Plexin structures are coming: opportunities for multilevel investigations of semaphorin guidance receptors, their cell signaling mechanisms, and functions

Abstract

Plexin transmembrane receptors and their semaphorin ligands, as well as their co-receptors (Neuropilin, Integrin, VEGFR2, ErbB2, and Met kinase) are emerging as key regulatory proteins in a wide variety of developmental, regenerative, but also pathological processes. The diverse arenas of plexin function are surveyed, including roles in the nervous, cardiovascular, bone and skeletal, and immune systems. Such different settings require considerable specificity among the plexin and semaphorin family members which in turn are accompanied by a variety of cell signaling networks. Underlying the latter are the mechanistic details of the interactions and catalytic events at the molecular level. Very recently, dramatic progress has been made in solving the structures of plexins and of their complexes with associated proteins. This molecular level information is now suggesting detailed mechanisms for the function of both the extracellular as well as the intracellular plexin regions. Specifically, several groups have solved structures for extracellular domains for plexin-A2, -B1, and -C1, many in complex with semaphorin ligands. On the intracellular side, the role of small Rho GTPases has been of particular interest. These directly associate with plexin and stimulate a GTPase activating (GAP) function in the plexin catalytic domain to downregulate Ras GTPases. Structures for the Rho GTPase binding domains have been presented for several plexins, some with Rnd1 bound. The entire intracellular domain structure of plexin-A1, -A3, and -B1 have also been solved alone and in complex with Rac1. However, key aspects of the interplay between GTPases and plexins remain far from clear. The structural information is helping the plexin field to focus on key questions at the protein structural, cellular, as well as organism level that collaboratoria of investigations are likely to answer.

Fig. 1

a, b Intracellular signaling networks surrounding vertebrate plexin-A and plexin-B function. Proteins that are known to directly interact with plexin-A and/or -B family members are encircled. Color scheme indicates type of protein as follows: red: GTPase or GTPase regulatory protein; blue: tyrosine kinase; green: serine/threonine kinase; light blue: enzyme involved with lipid second messenger; orange: protein functioning as adaptor, scaffold or involved with cytoskeleton [* in plexin-A4, ** in plexin-B3]. Double arrows indicate additional protein–protein interactions that may occur while bound to plexin. Single activating and inhibitory arrows pertain to the functional interaction of the two proteins involved only; e.g. R-Ras stimulates PI3K, even though in plexin signaling PI3K is downregulated because R-Ras is deactivated. Inhibitory arrow with “s” indicates a sequestration mechanism has been suggested. Cell signaling networks are not yet substantially understood for plexin-C1 and -D1. Although some common features are shared with plexin-A and -B family members, many others are likely to be distinct

Fig. 2

Domain organization of the extracellular regions of representatives of the plexin and semaphorin subfamilies. Shown in comparison are some of the proteins that also associate with plexins and/or semaphorins and that have some of the domains in common

Fig. 3

Mainchain folds of a Sema4D homodimer (pdb id 1OLZ), shown in three different orientations (i-iii). The PSI + Ig stalk is shown in brown/orange. The first and second insert regions are colored dark blue/green and red, respectively. b Plexin-A2 homodimer (pdb id 3AL9), color scheme similar as in (a), except plexin SEMA domains are shown in cyan/pink. c The Sema4D:plexin-B1 2:2 heterodimer (pdb id 3OL2) is shown in two orientations. Plexin-PSI/PSI-IPT domains are colored grey

Fig. 4

Mainchain folds showing a i–iii that binding of a Rho GTPase (colored red) destabilizes the plexin-B1 RBD dimer (magenta) (pdb ids 2R2O and 2REX). Schematics of the complexes are shown, including the GAP domains (green). A model of the RhoGTPase bound structure of the dimeric plexin structure in a.ii indicates large steric clashes, marked X, between the RhoGTPase and an opposing GAP domain in the entire intracellular region. The dimer is thus predicted to be highly unstable. b Entire intracellular region with R-Ras (yellow) modeled into the binding site of the plexin-B1 GAP region (green) (pdb id 3HM6). The coupling loop (cyan) and juxtamembrane (JM) helix (light brown) are also shown. c.i Trimeric structure of Siebold and coworkers, with the most right unit, shown in the same orientation as b. A closer look is provided in c ii of the putative second Rho GTPase binding site in plexin-B1 (region corresponds to an enlargement of the lower left side of c i, marked *). Binding at this site brings together the RBD (magenta) and switch I region of Rac1 (red) and part of the GAP domain (green) (pdb id 3SUA)