Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1

Abstract

The Plexin family of transmembrane receptors are unique in that their intracellular region interacts directly with small GTPases of the Rho family. The Rho GTPase binding domain of plexin (RBD)—which is responsible for these interactions—can bind with Rac1 as well as Rnd1 GTPases. GTPase complexes have been crystallized with the RBDs of plexinA1, -A2, and -B1. The protein association is thought to elicit different functional responses in a GTPase and plexin isoform specific manner, but the origin of this is unknown. In this project, we investigated complexes between several RBD and Rac1/Rnd1 GTPases using multimicrosecond length all atom molecular dynamics simulations, also with reference to the free forms of the RBDs and GTPases. In accord with the crystallographic data, the RBDs experience more structural changes than Rho-GTPases upon complex formation. Changes in protein dynamics and networks of correlated motions are revealed by analyzing dihedral angle fluctuations in the proteins. The extent of these changes differs between the different RBDs and also between the Rac1 and Rnd1 GTPases. While the RBDs in the free and bound states have similar—if not decreased—correlations, correlations within the GTPases are increased upon binding. Mapping highly correlated residues to the structures, it is found that the plexinA1, -B1, and -A2 RBDs all have similar communication pathways within the ubiquitin fold, but that different residues are involved. Dynamic network analyses indicate that plexinA1 and -B1 RBDs interact with small GTPases in a similar manner, whereas complexes with the plexinA2 RBD display different features. Importantly complexes with Rnd1 have a considerable number of dynamic correlations and network connections between the proteins, whereas such features are missing in the RBD–Rac1 complexes. Overall, the simulations suggest mechanisms that are consistent with the experimental data on plexinB1 and indicate RBD and GTPase isoform specific changes in protein dynamics upon complex formation.

Reduction of NgR in perforant path decreases amyloid-β peptide production and ameliorates synaptic and cognitive deficits in APP/PS1 mice

“…However, how NgR activates Rho/ROCK2 pathway is not well understood yet. The plexin receptors regulate cell adhesion, migration, and guidance, with their intracellular region interacts directly with small GTPases of the Rho family [57,58]. Plexins are widely expressed in neurons, performing critical functions in axon guidance and signal transduction [59].…”

Molecular dynamics simulations and functional studies reveal that hBD-2 binds SARS-CoV-2 spike RBD and blocks viral entry into ACE2 expressing cells

“…Furthermore, compared to the ring-ring (pi-pi) contact between residue side-chains, which is highly probable between the UK-mutant RBD and ACE2, stabilizing the interaction as shown by a deep mutagenesis study with the N501Y mutation enhancing binding (Starr et al, 2020), neither a sidechain ring or positively charged sidechain of hBD-2 appears to come near in our models of its complex with the (original) RBD. At the same time it should be noted that the interaction of the RBD with ACE2, and especially with hBD-2, is considerably dynamic (Zhang et al, 2016; Zhang and Buck, 2017). Although this has not yet been measured in the RBD:ACE2 or RBD:hBD-2 platforms, the entropy of the interaction is likely to be not as unfavorable as seen in complexes where one or both partner proteins have to become significantly rigid.…”

Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics

“…The highly conserved intracellular Ras-GAP domain of Plexins has been reported to inactivate small G proteins such as R-Ras, M-Ras, and Rap1/2 41 – 43 , whereas the C-terminus of Plexin-Bs contains a PDZ-binding motif for docking of PDZ-Rho-GEF and LARG, two guanine nucleotide exchange factors (GEFs) that can activate RhoA 44 . In addition, Plexins also contain a Rho-binding domain (RBD) where Rac1 or Rnd1/2/3 can bind, presumably to modulate Plexin activity 41 , 45 , 46 .…”