Versatile communication strategies among tandem WW domain repeats

Abstract

Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands.

Keywords: WW domain; WW domain containing oxidoreductase; Yes-associated protein; cooperative binding; peptide-mediated interactions; protein domain repeats; regulation of signaling.

Figure 1

The life cycle of a regulatory protein is determined by WW domains. Proteins that contain (multiple) WW domains are involved in the tight regulation of both activation and clearance of major players in critical regulatory pathways. A simplified scheme of this process consists of the following steps: The target protein (white ellipse) is activated (bold outline) by binding to an activator protein (gray trapezoid), and subsequently targeted for degradation (dotted outline) by binding to an E3 ubiquitin ligase (gray rectangle).^,, Both steps are regulated by competition with a sequestering protein (black triangle), as well as often by phosphorylation. All these interactions are mediated by interactions between WW domains (labeled dark gray rectangles) and the polyproline ligands on the target (black rectangles). The different targets, activators, and E3 ubiquitin ligases discussed in more detail in the text are shown, together with their number of WW domains. We note that interactions with different partners may involve different (numbers of) WW domains. See text for more details. (A color version of this figure is available in the online journal.)

Figure 2

Strategies for integration of input from different WW domains. Tandem WW domains in proteins can communicate in different ways during binding to their polyproline (and/or (pS/pT)P) ligand containing targets. This figure depicts the main strategies reported in literature and discussed in this review. In each example (except for (a)), the discussed WW domain is highlighted by a dotted rectangle and labeled in bold. For the WW domains, unstable domains are shown in dotted outline and the peptide binding site is indicated by a sickle. Different binding specificities are indicated by different fills (e.g. granite texture for Pin1-ligand binding to a (pS/pT)P ligand). Binding/nonbinding is shown by “v” and “x” signs, respectively. See text for more details. (a) Additive effect (as originally suggested for YAP2): Both tandem domains (e.g. WW1 and WW2 of YAP2) are independently capable of interaction with motifs on the target protein (e.g. ErbB4), but two such interactions significantly increase effective binding affinity. (b) Chaperone effect (e.g. WWOX):^, While only the first domain (e.g. WW1 of WWOX) is able to bind to the target (e.g. ErbB4), it is the second domain (WW2 of WWOX) that stabilizes this interaction to obtain the necessary binding affinity. The second domain has lost its ability to bind due to mutations at critical binding positions. (c) Binding-induced-binding (e.g. Nedd4L that outcompetes Pin1): In this case, the binding affinity of a weakly binding domain (e.g. WW2 domain of Nedd4L) is increased by positioning it next to its target peptide (e.g. on Smad2) after the first domain (e.g. WW3 domain of Nedd4L) has bound to an adjacent peptide motif. In this case, this binding event might outcompete an original, stronger interaction (trapezoid; e.g. with Pin1). (d) Modulation of binding conformation by adjacent WW domain (e.g. FBP11): An adjacent WW tandem domain (e.g. WW2 domain of FBP11) can change the stability as well as the dynamics of a WW domain (e.g. WW1 domain of FBP11), leading to changes in the target peptide bound conformation, and possibly in the binding specificity of the WW domain. (e) Integration of two binding events by competition between stabilization and binding (e.g. Su(dx)): A WW domain that can bind its polyproline target in isolation (e.g. WW4 domain of Su(dx)), loses this ability when connected to its tandem WW domain (e.g. WW3 domain of Su(dx)), due to stabilization of a binding-incompatible conformation. Upon binding of the tandem WW3 domain to its own polyproline target, the inhibition of the first is released. This results in an AND switch where full binding is only achieved when both WW domains are bound

Figure 3

Structures of tandem WW domains reveal a wide range of interdomain flexibility. A range of mobility between WW domains is observed in different solved tandem domain structures. (a) Yeast splicing factor Prp40 WW1–WW2 [Protein Data Bank (PDB) id 1o6w]. (b) E3 Ubiquitin ligase Su(dx) WW3–WW4 (PDB id 1tk7). (c) E3 Ubiquitin ligase Smurf2 WW3–WW4 bound to its peptide ligand (PDB id 2kxq). (d) Human Prp40 homologs FBP11 (PDB id 2l5f) and (e) FBP21 (PDB id 2jxw). The first WW domain, linker, and second WW domains are shown on the left in pink, in light gray, and to the right in cyan, respectively. The peptide is displayed as black trace (in (c)). Slight reorientations were performed to optimally display flexibility (in FBP21, the first domain is located in the center, in front of the rest). See text for more details. (A color version of this figure is available in the online journal.)