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Deciphering the BAR Code of Membrane Modulators

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Cell. Mol. Life Sci. DOI 10.1007/s00018-017-2478-0 Cellular and Molecular LifeSciences REVIEW Deciphering the BAR code of membrane modulators Ulrich Salzer1 · Julius Kostan2 · Kristina Djinović‑Carugo2,3 Received: 30 September 2016 / Revised: 25 January 2017 / Accepted: 27 January 2017 © The Author(s) 2017. This article is published with open access at Springerlink.com Abstract The BAR domain is the eponymous domain of Keywords N-BAR domain · F-BAR domain · I-BAR the “BAR-domain protein superfamily”, a large and diverse domain · lipid binding · Membrane remodelling · set of mostly multi-domain proteins that play eminent roles Membrane curvature at the membrane cytoskeleton interface. BAR domain homodimers are the functional units that peripherally asso- ciate with lipid membranes and are involved in membrane Introduction sculpting activities. Differences in their intrinsic curvatures and lipid-binding properties account for a large variety in Identification of sequence homology between the N-termi- membrane modulating properties. Membrane activities nal regions of the Bin, the amphiphysin, and the yeast Rvs of BAR domains are further modified and regulated by proteins led to the recognition of a novel protein domain intramolecular or inter-subunit domains, by intermolecu- which was named “BAR domain” as an acronym composed lar protein interactions, and by posttranslational modifica- of the first letters of these proteins [1]. This domain was tions. Rather than providing detailed cell biological infor- found in a large set of proteins which were classified as mation on single members of this superfamily, this review BAR domain proteins, later also termed N-BAR domain focuses on biochemical, biophysical, and structural aspects proteins, because several members of this protein family and on recent findings that paradigmatically promote our have an amphipathic helix at the N-terminus of the BAR understanding of processes driven and modulated by BAR domain [2]. The structure of the amphiphysin BAR domain domains. laid the basis for a mechanistic understanding of membrane deformation by this protein and of N-BAR domain proteins, in general: the BAR-domain homodimer displays a cres- cent shape that binds to the membrane bilayer with its con- cave side. In addition, an N-terminal amphipathic helix is thought to insert into the membrane like a “wedge”, thereby U. Salzer and J. Kostan contributed equally to the work. inducing membrane buckling [2]. Soon thereafter, the rela- tionship on the sequence level between N-BAR domains * Kristina Djinović-Carugo [email protected] and a protein domain that consisted of an N-terminal FCH (Fes/CIP4 homology) and a coiled-coil (CC) domain was 1 Max F. Perutz Laboratories, Department of Medical found and the term “F-BAR domain” was coined [3]. The Biochemistry, Medical University of Vienna, Dr. Bohr-Gasse alternative term “extended FC (EFC) domain” stressing the 9, 1030 Vienna, Austria 2 connection between the FCH and the CC region [4] is less Max F. Perutz Laboratories, Department of Structural used than “F-BAR domain”, because “BAR” is nowadays and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria well associated with the general notion of membrane mod- eling. Structural analyses of the IRSp53 protein identified 3 Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna the Rac-binding (RCB) domain/IRSp53-MIM homology pot 119, 1000 Ljubljana, Slovenia domain (IMD) as a member of yet another type of BAR Vol.:(0123456789)1 3 U. Salzer et al. domains [5, 6]. Here, in contrast to the crescent-shaped curvature opposite that of BAR domains and deforms dimer of the BAR-domain, the dimer of the RCB domain membranes by binding to the interior of the tubules, this of IRSp53 revealed a “zeppelin-like shape”. Similar to domain was renamed accordingly as “inverse-BAR” or BAR domains, this RCB/IMD domain which was known to I-BAR domain [7, 8] (Fig. 1a). bundle actin filaments and bind Rac, displayed membrane Most BAR domain proteins contain one or several addi- deforming activity. Since RCB/IMD induces a membrane tional domains with lipid-binding, protein-binding and/ Fig. 1 Structure of selected BAR domain dimers. The BAR domain dimers form an elongated structure with a core bundle of six α-helices gener- ated by antiparallel dimerisation of two BAR domain monomers. 3D structures of BAR domain dimers are shown as a ribbon. Monomers are depicted in different colors (yellow and dark magenta). Side view of the each BAR dimer is shown on left, while top view is on right. a Examples of BAR domain dimers representing N-BAR, F-BAR, and I-BAR domain fold. Different degrees of curvature adopted by each class of BAR domain dimers are depicted by grey lines. b Struc- tures of BAR domain dimers from different subfamilies with their accessory domains (PH, PX, PDZ, and SH3) shown in magenta. Note, for PICK1, that two SAXS analysis derived models are shown. In PICK1 model (SASDAB8), the PDZ domains are far apart and flexible with respect to the BAR domain. Here, overlay of three generated models is shown. In the PICK1 model of Madasu et al. [78], the position of the PDZ domain was found to be well constrained, and packed against BAR domain. c Structure of the Arfaptin-2 BAR domain dimer in complex with Arl1 GTPase, and Rac1-GDP, both shown in green 1 3 Deciphering the BAR code of membrane modulators Fig. 2 Schematic domain representation of selected BAR domain N-BAR domain proteins. PTB (phosphotyrosine-binding) domain proteins. Selected members of the N-BAR (BAR with an N-terminal binds to phosphotyrosine. GBD (GTPase‑binding domain) is required amphipathic helix) and I-BAR (inverse-BAR) domain family on left for binding to Rho small GTPases. WH2 (Wiskott-Aldrich syndrome and F-BAR (Fes/CIP4 homology-BAR) domain family on right are homology 2) domain binds to actin monomers and can facilitate the depicted. Most BAR domain proteins contain one or several addi- assembly of actin monomers into actin filaments. HR1 (protein kinase tional domains with lipid-binding, protein-binding, and/or enzymatic C-related kinase homology region 1) binds the small G protein Rho. activities. PDZ (PSD95/Dlg1/ZO-1) domain mediates protein–protein FX (F-BAR extension) domain in Fer was shown to bind phosphatidic interactions by binding to the C-terminus of other specific proteins. acid. SH2 (Src homology 2) domain allows binding to phosphoryl- SH3 (Src homology 3) domain confers binding to poly-proline motifs ated tyrosine residues on other proteins. RhoGAP (Rho GTPase acti- of target proteins, like N-WASP or dynamin. The phosphoinositides- vating protein) domain modulates the activity of Rho. Fer and Fes binding PX (phox homology) and PH (pleckstrin homology) domains possess a tyrosine kinase domain modulate membrane-binding specificities of different subsets of or enzymatic activities (Figs. 1b, 2). The most common BAR-domain proteins and small GTPases which are known domain combined with N-, F-, and I-BAR domains is the as master regulators of the actin cytoskeleton. The combi- Src Homology 3 domain (SH3) which confers binding to nation of BAR domains with additional functional domains poly-proline motifs of target proteins, like the cytoskel- within the same polypeptide constitutes the functional etal organizer N-WASP or the membrane vesicle scissor diversity of the members of this superfamily. BAR domain dynamin [9]. The phosphoinositide-binding phox homol- proteins are key players in processes like clathrin-depend- ogy (PX) and pleckstrin homology (PH) domains are ent [10] and clathrin-independent [11] endocytosis, caveo- present in different subsets of N-BAR domain proteins, lae formation [12, 13], intracellular vesicle formation [14], thereby modulating membrane-binding specificities of cell migration [15, 16], and cytokinesis [17] to name only these proteins. A Rho GTPase activating protein (RhoGAP) a few. The recognition of the full molecular significance of domain is found in the N-BAR domain proteins nadrin and BAR domain proteins is only slowly emerging. Overviews oligophrenin and the F-BAR domain proteins srGAP1-4 of our current knowledge on the cell biological function (Fig. 2) and HMHA1. N-BAR domain proteins ASAP1 and the (patho)-physiological impact of BAR domain pro- and centaurin contain an ArfGAP domain and the tuba teins are given in various excellent reviews [18–24]. protein contains a Rho guanine-nucleotide exchange factor In this review, we focus on the association of the BAR- domain (RhoGEF). This indicates a close linkage between domain dimer with intramolecular or intradimer domains 1 3 U. Salzer et al. as well as on its ligand-binding characteristics. Rather than Comparing the requirements of membrane association giving a broad overview on the functional diversity of BAR within the srGAP subfamily of F-BAR proteins, Coutinho- domain proteins, we here specifically present those stud- Budd et al. found that srGAP2 and srGAP3 differently ies that further our mechanistic understanding of processes depend on PIP2 for membrane association [29]. In contrast driven/modulated by BAR domain dimers. to srGAP3, srGAP2 remains largely membrane associated upon temporal cellular PIP2 depletion. Despite of a high degree of similarity between these two proteins, this differ- ential behavior is likely due to altered lipid-binding specifi- Interaction with membranes cities. The srGAP2 protein apparently has a broader spec- trum of affinities to negatively charged membrane lipids Lipid‑binding specificities and thus withstands conditions of a selective loss of PIP2 in the membranes. These data impressively show the differ- The excess of positively charged residues at the concave ential influence of membrane lipid composition on the sub- side of the crescent-shaped dimer is a hallmark of N- and cellular localization of BAR domain proteins and indicate F-BAR domain proteins and is suggestive for their prefer- a general regulatory impact of lipid metabolism on these ential binding to membrane regions rich in anionic phos- proteins.
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