Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers

Jang, Hyunbum; Muratcioğlu, Serena; Gürsoy, Attila; Keskin, Özlem; Nussinov, Ruth

doi:10.1042/bcj20160031

Cited by 91 publications

(100 citation statements)

References 70 publications

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“…The CHARMM program 22 was used to construct the set of initial conformations and to relax the systems for the atomistic MD simulations. Using the same MD protocols as in our previous works, 23–29 the dimer systems were solvated by the modified TIP3P water model and subsequently minimized using the steepest descent (SD) and adopted-basis Newton-Raphson (ABNR) methods, followed by consecutive cycles of dynamics in the pre-equilibrium stage. During the pre-equilibrium simulations, the initial crystal structures of SARAH dimers were gradually relaxed after solvation.…”

Section: Methodsmentioning

confidence: 99%

The dynamic mechanism of RASSF5 and MST kinase activation by Ras

Liao

Jang

Tsai

et al. 2017

Phys. Chem. Chem. Phys.

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As a tumor suppressor, RASSF5 (NORE1A) activates MST1/2 thereby modulating the Hippo pathway. Structurally, activation involves RASSF5 and MST1/2 swapping their SARAH domains to form a SARAH heterodimer. This exposes the MST1/2 kinase domain which homodimerizes, leading to trans-autophosphorylation. The SARAH-SARAH interaction shifts RASSF5 away from its autoinhibited state and relieves MST1/2 autoinhibition. Separate crystal structures are available for the RA (Ras association) domain and SARAH dimer, where SARAH is a long straight α-helix. Using all-atom molecular dynamics simulations, we modeled the RASSF5 RA with a covalently connected SARAH to elucidate the dynamic mechanism of how SARAH mediates between autoinhibition and Ras triggered-activation. Our results show that in inactive RASSF5 the RA domain retains SARAH, yielding a self-associated conformation in which SARAH is in a kinked α-helical motif that increases the binding interface. When RASSF5 binds K-Ras4B-GTP, the equilibrium shifts toward SARAH’s interacting with MST. Since the RA/SARAH affinity is relatively low, whereas that of the SARAH heterodimer is in the nM range, we suggest that RASSF5 exerts its tumor suppressor action through competition with other Ras effectors for Ras effector binding site, as well as coincidentally its recruitment to the membrane to help MST activation. Thus, SARAH plays a key role in RASSF5’s tumor suppression action by linking the two major pathways in tumor cell proliferation: Ras and the MAPK (tumor cell proliferation-promoting) pathway, and the Hippo (tumor cell proliferation-suppressing) pathway.

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Section: Methodsmentioning

confidence: 99%

The dynamic mechanism of RASSF5 and MST kinase activation by Ras

Liao

Jang

Tsai

et al. 2017

Phys. Chem. Chem. Phys.

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“…Further details of the calculation protocol are reported in our previous studies (58). The electrostatic and non-polar contributions to the solvation free energy are obtained from the GB approximation within the CHARMM program (55).…”

Section: Methodsmentioning

confidence: 99%

Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2

Ozdemir

Jang

Gürsoy

et al. 2018

Journal of Biological Chemistry

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IQ motif-containing GTPase-activating protein (IQGAP) scaffolding proteins play central roles in cell-cell adhesion, polarity, and motility. The Rho GTPases Cdc42 and Rac1, in their GTPbound active forms, interact with all three human IQGAPs. The IQGAP-Cdc42 interaction promotes metastasis by enhancing actin polymerization. However, despite their high sequence identity, Cdc42 and Rac1 differ in their interactions with IQGAP. Two Cdc42 molecules can bind to the Exdomain and the RasGAP site of the GTPaseactivating protein (GAP)-related domain (GRD) of IQGAP and promote IQGAP dimerization. Only one Rac1 molecule might bind to the RasGAP site of GRD and may not facilitate the dimerization, and the exact mechanism of Cdc42 and Rac1 binding to IQGAP is unclear. Using all-atom molecular dynamics simulations, site-directed mutagenesis, and Western blotting, we unraveled the detailed mechanisms of Cdc42 and Rac1 interactions with IQGAP2. We observed that Cdc42 binding to the Ex-domain of GRD of IQGAP2 (GRD2) releases the Ex-domain at the C-terminal region of GRD2, facilitating IQGAP2 dimerization. Cdc42 binding to the Ex-domain promoted allosteric changes in the RasGAP site, providing a binding site for the second Cdc42 in the RasGAP site. Of note, the Cdc42 "insert loop" was important for the interaction of the first Cdc42 with the Ex-domain. By contrast, differences in Rac1 insert loop sequence and structure precluded its interaction with the Ex-domain. Rac1 could bind only to the RasGAP site of apo-GRD2 and could not facilitate IQGAP2 dimerization. Our detailed mechanistic insights help decipher how Cdc42 can stimulate actin polymerization in metastasis.The Rho GTPase family is a subfamily of the Ras GTPase superfamily. Rho GTPases regulate multiple cellular processes such as growth, survival, cell invasion, cell motility and vesicle trafficking by interacting with effector molecules (1-4). To date, the mammalian Rho GTPase family includes 22 members; Cdc42, Rac1, and RhoA are the most studied among them (5).Rho GTPases are distinguished from other GTPases by the presence of an "insert loop" which is rich in charged residues in an α-helical motif (Fig. http://www.jbc.org/cgi

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“…As shown, our chimeric BirA*Ras proteins were expressed as expected, localized as predicted, and their localization patterns matched the patterns of the proteins they biotinylated (Figures 1-4). K-Ras proteins also have been reported to oligomerize (17,20,(89)(90)(91), and we observed that WT, G12D, and S17N BirA*Ras proteins biotinylated WT pAMCherry1-KRas proteins in trans ( Figure 5). These results are of interest in the context of data that show both GDPbound and GTP-bound K-Ras proteins oligomerize in cells (20).…”

Section: Discussionmentioning

confidence: 69%