Dataset Information

Analysis of XFEL serial diffraction data from individual crystalline fibrils.

ABSTRACT: Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.

SUBMITTER: Wojtas DH

PROVIDER: S-EPMC5668865 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Publications

Analysis of XFEL serial diffraction data from individual crystalline fibrils.

Wojtas David H DH Ayyer Kartik K Liang Mengning M Mossou Estelle E Romoli Filippo F Seuring Carolin C Beyerlein Kenneth R KR Bean Richard J RJ Morgan Andrew J AJ Oberthuer Dominik D Fleckenstein Holger H Heymann Michael M Gati Cornelius C Yefanov Oleksandr O Barthelmess Miriam M Ornithopoulou Eirini E Galli Lorenzo L Xavier P Lourdu PL Ling Wai Li WL Frank Matthias M Yoon Chun Hong CH White Thomas A TA Bajt Saša S Mitraki Anna A Boutet Sebastien S Aquila Andrew A Barty Anton A Forsyth V Trevor VT Chapman Henry N HN Millane Rick P RP

IUCrJ 20171020 Pt 6

Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to ...[more]

PMID: 29123682

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Project description:X-ray free-electron laser (XFEL) is the latest generation of the X-ray source that could become an invaluable technique in structural biology. XFEL has ultrashort pulse duration, extreme peak brilliance, and high spatial coherence, which could enable the observation of the biological molecules in near nature state at room temperature without crystallization. However, for biological systems, due to their low diffraction power and complexity of sample delivery, experiments and data analysis are not straightforward, making it extremely challenging to reconstruct three-dimensional (3D) structures from single particle XFEL data. Given the current limitations to the amount and resolution of the data from such XFEL experiments, we propose a new hybrid approach for characterizing biomolecular conformational transitions by using a single 2D low-resolution XFEL diffraction pattern in combination with another known conformation. In our method, we represent the molecular structure with a coarse-grained model, the Gaussian mixture model, to describe large conformational transitions from low-resolution XFEL data. We obtain plausible 3D structural models that are consistent with the XFEL diffraction pattern by deforming an initial structural model to maximize the similarity between the target pattern and the simulated diffraction patterns from the candidate models. We tested the proposed algorithm on two biomolecules of different sizes with different complexities of conformational transitions, adenylate kinase, and elongation factor 2, using synthetic XFEL data. The results show that, with the proposed algorithm, we can successfully describe the conformational transitions by flexibly fitting the coarse-grained model of one conformation to become consistent with an XFEL diffraction pattern simulated from another conformation. In addition, we showed that the incident beam orientation has some effect on the accuracy of the 3D structure modeling and discussed the reasons for the inaccuracies for certain orientations. The proposed method could serve as an alternative approach for retrieving information on 3D conformational transitions from the XFEL diffraction patterns to interpret experimental data. Since the molecules are represented by Gaussian kernels and no atomic structure is needed in principle, such a method could also be used as a tool to seek initial models for 3D reconstruction algorithms.

Dataset Information

Analysis of XFEL serial diffraction data from individual crystalline fibrils.

Publications

Analysis of XFEL serial diffraction data from individual crystalline fibrils.

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