Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology

Li, Zhenlu; Buck, Matthias

doi:10.1016/j.str.2017.02.007

Cited by 75 publications

(133 citation statements)

References 52 publications

(57 reference statements)

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“…We believe this mechanism applies not only to the consitituvely G12V but also to wild type K-Ras and other Ras isoforms, but there can be potential differences in the distribution of monomer, dimer/trimer and higher order organization due to GDP/GTP exchange or nucleotide dependent membrane binding. 50–53 We then wondered about the implication of oligomerization on the dynamic reorientation of the catalytic domain with respect to the membrane plane. 52,54,55 Inspection of our membrane-bound oligomer models yielded a surprising insight.…”

Section: Discussionmentioning

confidence: 99%

Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes

et al. 2017

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Self-assembly of plasma membrane-associated Ras GTPases has major implications to the regulation of cell signaling. However, the structural basis of homo-oligomerization and the fractional distribution of oligomeric states remained undetermined. We have addressed these issues by deciphering the distribution of dimers and higher-order oligomers of K-Ras4B, the most frequently mutated Ras isoform in human cancers. We focused on the constitutively active G12V K-Ras and two of its variants, K101E and K101C/E107C, which respectively destabilize and stabilize oligomers. Using raster image correlation spectroscopy and number and brightness analysis combined with fluorescence recovery after photobleaching, fluorescence correlation spectroscopy and electron microscopy in live cells, we show that G12V K-Ras exists as a mixture of monomers, dimers and larger oligomers, while the K101E mutant is predominantly monomeric and K101C/E107C is dominated by oligomers. This observation demonstrates the ability of K-Ras to exist in multiple oligomeric states whose population can be altered by interfacial mutations. Using molecular modeling and simulations we further show that K-Ras uses two partially overlapping interfaces to form compositionally and topologically diverse oligomers. Our results thus provide the first detailed insight into the multiplicity, structure, and membrane organization of K-Ras homomers.

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Section: Discussionmentioning

confidence: 99%

Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes

et al. 2017

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“…A recent study has uncovered that the function of K-Ras can be greatly influenced by the composition of phospholipids in the PM as they offer distinct affinity to the protein [12**]. Ras, a small GTPase that regulates multiple signaling pathways and is known to be linked to several cancers, is only fully functional once bound to the PM.…”

Section: Membrane Lipid Composition and Cell Signalingmentioning

confidence: 99%

“…Using all-atom molecular dynamics simulations, Li and Buck found that the association of K-Ras with distinct phospholipids modulates its orientation and therefore its function. The authors showed five possible cytosolic topologies of Ras depending on the type of anionic lipids present at the membrane, resulting in alterations in the exposure of the catalytic domain and therefore its ability to signal [12**]. Interestingly, it also appears that the affinity of K-Ras to membrane lipids is nucleotide-dependent [13].…”

Section: Membrane Lipid Composition and Cell Signalingmentioning

confidence: 99%

Membrane lipids and cell signaling

Sunshine

Iruela‐Arispe

2017

Current Opinion in Lipidology

183

126

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Purpose of review Reception and transmission of signals across the plasma membrane has been a function generally attributed to transmembrane proteins. In the last three years, however, a growing number of reports have further acknowledged important contributions played by membrane lipids in the process of signal transduction. Recent findings In particular, the constituency of membrane lipids can regulate how proteins with SH2 domains and molecules like K-Ras expose their catalytic domains to the cytosol and interact with effectors and second messengers. Recent reports have also shown that the degree of saturation of phospholipids can reduce the activation of certain G-protein coupled receptors, as well as signaling downstream to Toll-like receptor 4 with consequences to NFkB activation and inflammation. Levels of specific gangliosides in the membrane were reported to activate integrins in a cell-autonomous manner affecting tumor cell migration. Furthermore, high resolution of the association of cholesterol with the Smoothened receptor has clarified its participation in sonic hedgehog signaling. These are some of the key advancements that have further propelled our understanding of the broad versatile contributions of membrane lipids in signal transduction. Summary As we gain definitive detail regarding the impact of lipid-protein interactions and their consequences to cell function, the options for therapeutic targeting expand with the possibility of greater specificity.

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“…12 Both lobes bind to the membrane, based on the results of computational modeling, NMR and FRET. [17][18][19][20][21][22] For functional activity via the ERK or the MAPK pathway, the effector lobe needs to associate with down-stream effector proteins, such as Raf and PI3K. 23,24 Therefore, membrane binding of the effector lobe will occlude the association of an effector protein with this region of the GTPase, and thus attenuate the activity of K-Ras.…”

Section: Introductionmentioning

confidence: 99%

“…[27][28][29] In our prior study of K-Ras, we have found that "off-plane" negative potentials generated by PIP2 at the membrane surface, alter the orientational preference of K-Ras4B, leading to an increased exposure of its effector lobe to the solvent. 20 As an inference, the opposite, i.e. "off-plane" positive potentials at the membrane surface may effectively also trap the negatively charged effector lobe onto the membrane.…”

Section: Introductionmentioning

confidence: 99%

Computational Design of Myristoylated Cell Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector Binding Membrane Interface

Buck

2019

Preprint

Self Cite

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A number of small inhibitors have been developed in the recent years to target the cancer driving protein, K-Ras. In this study, we propose and design a novel way of targeting oncogenic K-Ras4B.G12D with myristoylated cell penetrating peptides which become membrane anchored and lock the protein into an inactive state. In all atom molecular dynamics simulations such peptides associate with K-Ras4B exclusively at the effector binding region, which, in turn, hinders the binding of down-stream effector proteins (e.g. C-Raf). The myristoylated R9 (Arg 9 ) peptide strongly locks K-Ras4B.G12D into orientations that are unfavorable for effector binding. After breaking the cyclic structure and myristoylation, a cell penetrating peptide cyclorasin 9A5, which was designed for targeting the Ras: Raf interface, is also found to be effective in targeting the Ras: membrane interface. The myristolyated peptides likely have high cell permeability due to their mixed cationic/hydrophobic character at the Nterminus, while simultaneously the subsequent multiple charges help to maintain a strong association of the peptide with the K-Ras4B.G12D effector binding lobe. Targeting protein-membrane interfaces is starting to attract attention very recently, thanks to our understanding of the signal mechanism of an increased number of peripheral membrane proteins. The strategy used in this study should have potential applications in the design of drugs against K-Ras4B driven cancers. It also provides insights into the general principles of targeting protein-membrane interfaces.

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Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology

Cited by 75 publications

References 52 publications

Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes

Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes

Membrane lipids and cell signaling

Computational Design of Myristoylated Cell Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector Binding Membrane Interface

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