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One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.

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Fischer M, Shoichet BK, Fraser JS
OpenAccess logo Chembiochem 16 1560-4 (2015)
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Cited: 35 times
EuropePMC logo PMID: 26032594

Abstract

Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiation damage. However, it might also perturb protein conformations that can be accessed at room temperature. Using data from crystals measured consecutively at room temperature and at cryogenic temperature, we found that transient binding sites could be abolished at the cryogenic temperatures employed by standard approaches. Changing the temperature at which the crystallographic data was collected could provide a deliberate perturbation to the equilibrium of protein conformations and help to visualize hidden sites with great potential to allosterically modulate protein function.

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  3. Enhanced sampling without borders: on global biasing functions and how to reweight them. Kamenik AS, Linker SM, Riniker S. Phys Chem Chem Phys 24 1225-1236 (2022)

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  17. Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography. Huang CY, Aumonier S, Engilberge S, Eris D, Smith KML, Leonarski F, Wojdyla JA, Beale JH, Buntschu D, Pauluhn A, Sharpe ME, Metz A, Olieric V, Wang M. Acta Crystallogr D Struct Biol 78 964-974 (2022)
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  19. Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics. Sasmal S, Gill SC, Lim NM, Mobley DL. J Chem Theory Comput 16 1854-1865 (2020)
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Related citations provided by authors (1)

  1. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.. Fischer M, Coleman RG, Fraser JS, Shoichet BK Nat Chem 6 575-83 (2014)

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