Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Jason R. Stagno,Thomas A. White,Sébastien Boutet,Suraj Pandey,Chufeng Li,Thomas D. Grant,Xiaobing Zuo,Stephen Lockett,Chelsie E. Conrad,Yun Xing Wang ,J. Knoška ,Yun-Tzai Lee,Anton Barty,Saminathan Ramakrishnan,William F. Heinz,Max O. Wiedorn,Yuba R. Bhandari,Marius Schmidt,Oleksandr Yefanov,Dominik Oberthür,Jienyu Ding,Nadia A. Zatsepin,Gary T. Pauly ,Valerio Mariani,Valentin Magidson,Wolfgang Brehm,Henry N. Chapman,Mark S. Hunter,Ping Yü ,John C. H. Spence

doi:10.1038/s41467-021-21838-5

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.

Highlights

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice
Further direct visualization and image analysis at the molecular level using solution atomic force microscopy (AFM) reveal the distinct molecular arrangements and lattice constants at various stages of the transition. These microscopy data corroborate the TRX data that detect the difference electron density (DED) and evolution of intermediate structures. These results describe in detail the SS transition in the riboA crystals, and demonstrate the molecular cooperativity associated with the large conformational changes triggered by ligand binding
The ROI, which contains ~400 million RNA molecules, is about the typical size of crystals used in the Xray-free electron laser (XFEL) experiments[14]

Summary

Introduction

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. The majority of biological processes involve interactions that result in large conformational changes greater than several angstroms, which are likely to alter lattice interfaces and trigger phase transitions in crystal[14,19,20,21,22]. These results describe in detail the SS transition in the riboA crystals, and demonstrate the molecular cooperativity associated with the large conformational changes triggered by ligand binding.

Results

Conclusion