Advances in NMR Methods to Identify Allosteric Sites and Allosteric Ligands

  • Hazem Abdelkarim
  • Ben Hitchinson
  • Avik Banerjee
  • Vadim GaponenkoEmail author
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1163)


NMR allows assessment of protein structure in solution. Unlike conventional X-ray crystallography that provides snapshots of protein conformations, all conformational states are simultaneously accessible to analysis by NMR. This is a significant advantage for discovery and characterization of allosteric effects. These effects are observed when binding at one site of the protein affects another distinct site through conformational transitions. Allosteric regulation of proteins has been observed in multiple physiological processes in health and disease, providing an opportunity for the development of allosteric inhibitors. These compounds do not directly interact with the orthosteric site of the protein but influence its structure and function. In this book chapter, we provide an overview on how NMR methods are utilized to identify allosteric sites and to discover novel inhibitors, highlighting examples from the field. We also describe how NMR has contributed to understanding of allosteric mechanisms and propose that it is likely to play an important role in clarification and further development of key concepts of allostery.


NMR Allosteric ligands Allosteric sites NMR methods 



Conserved regulatory/adaptive proteins


Fluorine NMR spectroscopy






Chemical shift covariance analysis


Conformational exchange matrix analysis of saturation transfer






Dihydrofolate reductase


Dihydropteroate synthase


Deoxyribonucleic acid


Plus-end-directed kinesin-related protein


Exchange protein directly activated by cAMP




Fluorine chemical shift anisotropy and exchange for screening


Guanosine diphosphate


β, γ-Methyleneguanosine triphosphate


G-protein-coupled receptors


Guanosine triphosphate




Histo-blood antigens


Heteronuclear single/multiple quantum coherence/correlation


Interleukin-2-inducible T-cell kinase


Koshland, Némethy, and Filmer


Molecular dynamics


The bacterial mercury resistance






Nuclear magnetic resonance


Nuclear Overhauser effects


p-Aminobenzoic acid


Pseudocontact shifts


Phosphoinositide-dependent kinase-1


PDK1 interacting fragment


Paramagnetic relaxation enhancements


15N spin-lattice relaxation experiments


Spin-spin relaxation experiments


Residual dipolar couplings


Ribonucleic acid


Son of sevenless


Saturation transfer difference






Transverse relaxation optimized spectroscopy


Norovirus virus-like particles


Water ligand observed via gradient spectroscopy



This work was funded by the National Institutes of Health (NIH)–National Cancer Institute (NCI) R01CA188427 grant to V.G., the American Cancer Society Postdoctoral Fellowship (132722-PF-18-196-01-DMC) to HA, and the Horizon award under the Congressionally Directed Medical Research Program (CDMPRP), Department of Defense (DoD) (W81XWH-17-10509) to A.B.


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Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Hazem Abdelkarim
    • 1
  • Ben Hitchinson
    • 1
  • Avik Banerjee
    • 2
  • Vadim Gaponenko
    • 1
    Email author
  1. 1.Department of Biochemistry and Molecular Genetics, College of MedicineUniversity of Illinois at ChicagoChicagoUSA
  2. 2.Department of ChemistryUniversity of Illinois at ChicagoChicagoUSA

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