Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

Kern, Jan; Yachandra, Vittal K.; Yano, Junko

doi:10.1016/j.sbi.2015.07.014

Cited by 39 publications

(26 citation statements)

References 60 publications

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“…As far as metalloproteins are concerned, the status of fs X-ray studies has recently been reviewed by Kern et al 339 Here we focus on the more recent developments of the last few months. Because local structural changes (i.e.…”

Section: Femtosecond Studiesmentioning

confidence: 99%

Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods

2017

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ABSTRACT:We review the tremendous advances in ultrafast X-ray science, over the past 15 years, making the best use of new ultrashort x-ray sources including table-top or large-scale facilities. Different complementary x-ray based techniques, including spectroscopy, scattering and diffraction, are presented. The broad and expanding spectrum of these techniques in the ultrafast time domain, is delivering new insight into the dynamics of molecular systems, of solutions, of solids and of Biosystems. Probing the time evolution of the electronic and structural degrees of freedom of these systems on the timescales of femtosecond to picoseconds delivers new insight into our understanding of dynamical matter.

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Section: Femtosecond Studiesmentioning

confidence: 99%

Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods

2017

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“…In this context a complete review concerning the most biochemical relevant papers is offered by Kern and collaborators [109]. Despite most of the works rely on XFEL exploitation for crystallographic studies, recently also XAS and X-ray Emission Spectroscopy (XES) applications have been reported [109,110]. As demonstrated by Alonso, Kern and their groups, two are the main advantage of XFEL-XAS.…”

Section: X-ray Free Electron Laser Xasmentioning

confidence: 99%

“…However, it is important to stress that the biggest advantage is also the most limiting issue: indeed, the beam is so energetic that the sample is destroyed after each measurement. Secondly, the femto-second time scale definitively pushes further the limits of reaction process kinetics study compare to the pico-second time of the best conventional synchrotron XAS beamline [109,110]. In Alonso's paper, XFEL-XES were successful used for the first time to probe the charge and spin states as well as the ligand environment of Mn(II) and binuclear Mn 2 (III-IV) complexes at room temperature.…”

Section: X-ray Free Electron Laser Xasmentioning

confidence: 99%

Advances in element speciation analysis of biomedical samples using synchrotron-based techniques

Porcaro

Roudeau

Carmona

et al. 2018

TrAC Trends in Analytical Chemistry

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Advances in element speciation analysis of biomedical samples using synchrotron-based techniques. Trends in Analytical Chemistry, Elsevier, 2018, 104, pp. Highlights principle of direct element speciation with synchrotron X-ray absorption spectroscopy (XAS)  experimental modalities for bulk-and micro-XAS speciation and their limitations  review (2012-2017) of XAS in pharmacology, metals and nanoparticles toxicology, physiopathology  future directions and developments of XAS speciation for biomedical research AbstractSynchrotron-radiation X-ray absorption spectroscopy (XAS) is a direct method for speciation analysis with atomic resolution, providing information about the local chemical environment of the probed element. This article gives an overview of the basic principles of XAS and its application to element speciation in biomedical research. The basic principle and experimental modalities of XAS are introduced, followed by a discussion of both its limitations, such as beam damage or detection limits, and practical advices to improve experiments. An updated review of biomedical studies involving XAS published over the last 5 years is then provided, paying special attention to metal-based drug biotransformation, metal and nanoparticle toxicology, and element speciation in cancer, neurological, and general pathophysiology. Finally, trends and future developments such as hyphenated methods, in situ correlative imaging and speciation, in vivo X-ray Absorption Near Edge Spectroscopy (XANES), full-field XANES, and X-ray Free Electron Laser (XFEL) XAS are presented.

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“…For proteins containing transition metal sites, a complete understanding of function requires not only the atomic structure, but also the electronic structure and chemical environment of the metal atoms (Kern et al, 2015). X-ray absorption spectroscopy has been highly informative, with the extended X-ray absorption fine structure (EXAFS) offering a sensitive measurement of metal-metal and metal-ligand distances, whereas the X-ray absorption near-edge structure (XANES) classically reveals the oxidation state and coordination geometry (Yano et al, 2005;.…”

Section: Introductionmentioning

confidence: 99%

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Sauter

Kern

Yano

et al. 2020

Acta Crystallogr D Struct Biol

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Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2-3 Â 10 À4 (ÁE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ÁE/E = 3 Â 10 À3 ) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

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Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

Cited by 39 publications

References 60 publications

Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods

Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods

Advances in element speciation analysis of biomedical samples using synchrotron-based techniques

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

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