Binding of small molecules to an adaptive protein-protein interface.
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.
Arkin
Michelle R
MR
Department of Biology, Sunesis Pharmaceuticals, South San Francisco, CA 94080-1913, USA. mra@sunesis.com
Randal
Mike
M
DeLano
Warren L
WL
Hyde
Jennifer
J
Luong
Tinh N
TN
Oslob
Johan D
JD
Raphael
Darren R
DR
Taylor
Lisa
L
Wang
Jun
J
McDowell
Robert S
RS
Wells
James A
JA
Braisted
Andrew C
AC
D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D006801:Humans; D007376:Interleukin-2 / Q000235:genetics / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D015375:Receptors, Interleukin-2 / Q000378:metabolism; D020349:Surface Plasmon Resonance; D013816:Thermodynamics
D007376:Interleukin-2; D008024:Ligands; D015375:Receptors, Interleukin-2