PDBsum entry 1m4c

Cytokine

PDB id: 1m4c

Contents

Protein chains

114 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Binding of small molecules to an adaptive protein-Protein interface.

Authors

M.R.Arkin, M.Randal, W.L.Delano, J.Hyde, T.N.Luong, J.D.Oslob, D.R.Raphael, L.Taylor, J.Wang, R.S.Mcdowell, J.A.Wells, A.C.Braisted.

Ref.

Proc Natl Acad Sci U S A, 2003, 100, 1603-1608. [DOI no: 10.1073/pnas.252756299]

PubMed id

12582206

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 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.

Figure 1.
Fig. 1. (a) Compound 1/IL-2 complex determined by x-ray crystallography (Table 1). Compound 1 is shown in green sticks, IL-2 in white ribbon. The B-C loop is not defined by the electron density and is shown schematically in white spheres. (b) Interaction of Compound 1 (green sticks) with IL-2 (white sticks) taken from x-ray coordinates. Key contact side chains are labeled; H-bonds and distances are shown by yellow dotted lines. All molecular graphic images were produced with PYMOL (W. L. DeLano, San Carlos, CA).

Figure 2.
Fig. 2. Adaptivity of the IL-2-binding surface. (a) Structure of the complex of IL-2 and Compound 1, shown as a surface representation of IL-2 (white and orange) and stick representation of Compound 1 (green). The residues that comprise the IL-2R -binding hot spot are shown in orange. Residues contacting the molecule are labeled. (b-d) Surface representation of three different unliganded structures (21) (b) and Native I and II (c and d; Table 1). Compound 1 is overlaid to emphasize the extent of rearrangement that occurs in both of the unliganded structures and in the liganded form. Movie 1 (RIGIMOL, W. L. DeLano) highlights the dynamic nature of this site across this series of structures.