Ultrafast structural changes within a photosynthetic reaction centre

Dods, Robert; Båth, Petra; Morozov, Dmitry; Gagnér, Viktor Ahlberg; Arnlund, David; Luk, Hoi Ling; Kübel, Joachim; Maj, Michał; Vallejos, Adams; Wickstrand, Cecilia; Bosman, Robert; Beyerlein, Kenneth R.; Nelson, Garrett; Liang, Mao; Milathianaki, Despina; Robinson, Joseph S.; Harimoorthy, Rajiv; Berntsen, Peter; Malmerberg, Erik; Johansson, Linda C.; Andersson, Rebecka; Carbajo, Sergio; Claesson, Elin; Conrad, Chelsie E.; Dahl, Peter; Hammarin, Greger; Hunter, Mark S.; Li, Chufeng; Lisova, Stella; Royant, Antoine; Safari, Cecilia; Sharma, Amit; Williams, Garth J.; Yefanov, Oleksandr; Westenhoff, Sebastian; Davidsson, Jan; DePonte, Daniel P.; Boutet, Sébastien; Barty, Anton; Katona, Gergely; Groenhof, Gerrit; Brändén, Gisela; Neutze, Richard

doi:10.1038/s41586-020-3000-7

Cited by 80 publications

(71 citation statements)

References 72 publications

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“…An optical laser pulse triggers a reaction in the crystallized molecules. Structures are probed by X-ray pulses after a controlled delay (Tenboer et al, 2014;Barends et al, 2015;Coquelle et al, 2018;Nogly et al, 2018;Kern et al, 2018;Pandey et al, 2019;Skopintsev et al, 2020;Dods et al, 2021;Yun et al, 2021). Due to the ultrashort nature of both X-ray and optical laser pulses, the experiments can reach subpicosecond time resolutions (Hartmann et al, 2014;Barends et al, 2015;Pande et al, 2016;Skopintsev et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Pandey

Calvey

Katz

et al. 2021

IUCrJ

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Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL). The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the Mycobacterium tuberculosis β-lactamase to be followed using time-resolved crystallography in real time. It is shown how a diffusion coefficient in enzyme crystals can be derived directly from the X-ray data, enabling the determination of ligand and enzyme–ligand concentrations at any position in the crystal volume as a function of time. In addition, the structure of the irreversible inhibitor sulbactam bound to the enzyme at a 66 ms time delay after mixing is described. This demonstrates that the EuXFEL can be used as an important tool for biomedically relevant research.

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Section: Introductionmentioning

confidence: 99%

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Pandey

Calvey

Katz

et al. 2021

IUCrJ

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“…By the short duration of highly intense X-ray pulses the crystals are vaporized before radiation damage can occur [94], thus facilitating the time-resolved characterization of dynamic structural transitions in crystallized proteins [96]. These studies have provided remarkable insight into the activation of different photoreceptors, by visualizing the so-called protein quake [97][98][99]. In addition to SFX, another method that has been show to provide high-resolution structural data of microcrystalline membrane proteins is so-called microcrystal electron diffraction (Micro ED) [100,101], which was recently applied to study the tetrameric sodium channel NaK in DDM based crystals [102] as well as the human adenosine A 2A receptor in LCP [103].…”

Section: D Crystals and Lipidic Cubic Phasementioning

confidence: 99%

Fake It ‘Till You Make It—The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics

Thoma

Burmann

2020

IJMS

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Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.

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“…Indeed, fs-TRXSS has been used to disclose the ultrafast structural dynamics of small molecules 19 – 25 and proteins 26 , 27 . In spite of its strong potential, however, fs-TRXSS has been applied to a limited number of model protein systems such as myoglobin (Mb) and photosynthetic reaction center unlike time-resolved serial femtosecond X-ray crystallography (TR-SFX), which has been used for various protein systems 28 – 34 . Moreover, the interpretation of fs-TRXSS data is still under debate.…”

Section: Introductionmentioning

confidence: 99%

Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering

et al. 2021

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Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.

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Ultrafast structural changes within a photosynthetic reaction centre

Cited by 80 publications

References 72 publications

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Fake It ‘Till You Make It—The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics

Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering

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