Interrogating protein interaction networks through structural biology

Abstract

Protein-protein interactions are central to most biological processes. Although much recent effort has been put into methods to identify interacting partners, there has been a limited focus on how these interactions compare with those known from three-dimensional (3D) structures. Because comparison of protein interactions often involves considering homologous, but not identical, proteins, a key issue is whether proteins that are homologous to an interacting pair will interact in the same way, or interact at all. Accordingly, we describe a method to test putative interactions on complexes of known 3D structure. Given a 3D complex and alignments of homologues of the interacting proteins, we assess the fit of any possible interacting pair on the complex by using empirical potentials. For studies of interacting protein families that show different specificities, the method provides a ranking of interacting pairs useful for prioritizing experiments. We evaluate the method on interacting families of proteins with multiple complex structures. We then consider the fibroblast growth factor/receptor system and explore the intersection between complexes of known structure and interactions proposed between yeast proteins by methods such as two-hybrids. We provide confirmation for several interactions, in addition to suggesting molecular details of how they occur.

Figure 1

Interaction types across the four classes.

Figure 2

The FGFR system. alscript (37) alignment and molscript (38) structure figures showing the FGF (Upper)/receptor (Lower) interaction. Sequences are denoted by SWISSPROT or PDB identifiers. Residues are colored according to property conservation: hydrophobic, yellow background; small, blue background; and polar, red characters. Residues in the known structure (FGF-2/FGFR-1; PDB code 1cvs (26) participating in side-chain to side-chain contacts are shown and colored: positive, blue; negative, red; hydrophobic, yellow; and tyrosine, green. Residues participating in side-chain to main-chain contacts are boxed. Contacts between side-chains are listed.

Figure 3

Yeast interactions mapped onto known 3D complexes. Yeast proteins are given by their YPD names, codes, and Pfam families. Thick lines denote interactions significant at ≤0.01, thin lines 0.01–0.1, and dashed lines >0.1.

Figure 4

The kinase/cyclase system in yeast. Sequences are denoted by YPD or PDB codes. The known structure [1fin (35)] is that of human CDK2 (Upper)/cyclin A (Lower). Details are otherwise as for Fig. 2.