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Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

By Alexander M. Wolff, Eriko Nango, Iris Diane Young1, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James Holton2, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, James Fraser3, Michael Thompson1

1. University of California - San Francisco 2. University of California San Francisco 3. University of California-San Francisco

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Category

BioXFEL Publications

Published on

Type

journal-article

Author

Alexander M. Wolff and Eriko Nango and Iris D. Young and Aaron S. Brewster and Minoru Kubo and Takashi Nomura and Michihiro Sugahara and Shigeki Owada and Benjamin A. Barad and Kazutaka Ito and Asmit Bhowmick and Sergio Carbajo and Tomoya Hino and James M. Holton and Dohyun Im and Lee J. O’Riordan and Tomoyuki Tanaka and Rie Tanaka and Raymond G. Sierra and Fumiaki Yumoto and Kensuke Tono and So Iwata and Nicholas K. Sauter and James S. Fraser and Michael C. Thompson

Citation

Wolff, A. M., Nango, E., Young, I. D., Brewster, A. S., Kubo, M., Nomura, T., Sugahara, M., Owada, S., Barad, B. A., Ito, K., Bhowmick, A., Carbajo, S., Hino, T., Holton, J. M., Im, D., O’Riordan, L. J., Tanaka, T., Tanaka, R., Sierra, R. G., … Thompson, M. C. (2023). Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nature Chemistry. https://doi.org/10.1038/s41557-023-01329-4

Abstract

AbstractUnderstanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

DOI

http://dx.doi.org/10.1038/s41557-023-01329-4

Funding

NSF-STC Biology with X-ray Lasers (NSF-1231306)