Abstract
Knowledge of how effectors interact with RAS GTPases is key to understanding how these switch-like proteins function in cells. Effectors bind specifically to GTP-loaded RAS using RAS association (RA) or RAS binding domains (RBDs) that show wide-ranging affinities and thermodynamic characteristics. Both normal development and RAS-induced tumorigenesis depend on multiple distinct effector proteins that are frequently co-expressed and co-localized, suggesting an antagonistic nature to signaling whereby multiple proteins compete for a limited pool of activated GTPase. NMR spectroscopy offers a powerful approach to multiplex effectors and/or regulatory enzymes and quantifies their interaction with RAS, expanding our biophysical and systems-level understanding of RAS signaling in a more integrated and physiologically relevant setting. Here we describe a method to directly quantitate GTPase binding to competing effectors, using wild-type KRAS complex with ARAF and PLCε1 as a model. Unlabeled RBD/RA domains are added simultaneously to isotopically labeled RAS, and peak intensities at chemical shifts characteristic of individually bound domains provide quantitation. Similar competition-based assays can be run with small molecule interactors, GEF/GAP domains, or regulatory enzymes that drive posttranslational modifications. Such efforts bring in vitro interaction experiments in line with more complex cellular environments.
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References
Gimple RC, Wang X (2019) RAS: striking at the core of the oncogenic circuitry. Front Oncol 9:965. https://doi.org/10.3389/fonc.2019.00965
De Luca A, Maiello MR, D’Alessio A et al (2012) The RAS/RAF/MEK/ERK and the PI3K/AKT signalling pathways: role in cancer pathogenesis and implications for therapeutic approaches. Expert Opin Ther Targets 16:S17–S27. https://doi.org/10.1517/14728222.2011.639361
Wohlgemuth S, Kiel C, Krämer A et al (2005) Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol 348:741–758. https://doi.org/10.1016/j.jmb.2005.02.048
Smith MJ, Neel BG, Ikura M (2013) NMR-based functional profiling of RASopathies and oncogenic RAS mutations. Proc Natl Acad Sci 110:4574–4579. https://doi.org/10.1073/pnas.1218173110
Marshall CB, Meiri D, Smith MJ et al (2012) Probing the GTPase cycle with real-time NMR: GAP and GEF activities in cell extracts. Methods 57:473–485. https://doi.org/10.1016/j.ymeth.2012.06.014
Smith MJ, Ikura M (2014) Integrated RAS signaling defined by parallel NMR detection of effectors and regulators. Nat Chem Biol 10:223–230. https://doi.org/10.1038/nchembio.1435
Smith MJ, Marshall CB, Theillet F-X et al (2015) Real-time NMR monitoring of biological activities in complex physiological environments. Curr Opin Struct Biol 32:39–47. https://doi.org/10.1016/j.sbi.2015.02.003
Killoran RC, Smith MJ (2019) Conformational resolution of nucleotide cycling and effector interactions for multiple small GTPases determined in parallel. J Biol Chem 294:9937–9948. https://doi.org/10.1074/jbc.RA119.008653
Gardner KH, Kay LE (1997) Production and incorporation of 15N, 13C, 2H (1H-δ1 methyl) isoleucine into proteins for multidimensional NMR studies. J Am Chem Soc 119:7599–7600. https://doi.org/10.1021/ja9706514
Rowlinson B, Crublet E, Kerfah R, Plevin MJ (2022) Specific isotopic labelling and reverse labelling for protein NMR spectroscopy: using metabolic precursors in sample preparation. Biochem Soc Trans 50:1555–1567. https://doi.org/10.1042/BST20210586
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Strakhova, R., Smith, M.J. (2024). Profiling Complex RAS-Effector Interactions Using NMR Spectroscopy. In: Stephen, A.G., Esposito, D. (eds) KRAS. Methods in Molecular Biology, vol 2797. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3822-4_14
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DOI: https://doi.org/10.1007/978-1-0716-3822-4_14
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