements that 
address these problems. These methods are applied to Lys48-linked di-ubiquitin, which in solution exists in dynamic 
equilibrium between a closed and one or more open conformations. I will present a detailed, NMR-derived picture of 
the process of opening/closing of the protein and show that using 15N relaxation measurements combined with physical 
models, it is possible to not only characterize the interdomain dynamics but also to determine the structure 
(i.e. domain positioning and orientation) of the interconverting states.