Abstract
Fragment-based screening by ligand-observed 1D NMR and binding interface map** by protein-observed 2D NMR are popular methods used in drug discovery. These methods allow researchers to detect compound binding over a wide range of affinities and offer a simultaneous assessment of solubility, purity, and chemical formula accuracy of the target compounds and the 15N-labeled protein when examined by 1D and 2D NMR, respectively. These methods can be applied for screening fragment binding to the active (GMPPNP-bound) and inactive (GDP-bound) states of oncogenic KRAS mutants.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dalvit C, Fogliatto G, Stewart A, Veronesi M, Stockman B (2001) WaterLOGSY as a method for primary NMR screening: practical aspects and range of applicability. J Biomol NMR 21(4):349–359
Mayer M, Mayer B (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Ed 38:1784–1788
Hajduk PJ, Olejniczak ET, Fesik SW (1997) One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J Am Chem Soc 119(50):12257–12261
Cala O, Krimm I (2015) Ligand-orientation based fragment selection in STD NMR screening. J Med Chem 58(21):8739–8742
Raingeval C, Cala O, Brion B, Le Borgne M, Hubbard RE, Krimm I (2019) 1D NMR WaterLOGSY as an efficient method for fragment-based lead discovery. J Enzyme Inhib Med Chem 34(1):1218–1225
Agamasu C, Ghirlando R, Taylor T, Messing S, Tran TH, Bindu L et al (2019) KRAS prenylation is required for bivalent binding with calmodulin in a nucleotide-independent manner. Biophys J 116(6):1049–1063
Travers T, López CA, Van QN, Neale C, Tonelli M, Stephen AG et al (2018) Molecular recognition of RAS/RAF complex at the membrane: role of RAF cysteine-rich domain. Sci Rep 8(1):8461
Chao FA, Dharmaiah S, Taylor T, Messing S, Gillette W, Esposito D et al (2022) Insights into the cross talk between effector and allosteric lobes of KRAS from methyl conformational dynamics. J Am Chem Soc 144(9):4196–4205
Li J, Byrd RA (2022) A simple protocol for the production of highly deuterated proteins for biophysical studies. J Biol Chem 298(8):102253
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6(3):277–293
Lee W, Rahimi M, Lee Y, Chiu A (2021) POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Bioinformatics 37(18):3041–3042
DeLano WL (2002) The PyMOL molecular graphics system, Version 2.0. Schrödinger, LLC
Acknowledgments
This project was funded in part with federal funds from the National Cancer Institute, National Institutes of Health under contract 75N91019D00024. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, and the mention of trade names, commercial products, or organizations does not imply endorsement by the US government.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Cornilescu, G. (2024). 1D and 2D NMR for KRAS:Ligand Binding. 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_9
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3822-4_9
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3821-7
Online ISBN: 978-1-0716-3822-4
eBook Packages: Springer Protocols