Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Saminathan Ramakrishnan, Jason R. Stagno, Chelsie E. Conrad, Jienyu Ding, Ping Yu, Yuba R. Bhandari, Yun-Tzai Lee, Gary Pauly, Oleksandr Yefanov, Max O. Wiedorn, Juraj Knoska, Dominik Oberthür, Thomas A. White, Anton Barty, Valerio Mariani, Chufeng Li, Wolfgang Brehm, William F. Heinz, Valentin Magidson, Stephen Lockett, Mark S. Hunter, Sébastien Boutet, Nadia A. Zatsepin, Xiaobing Zuo, Thomas D. Grant, Suraj Pandey, Marius Schmidt, John C. H. Spence, Henry N. Chapman and Yun-Xing Wang ()
Additional contact information
Saminathan Ramakrishnan: National Cancer Institute
Jason R. Stagno: National Cancer Institute
Chelsie E. Conrad: National Cancer Institute
Jienyu Ding: National Cancer Institute
Ping Yu: National Cancer Institute
Yuba R. Bhandari: National Cancer Institute
Yun-Tzai Lee: National Cancer Institute
Gary Pauly: National Cancer Institute
Oleksandr Yefanov: Deutsches Elektronen-Synchrotron DESY
Max O. Wiedorn: Deutsches Elektronen-Synchrotron DESY
Juraj Knoska: Deutsches Elektronen-Synchrotron DESY
Dominik Oberthür: Deutsches Elektronen-Synchrotron DESY
Thomas A. White: Deutsches Elektronen-Synchrotron DESY
Anton Barty: Deutsches Elektronen-Synchrotron DESY
Valerio Mariani: Deutsches Elektronen-Synchrotron DESY
Chufeng Li: Deutsches Elektronen-Synchrotron DESY
Wolfgang Brehm: Deutsches Elektronen-Synchrotron DESY
William F. Heinz: Frederick National Laboratory for Cancer Research
Valentin Magidson: Frederick National Laboratory for Cancer Research
Stephen Lockett: Frederick National Laboratory for Cancer Research
Mark S. Hunter: SLAC National Accelerator Laboratory
Sébastien Boutet: SLAC National Accelerator Laboratory
Nadia A. Zatsepin: Arizona State University
Xiaobing Zuo: Argonne National Laboratory
Thomas D. Grant: SUNY University at Buffalo
Suraj Pandey: University of Wisconsin-Milwaukee
Marius Schmidt: University of Wisconsin-Milwaukee
John C. H. Spence: Arizona State University
Henry N. Chapman: Deutsches Elektronen-Synchrotron DESY
Yun-Xing Wang: National Cancer Institute

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

Date: 2021
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DOI: 10.1038/s41467-021-21838-5

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