Dataset Information

Synchronous RNA conformational changes trigger ordered phase transitions in crystals.

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.

SUBMITTER: Ramakrishnan S

PROVIDER: S-EPMC7979858 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Synchronous RNA conformational changes trigger ordered phase transitions in crystals.

Ramakrishnan Saminathan S Stagno Jason R JR Conrad Chelsie E CE Ding Jienyu J Yu Ping P Bhandari Yuba R YR Lee Yun-Tzai YT Pauly Gary G Yefanov Oleksandr O Wiedorn Max O MO Knoska Juraj J Oberthür Dominik D White Thomas A TA Barty Anton A Mariani Valerio V Li Chufeng C Brehm Wolfgang W Heinz William F WF Magidson Valentin V Lockett Stephen S Hunter Mark S MS Boutet Sébastien S Zatsepin Nadia A NA Zuo Xiaobing X Grant Thomas D TD Pandey Suraj S Schmidt Marius M Spence John C H JCH Chapman Henry N HN Wang Yun-Xing YX

Nature communications 20210319 1

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 i ...[more]

PMID: 33741910

Similar Datasets

Project description:Crystallographic observation of structural changes in real time requires that those changes be uniform both spatially and temporally. A primary challenge with time-resolved ligand-mixing diffraction experiments is asynchrony caused by variable factors, such as efficiency of mixing, rate of diffusion, crystal size, and subsequently, conformational heterogeneity. One method of minimizing such variability is use of a photolabile caged ligand, which can fully saturate the crystal environment (spatially), and whose photoactivation can rapidly (temporally) trigger the reaction in a controlled manner. Our recently published results on a ligand-mixing experiment using time-resolved X-ray crystallography (TRX) with an X-ray free electron laser (XFEL) demonstrated that large conformational changes upon ligand binding resulted in a solid-to-solid phase transition (SSPT), while maintaining Bragg diffraction. Here we investigate this SSPT by polarized video microscopy (PVM) after light-triggered release of a photo-caged adenine (pcADE). In general, the mean transition times and transition widths of the SSPT were less dependent on crystal size than what was observed in previous PVM studies with direct ADE mixing. Instead, the photo-induced transition appears to be heavily influenced by the equilibrium between caged and uncaged ADE due to relatively low sample exposure and uncaging efficiency. Nevertheless, we successfully demonstrate a method for the characterization of phase transitions in RNA crystals that are inducible with a photocaged ligand. The transition data for three crystals of different sizes were then applied to kinetic analysis by fitting to the known four-state model associated with ligand-induced conformational changes, revealing an apparent concentration of uncaged ADE in crystal of 0.43-0.46 mM. These results provide further insight into approaches to study time-resolved ligand-induced conformational changes in crystals, and in particular, highlight the feasibility of triggering phase transitions using a light-inducible system. Developing such approaches may be paramount for the rapidly emerging field of time-resolved crystallography.

Dataset Information

Synchronous RNA conformational changes trigger ordered phase transitions in crystals.

Publications

Synchronous RNA conformational changes trigger ordered phase transitions in crystals.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets