Binding of small molecules to an adaptive protein-protein interfaceArkin, M.A., Randal, M., DeLano, W.L., Hyde, J., Luong, T.N., Oslob, J.D., Raphael, D.R., Taylor, L., Wang, J., McDowell, R.S., Wells, J.A., Braisted, A.C.
(2003) Proc.Natl.Acad.Sci.USA 100: 1603-1608
- PubMed: 12582206
- DOI: 10.1073/pnas.252756299
- Primary Citation of Related Structures:  1M47, 1M48, 1M4A, 1M4B, 1M4C
- PubMed Abstract:
Understanding binding properties at protein-protein interfaces has been limited to structural and mutational analyses of natural binding partners or small peptides identified by phage display. Here, we present a high-resolution analysis of a nonpepti ...
Understanding binding properties at protein-protein interfaces has been limited to structural and mutational analyses of natural binding partners or small peptides identified by phage display. Here, we present a high-resolution analysis of a nonpeptidyl small molecule, previously discovered by medicinal chemistry [Tilley, J. W., et al. (1997) J. Am. Chem. Soc. 119, 7589-7590], which binds to the cytokine IL-2. The small molecule binds to the same site that binds the IL-2 alpha receptor and buries into a groove not seen in the free structure of IL-2. Comparison of the bound and several free structures shows this site to be composed of two subsites: one is rigid, and the other is highly adaptive. Thermodynamic data suggest the energy barriers between these conformations are low. The subsites were dissected by using a site-directed screening method called tethering, in which small fragments were captured by disulfide interchange with cysteines introduced into IL-2 around these subsites. X-ray structures with the tethered fragments show that the subsite-binding interactions are similar to those observed with the original small molecule. Moreover, the adaptive subsite tethered many more compounds than did the rigid one. Thus, the adaptive nature of a protein-protein interface provides sites for small molecules to bind and underscores the challenge of applying structure-based design strategies that cannot accurately predict a dynamic protein surface.
Department of Biology, Sunesis Pharmaceuticals, South San Francisco, CA 94080-1913, USA. firstname.lastname@example.org