Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement

Many biological macromolecular interactions proceed via lowly-populated, highly transient species that arise from rare excursions between the minimum free energy configuration and other local minima of the free energy landscape. Little is known about the structural properties of such lowly-occupied states since they are difficult to trap and hence inaccessible to conventional structural and biophysical techniques. Yet these states play a crucial role in a variety of dynamical processes including molecular recognition and binding, allostery, induced-fit and self-assembly. Here we highlight recent progress in paramagnetic nuclear magnetic resonance to detect, visualize and characterize lowly-populated transient species at equilibrium. We have used the PRE (a) to detect and characterize the stochastic target search process whereby a sequence-specific transcription factor binds to non-cognate DNA sites as a means of enhancing the rate of specific association via intramolecular sliding and intermolecular translocation1; (b) to directly visualize the distribution of non-specific transient encounter complexes involved in the formation of stereospecific protein-protein complexes2; (c) to determine the structure of a minor species for a multidomain protein (maltose binding protein) where large interdomain motions are associated with ligand binding;3 and (d) to characterize early transient events involved in N-terminal auto-processing of HIV-1 protease.4 The PRE offers unique opportunities to directly probe and explore in structural terms lowly-populated regions of the free energy landscape and promises to yield fundamental new insights into biophysical processes.

References and Footnotes
  1. Iwahara, J. & Clore, G. M. Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440: 1227-1230 (2006).
  2. Tang, C., Iwahara, J. & Clore, G.M. Visualization of transient encounter complexes in protein-protein association. Nature 444: 383-386 (2006)
  3. Tang, C., Schwieters, C.D. & Clore, G.M. Open to closed transition in apo maltose-binding protein visualized by paramagnetic NMR. Nature 449: 1078-1082 (2007).
  4. Tang, C., Louis, J.M., Aniana, A., Suh, J.-Y. & Clore, G.M, Visualizing transient events in N-terminal auto-processing of HIV-1 protease. Nature 455: 693-696 (2008).

G. Marius Clore

Laboratory of Chemical Physics
NIDDK, National Institutes of Health
Bethesda, MD 20892-0520

Tel: (301) 496 0782
email Marius Clore