Conformational landscape of a virus by single-particle X-ray scattering

Hosseinizadeh, Ahmad; Mashayekhi, Ghoncheh; Copperman, Jeremy; Schwander, Peter; Dashti, Ali A.; Sepehr, Reyhaneh; Fung, Russell; Schmidt, Marius; Yoon, Chun Hong; Hogue, Brenda G.; Williams, Garth J.; Aquila, Andrew; Ourmazd, A.

doi:10.1038/nmeth.4395

Cited by 69 publications

(53 citation statements)

References 45 publications

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“…The combination of the high number of photons (%10 12 ) per pulse with femtosecond pulse lengths allows the recording of diffraction images of nanometer-sized samples with single x-ray flashes. From the two-dimensional x-ray diffraction patterns, threedimensional information can be obtained 5 and biological function revealed 6 . Combining the single-shot imaging approach with an optical pump laser yields insight into non-thermal processes on the nanoscale with femtosecond resolution 7 .…”

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confidence: 99%

The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters

Daurer

Hantke

et al. 2020

Nat Commun

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Intense x-ray free-electron laser (XFEL) pulses hold great promise for imaging function in nanoscale and biological systems with atomic resolution. So far, however, the spatial resolution obtained from single shot experiments lags averaging static experiments. Here we report on a combined computational and experimental study about ultrafast diffractive imaging of sucrose clusters which are benchmark organic samples. Our theoretical model matches the experimental data from the water window to the keV x-ray regime. The largescale dynamic scattering calculations reveal that transient phenomena driven by non-linear xray interaction are decisive for ultrafast imaging applications. Our study illuminates the complex interplay of the imaging process with the rapidly changing transient electronic structures in XFEL experiments and shows how computational models allow optimization of the parameters for ultrafast imaging experiments.

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confidence: 99%

The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters

Daurer

Hantke

et al. 2020

Nat Commun

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“…The initiative consists of over 100 scientists from 20 international institutions and covers all aspects of SPI, from ultrafast X-ray induced damage processes to sample delivery and algorithm development. Recently, the SPI initiative reported scattering data from rice dwarf virus particles out to 3.0 Å (with scattering signals significantly above background) [65], and have pushed the state-of-the-art for 3D image reconstruction to below 10 nm [66].…”

Section: Coherent X-ray Imaging At the Nanoscale-heterogeneity And Dymentioning

confidence: 99%

The Linac Coherent Light Source: Recent Developments and Future Plans

et al. 2017

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Abstract:The development of X-ray free-electron lasers (XFELs) has launched a new era in X-ray science by providing ultrafast coherent X-ray pulses with a peak brightness that is approximately one billion times higher than previous X-ray sources. The Linac Coherent Light Source (LCLS) facility at the SLAC National Accelerator Laboratory, the world's first hard X-ray FEL, has already demonstrated a tremendous scientific impact across broad areas of science. Here, a few of the more recent representative highlights from LCLS are presented in the areas of atomic, molecular, and optical science; chemistry; condensed matter physics; matter in extreme conditions; and biology. This paper also outlines the near term upgrade (LCLS-II) and motivating science opportunities for ultrafast X-rays in the 0.25-5 keV range at repetition rates up to 1 MHz. Future plans to extend the X-ray energy reach to beyond 13 keV (<1 Å) at high repetition rate (LCLS-II-HE) are envisioned, motivated by compelling new science of structural dynamics at the atomic scale.

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“…This article is organized as follows. We first outline how manifold-based geometric machine learning (1,(11)(12)(13)(14) can be used to determine the experimental energy landscapes of RyR1 with and without ligands in terms of rigorously derived, mutually orthogonal conformational reaction coordinates associated with ligand binding. This provides important insights into the mechanisms underlying the process of ligand binding,…”

Section: Main Text: Introductionmentioning

confidence: 99%

Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots

Dashti¹,

Shekhar²,

Ben-Hail³

et al. 2018

Preprint

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We present a new approach to determining the conformational changes associated with biological function, and demonstrate its capabilities in the context of experimental single-particle cryo-EM snapshots of ryanodine receptor (RyR1), a Ca 2+channel involved in skeletal muscle excitation/contraction coupling. These results include the detailed conformational motions associated with functional paths including transitions between energy landscapes. The functional motions differ substantially from those inferred from discrete structures, shedding new light on the gating mechanism in RyR1.The differences include the conformationally active structural domains, the nature, sequence, and extent of conformational motions involved in function, and the way allosteric signals are transduced within and between domains. The approach is general, and applicable to a wide range of systems and processes.

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Conformational landscape of a virus by single-particle X-ray scattering

Cited by 69 publications

References 45 publications

The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters

The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters

The Linac Coherent Light Source: Recent Developments and Future Plans

Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots

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