Accessing protein conformational ensembles using room-temperature X-ray crystallography
10.1073/pnas.1111325108
Crossref journal-article
Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences (341)
Abstract

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation.

Bibliography

Fraser, J. S., van den Bedem, H., Samelson, A. J., Lang, P. T., Holton, J. M., Echols, N., & Alber, T. (2011). Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proceedings of the National Academy of Sciences, 108(39), 16247–16252.

Authors 7
  1. James S. Fraser (first)
  2. Henry van den Bedem (additional)
  3. Avi J. Samelson (additional)
  4. P. Therese Lang (additional)
  5. James M. Holton (additional)
  6. Nathaniel Echols (additional)
  7. Tom Alber (additional)
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Dates
Type When
Created 13 years, 11 months ago (Sept. 15, 2011, 4:37 a.m.)
Deposited 3 years, 2 months ago (June 7, 2022, 4:01 a.m.)
Indexed 1 day, 13 hours ago (Sept. 3, 2025, 7 a.m.)
Issued 13 years, 11 months ago (Sept. 14, 2011)
Published 13 years, 11 months ago (Sept. 14, 2011)
Published Online 13 years, 11 months ago (Sept. 14, 2011)
Published Print 13 years, 11 months ago (Sept. 27, 2011)
Funders 0

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@article{Fraser_2011, title={Accessing protein conformational ensembles using room-temperature X-ray crystallography}, volume={108}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.1111325108}, DOI={10.1073/pnas.1111325108}, number={39}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Fraser, James S. and van den Bedem, Henry and Samelson, Avi J. and Lang, P. Therese and Holton, James M. and Echols, Nathaniel and Alber, Tom}, year={2011}, month=sep, pages={16247–16252} }