Protein Dynamics:

Protein structures are not static. Many of the bonds in a protein can rotate and flex, and entire structural segments of the protein can move on a variety of timescales. The types and timescales of motion that the protein experiences can play a significant role in the way that the protein functions. For example, some proteins such as the Ras-like GTPases are capable of interacting with a variety of different proteins using the same binding surface (1-6). This suggests that some proteins must have binding regions that are able to adjust to a variety of different incoming ligands.

In a collaboration with Dr. Robert Oswald at Cornell University, we are studying the dynamics of the G-protein Cdc42Hs, a protein is involved in a variety of cytoskeletal and growth functions. Cdc42Hs acts like a molecular switch that is off (inactive) when a molecule of GDP is bound, and on (active) when a molecule of GTP is bound. When active, Cdc42Hs can bind a variety of other proteins, in turn switching them on, thus initiating a functional cascade.

The dynamics of protein motion can be characterized using multidimensional NMR spectroscopy (xx). NMR spectroscopy is a particularly useful tool for investigating protein motions because it is sensitive to molecular motion over a wide variety of timescales. In one such study, we characterized the dynamics experienced by the backbone nitrogen atoms in three constructs of 15N-labeled Cdc42Hs (inactive, active, and active with a bound protein fragment) by measuring several relaxation parameters using 15N-1H NMR spectroscopy. This data yielded information on the type and timescale of backbone motions experienced by Cdc42Hs (Figure 1). Overall, significant flexibility was observed mainly in the regions of Cdc42Hs that are involved in protein-protein interactions. This flexibility was reduced upon interaction with a protein ligand, indicating that segmental flexibility is essential for high affinity binding interactions.

 

Figure 1: Best fit models for the dynamic behaviors of the backbone nitrogen atoms in the three constructs of Cdc42Hs . White: unassigned residues; Blue: model 1 (simple motion on a very fast timescale); Green: model 2 (simple motion on moderately fast timescale); Yellow: model 5 (complex motion on two timescales); Orange: model 3 (simple motion on a very fast timescale, and motion between two or more distinct chemical environments); Red: model 4 (simple motion on a moderate timescale, and motion between two or more distinct chemical environments).