1D and 2D NMR for KRAS:Ligand Binding

  • Protocol
  • First Online:
KRAS

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2797))

  • 431 Accesses

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. 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

    Article  CAS  PubMed  Google Scholar 

  2. Mayer M, Mayer B (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Ed 38:1784–1788

    Article  CAS  Google Scholar 

  3. 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

    Article  CAS  Google Scholar 

  4. Cala O, Krimm I (2015) Ligand-orientation based fragment selection in STD NMR screening. J Med Chem 58(21):8739–8742

    Article  CAS  PubMed  Google Scholar 

  5. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. 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

    Article  PubMed  PubMed Central  Google Scholar 

  8. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Li J, Byrd RA (2022) A simple protocol for the production of highly deuterated proteins for biophysical studies. J Biol Chem 298(8):102253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. 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

    Article  CAS  PubMed  Google Scholar 

  11. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. DeLano WL (2002) The PyMOL molecular graphics system, Version 2.0. Schrödinger, LLC

    Google Scholar 

Download references

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

Authors

Corresponding author

Correspondence to Gabriel Cornilescu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

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

Publish with us

Policies and ethics

Navigation