Macromolecular crystallography at synchrotron radiation sources: current status and future developments

Duke, Elizabeth; Johnson, L.N.

doi:10.1098/rspa.2010.0448

Cited by 33 publications

(34 citation statements)

References 129 publications

(148 reference statements)

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“…The availability in the near future of hard X-ray FEL facilities [220][221][222][223][224][225][226][227][228][229] will represent an impressive improvement in the potentialities of both TR-XSS and TR-XAS techniques, both in terms of photon flux (moving from 10 6 to 10 12 photons per electron bunch) and ultimate time resolution (the typical bunch width moving from 10 −10 down to 10 −14 s). The development of adequate measurement techniques and data-acquisition schemes for measuring X-ray scattering/absorption data at FELs will be essential to derive full benefit from these new-generation photon sources.…”

Section: Discussionmentioning

confidence: 99%

“…However, for the time being, this apparently simple solution is not feasible since, for q > 7 Å −1 , the experimental q I(q) data are dominated by noise and the interval 4 Å −1 < q < 7 Å −1 is too limited for extracting any reliable structural information. This situation will change in the future, with the availability of hard X-ray free electron lasers (FELs) [220][221][222][223][224][225][226][227][228][229], where the number of photons per electron pulse will reach values as high as 10 12 , compared with 10 6 for third-generation synchrotron radiation sources.…”

Section: Tr-xssmentioning

confidence: 99%

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Synchrotron ultrafast techniques for photoactive transition metal complexes

Borfecchia

Garino

Salassa

et al. 2013

Phil. Trans. R. Soc. A.

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In the last decade, the use of time-resolved X-ray techniques has revealed the structure of lightgenerated transient species for a wide range of samples, from small organic molecules to proteins. Time resolutions of the order of 100 ps are typically reached, allowing one to monitor thermally equilibrated excited states and capture their structure as a function of time. This review aims at providing a general overview of the application of timeresolved X-ray solution scattering (TR-XSS) and time-resolved X-ray absorption spectroscopy (TR-XAS), the two techniques prevalently employed in the investigation of light-triggered structural changes of transition metal complexes. In particular, we herein describe the fundamental physical principles for static XSS and XAS and illustrate the theory of timeresolved XSS and XAS together with data acquisition and analysis strategies. Selected pioneering examples of photoactive transition metal complexes studied by TR-XSS and TR-XAS are discussed in depth.

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Section: Discussionmentioning

confidence: 99%

Section: Tr-xssmentioning

confidence: 99%

Synchrotron ultrafast techniques for photoactive transition metal complexes

Borfecchia

Garino

Salassa

et al. 2013

Phil. Trans. R. Soc. A.

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“…The current and developing state of the art of X-ray diffraction promises more high-resolution, high-quality data of proteins in the future (Duke & Johnson, 2010;Dauter et al, 2010;Mueller et al, 2012;Garman & Weik, 2013). One factor limiting the number of very high-resolution data sets in the Protein Data Bank (PDB; Berman et al, 2000) is the geometry of many diffractometers for protein diffraction.…”

Section: Introductionmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Cryst D Biol Crystallogr

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Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

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“…Here, we intentionally neglected other effects of the synchrotron radiation on protein crystals, such as cleavage of specific bonds, etc. [4,17], for the sake of simplicity of the obtained computer model. The observed dependence means that the effect of insufficient scattering intensity of smaller crystal is prevalent.…”

Section: Radiation Stability Of Protein Crystalsmentioning

confidence: 99%

Stability and Radiation Damage of Protein Crystals as Studied by Means of Molecular Dynamics and Monte Carlo Simulation

Orekhov¹,

Bozdaganyan²,

Pechkova³

et al. 2017

NanoWorld J

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Molecular Dynamics (MD) and Monte Carlo (MC) simulations of crystals can help in interpretation of experimental X-ray crystallography data. Particularly, they can be useful for understanding how various crystallization techniques affect protein conformational plasticity within the crystal lattice and the stability of biomolecular crystals. The latter has become especially important since the modern and extremely intense X-ray radiation sources (such as free electron lasers, FELs) appeared recently.In the present study we were able to show by means of computer simulations that the lysozyme crystals obtained using the Langmuir-Blodgett technique have an advantage over the classical ones ("Hanging Drop") in terms of their thermal stability as well as their stability against the radiation damage. We also demonstrate an important role of crystal water dynamics for stability of protein crystals.

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Macromolecular crystallography at synchrotron radiation sources: current status and future developments

Cited by 33 publications

References 129 publications

Synchrotron ultrafast techniques for photoactive transition metal complexes

Synchrotron ultrafast techniques for photoactive transition metal complexes

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Stability and Radiation Damage of Protein Crystals as Studied by Means of Molecular Dynamics and Monte Carlo Simulation

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