The juxtamembrane regions of human receptor tyrosine kinases exhibit conserved interaction sites with anionic lipids

Hedger, George; Sansom, Mark S. P.; Koldsø, Heidi

doi:10.1038/srep09198

Cited by 105 publications

(110 citation statements)

References 74 publications

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“…Thus, by way of comparison with experiments, (1) anionic lipids can promote GPCR/G protein interactions, and (2) in the absence of PIP 2 the K d is sub-micromolar, both of which agree with our simulations. Interactions with PIP 2 are known for other membrane signaling proteins, e.g., ion channels (Hansen, 2015), receptor tyrosine kinases (Hedger et al, 2015), and neurotransmitter transporters (Khelashvili et al, 2015). Thus, our studies raise the possibility of PIP 2 -mediated crosstalk between GPCRs and other signaling systems (Fu et al, 2017) in cell membranes.…”

Section: Discussionmentioning

confidence: 57%

State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes

et al. 2019

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Graphical Abstract Highlights d MD simulations show state-dependent binding of lipids to the Adenosine A2a receptor d Nine lipid interaction sites were revealed, for GM3, cholesterol and PIP 2 d Binding of PIP 2 enhanced the association of mini-Gs with the A2a receptor d These results indicate lipids may allosterically regulate GPCRs SUMMARY Membranes are known to have modulatory effects on G protein-coupled receptors (GPCRs) via specific lipid interactions. However, the mechanisms of such modulations in physiological conditions and how they influence GPCR functions remain unclear.Here we report coarse-grained molecular dynamics simulations on the Adenosine A2a receptor in different conformational states embedded in an in vivo-mimetic membrane model. Nine lipid interaction sites were revealed. The strength of lipid interactions with these sites showed a degree of dependence on the conformational states of the receptor, suggesting that these lipids may regulate the conformational dynamics of the receptor. In particular, we revealed a dual role of PIP 2 on A2aR activation that involves both stabilization of the characteristic outward tilt of TM6 and enhancement of A2aR-mini-Gs association. Our results demonstrated that the bound lipids allosterically regulate the functional properties of GPCRs. These protein-lipid interactions provide a springboard for design of allosteric modulators of GPCRs. which are governed by both the protein receptor and its bound lipids. This opens up new prospects for the pharmacology of GPCRs as their druggable space is expanded to include the bound lipids. The sensitivity of protein-lipid interactions toward the receptor conformational state and the lipid environment may thus provide a platform for designing subtype-selective and cell type-selective drugs. STAR+METHODSDetailed methods are provided in the online version of this paper and include the following:

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Section: Discussionmentioning

confidence: 57%

State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes

et al. 2019

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“…Despite these limitations, the approaches discussed have achieved significant success in identifying a range of lipid interaction sites on membrane proteins, controlled and tested against experimental data including mass spectrometry (Gupta et al, 2017;Liko et al, 2016;Yen et al, 2018), crystallographic (Arnarez et al, 2013a;Schmidt et al, 2013;Van Eerden et al, 2017;Zeppelin et al, 2018), NMR spectroscopy Hedger et al, 2016b), and mutational functional data (Hedger et al, 2016a;Hedger et al, 2015;Stansfeld et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

“…Simulation data was analysed using VMD (Humphrey et al, 1996), tools implemented in GROMACS (Hess et al, 2008), and in-house protocols. Protein-lipid contact analysis employed a cutoff distance of 0.6 nm, based on radial distribution functions for CG lipid molecules (Hedger et al, 2015). Likewise, annular lipids were calculated as those within 0.6 nm of the protein surface.…”

Section: Coarse-grained Simulationsmentioning

confidence: 99%

Cholesterol interaction sites on the transmembrane domain of the hedgehog signal transducer and Class F G protein-coupled receptor Smoothened

Hedger

Koldsoe

Chavent

et al. 2018

Preprint

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Transduction of hedgehog signals across the plasma membrane is a key process during animal development. This is facilitated by the Class F G-protein-coupled-receptor (GPCR) Smoothened (SMO), a major drug target in the treatment of basal cell carcinomas. Recent studies have suggested that SMO is modulated via interactions of its transmembrane (TM) domain with cholesterol. Long time scale (>0.35 ms of simulation time) molecular dynamics simulations of SMO embedded in two different cholesterol containing lipid bilayers reveal direct interactions of cholesterol with the transmembrane domain at regions distinct from those observed in Class A GPCRs. In particular the extracellular tips of helices TM2 and TM3 form a well-defined cholesterol interaction site, robust to changes in membrane composition and in force field parameters. Potential of mean force calculations for cholesterol interactions yield a free energy landscape for cholesterol binding.Combined with analysis of equilibrium cholesterol occupancy these results reveal the existence of a dynamic 'greasy patch' interaction with the TM domain of SMO, which may be compared to previously identified lipid interaction sites on other membrane proteins. These predictions provide molecular level insights into cholesterol interactions with a biomedically relevant Class F GPCR, suggesting potential druggable sites.

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“…In the context of cancer, phosphoinositides were shown to be major regulators of cell motility, invasion, and metastasis [Yamaguchi et al, 2010; Gagliardi et al, 2015; Lien et al, 2017]. Recent studies revealed, several classes of transmembrane receptors and ion channels might be regulated by PIP2, or at least bind this signaling lipid with considerable affinity [Hedger et al, 2015;Kolay et al, 2016, Chadli et al, 2017. Thus, PIP2 signaling may results in a cell-global concerted response to environmental changes.…”

Section: Introductionmentioning

confidence: 99%

K-Ras G-domain binding with signaling lipid phosphoinositides: PIP2 association, orientation, function

Cao

Chung

Kim

et al. 2018

Preprint

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Ras genes are potent drivers of human cancers, with mutated K-Ras4B being the most abundant isoform. Targeted inhibition of oncogenic gene products is considered the "holy grail" of present-day cancer therapy, and recent discoveries of small molecule inhibitors for KRas4B greatly benefited from a deeper understanding of the protein structure and dynamics of the GTPase. Since interactions with biological membranes are key for Ras function, the details of Ras -lipid interactions have become a major focus of study, especially since it is becoming clear that such interactions not only involve the Ras C-terminus for lipid anchoring, but also the G-protein domain. Here we investigated the interaction between K-Ras4B with the signaling lipid phosphatidyl inositol (4,5) phosphate (PIP2) using NMR spectroscopy and molecular dynamics simulations, complemented by biophysical and cell biology assays. We discovered that the β2 and β3 strands as well as helices 4 and 5 of the GTPase G-domain bind to PIP2, and that these secondary structural elements employ specific residues for these interactions. These likely occur in two orientation states of the protein relative to the membrane. Importantly, we found that some of these residues, which are known to be oncogenic when mutated (D47K, D92N, K104M and D126N), are critical for K-Ras-mediated transformation of fibroblast cells, while not substantially affecting basal and assisted nucleotide hydrolysis and exchange. We further showed that mutation K104M can indeed abolish localization of mutant K-Ras to the plasma membrane. These findings suggest that specific G-domain residues play an important, previously-unknown role in regulating Ras function by mediating interactions with membrane PIP2 lipids. Thus, a detailed description of the novel K-Ras-PIP2 binding surfaces is likely to inform the future design of therapeutic reagents.

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The juxtamembrane regions of human receptor tyrosine kinases exhibit conserved interaction sites with anionic lipids

Cited by 105 publications

References 74 publications

State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes

State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes

Cholesterol interaction sites on the transmembrane domain of the hedgehog signal transducer and Class F G protein-coupled receptor Smoothened

K-Ras G-domain binding with signaling lipid phosphoinositides: PIP2 association, orientation, function

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