The BAR-domain family of proteins: a case of bending and binding?

Abstract

BAR-domains recently took centre stage in science through a report on the crystal structure of this domain in Drosophila Amphiphysin. Though only weakly conserved at the sequence level, the structure of the BAR domain shows striking similarity to the GTPase-binding domain of Arfaptin 2, an effector of Rho- and Arf- GTPases. On the basis of this sequence and structural similarity, these two proteins have been classified as belonging to the same family, the BAR-domain family, and they probably also have similar functional characteristics. Presented here are the results of a database search for the sequence of the BAR domain of Amphiphysin and Arfaptin 2. This search identified a variety of related proteins, most of which are involved in intracellular transport and especially in endocytosis. For example, the BAR-domain family includes Endophilins, GTPase-activating proteins of the Centaurinbeta family and Oligophrenins, the adaptor proteins APPL1 and APPL2 that were recently shown to interact with the small GTPase Rab5, as well as members of the Sorting nexin family. On the basis of the structures of Amphiphysin and Arfaptin 2 and the cellular role of Amphiphysins in the early steps of endocytosis, the functions of the BAR domain have been defined as a dimerization motif and as sensing and inducing membrane curvature. However, data on Arfaptin 2 and now also on the Adaptor proteins APPL1 and 2 suggest that another function of the BAR domain is to bind to small GTPases.

Figure 1

Crystal structures of Arfaptin 2 complexed with Rac and Amphiphysin. Both proteins form a crescent-shaped dimer. Rac (light grey) binds to the centre of the Arfaptin 2 dimer. One monomer of each homodimer is highlighted in red. Protein Data Bank accession numbers: Arfaptin 2:Rac1, ; Amphiphysin, .

Figure 2

Phylogenetic tree of proteins belonging to the BAR-domain family. Six families can be distinguished: the Arfaptin family, which contains the Arfaptins, Protein kinase C-binding protein 1 (PICK1) and the islet cell antigen Ica69; the Amphiphysin family, which contains Amphiphysin I and II, as well as their paralogue BRAP1 and the RhoGEF Tuba; the third family is composed of the GTPase-activating proteins Centaurinβ 1, β 2 and β 5, Oligophrenins and the adaptor proteins APPL1 and APPL2; the Rac-binding proteins Bap2α and Bap2-like seem to form a separate family; the Sorting nexins (1, 2, 4, 5, 6, 7, 8, 9 and 18), which are the most divergent members of the BAR-domain family; and finally the Endophilin and Nadrin family, which includes Endophilin I, II and III, Endophilin B, as well as Nadrin and SH3-BP1. Those depicted in red indicate experimentally determined GTPase-binding, double circles indicate experimentally proven dimerization. Helices indicate helical fold as determined by the program 3D-PSSM (Kelley et al, 2000). When the structure of Arfaptin 2 (1I4T) was identified as the top hit, a red helix is shown. When related structures (Phospholipase Cβ (1JAD), Alpha-Spectrin (1CUN), Syntaxin 1A (1DN1) and Interferon-induced guanylate-binding protein 1 (1DG3)) were identified, a grey helix is shown. For details of database searching and accession numbers, see supplementary information online.

Figure 3

Multiple sequence alignment of the BAR domains from Amphiphysins and from the subset of BAR domain family members that were shown to bind to a small GTPase. Residues with related sequences in the Amphiphysins and the Arfaptins are highlighted in grey; secondary structure elements, as determined from the crystal structures, are indicated at the top of the Amphiphysin and Arfaptin families, respectively as blue and red helices. Red dots indicate GTPase-binding sites of Arfaptin 2, blue dots indicate residues in Amphiphysin involved in the formation of tubules in the membrane. The alignment was generated on the basis of a structural alignment between Amphiphysin and Arfaptin 2, using the COMPARER server (Sali & Blundell, 1990). The remaining sequences were aligned manually. d, Drosophila melanogaster; h, human; x, Xenopus laevis. An alignment of human orthologues of all BAR domain-containing proteins is available in the supplementary information online.

Figure 4

Models for the separation or the interplay between membrane curvature sensing and bending and small GTPase-binding of BAR-domain proteins. In the exclusive model, the BAR domain is either a sensor of membrane curvature or a binding platform for a small GTPase. In the sequential model I, sensing membrane curvature takes place before interaction with a small GTPase, possibly as a means for proper localization. In the sequential model II, GTPase binding would take place before inducing membrane curvature.