In vivo protein crystallization opens new routes in structural biology

Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; DePonte, Daniel P.; White, Thomas A.; Stellato, Francesco; Rehders, Dirk; Liang, Mao; Andreasson, Jakob; Aquila, Andrew; Bajt, Saša; Barthelmeß, Miriam; Barty, Anton; Bogan, Michael J.; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D.; Caleman, Carl; Coppola, N.; Davidsson, Jan; Doak, R. Bruce; Ekeberg, Tomas; Epp, Sascha W.; Erk, Benjamin; Fleckenstein, H.; Foucar, L.; Graafsma, H.; Gumprecht, Lars; Hajdu, János; Hampton, Christina Y.; Hartmann, Andreas; Hartmann, R.; Hauser, Günter; Hirsemann, H.; Holl, P.; Hunter, Mark S.; Kassemeyer, Stephan; Kirian, Richard A.; Lomb, Lukas; Maia, Filipe R. N. C.; Kimmel, Nils; Martin, Andrew V.; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M.; Shoeman, Robert L.; Sierra, Raymond G.; Soltau, H.; Stern, Stephan; Strüder, L.; Tı̂mneanu, Nicuşor; Ullrich, J.; Wang, Xiaoyu; Weidenspointner, G.; Weierstall, Uwe; Williams, Garth J.; Wunderer, C.; Fromme, Petra; Spence, John C. H.; Stehle, Thilo; Chapman, Henry N.; Betzel, Christian; Duszenko, Michael

doi:10.1038/nmeth.1859

Cited by 197 publications

(200 citation statements)

References 27 publications

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“…Coherent diffraction imaging (CDI) [11] with hard x rays can determine the structure of noncrystallizing biomolecules or other nanoparticles at atomic resolution [12][13][14][15][16][17][18][19][20][21][22][23][24][25]. The high fluence of a strongly focused XFEL pulse enables the efficient scattering of radiation photons from a molecule, sufficient to obtain a "readable" diffraction pattern of the object.…”

Section: Introductionmentioning

confidence: 99%

Effect of screening by external charges on the atomic orbitals and photoinduced processes within the Hartree-Fock-Slater atom

et al. 2012

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X-ray free-electron lasers (XFELs) are a promising tool for the structural determination of macro-and biomolecules, using coherent diffractive imaging. During imaging, the intense XFEL pulses also efficiently ionize the molecules, so it is important to estimate how the charged environment within the molecule modifies atomic properties, in comparison to the case of an isolated atom. Here, we apply the XATOM toolkit to obtain predictions on the modified ionization thresholds and rates of some photoinduced processes in carbon. The Hartree-Fock-Slater model is extended to include the electron screening and ion correlation effects, induced by external charges. With this extended model, we obtain predictions on modifications of orbital energies, photoabsorption cross sections, Auger decay rates, fluorescence emission rates, and atomic scattering factors as a function of the density and temperature of the surrounding charges. Our results have implications for the studies of dynamics within XFEL irradiated samples, in particular for those dedicated to coherent diffraction imaging.

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Section: Introductionmentioning

confidence: 99%

Effect of screening by external charges on the atomic orbitals and photoinduced processes within the Hartree-Fock-Slater atom

et al. 2012

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“…In the past few years there has been a veritable explosion of interest in nucleation due to the development of new techniques, such as microfluidics, that bring us the opportunity to probe the very small and the very fast. Besides, nucleation in confined environments is important for biological processes such as bone formation [35,36], in vivo protein crystallization [37,38], or cavitation in lipid bilayers [39], to name but a few. However, CNT is based on assumptions that are violated for small systems.…”

Section: Introductionmentioning

confidence: 99%

Mesoscopic nucleation theory for confined systems: A one-parameter model

Durán-Olivencia

Lutsko

2015

Phys. Rev. E

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Classical nucleation theory has been recently reformulated based on fluctuating hydrodynamics [J. F. Lutsko and M. A. Durán-Olivencia, Classical nucleation theory from a dynamical approach to nucleation, J. Chem. Phys. 138, 244908 (2013).]. The present work extends this effort to the case of nucleation in confined systems such as small pores and vesicles. The finite available mass imposes a maximal supercritical cluster size and prohibits nucleation altogether if the system is too small. We quantity the effect of system size on the nucleation rate. We also discuss the effect of relaxing the capillary-model assumption of zero interfacial width resulting in significant changes in the nucleation barrier and nucleation rate.

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“…An appealing alternative, made possible by recent advances in light source technology, is X-ray nanocrystallography, which is able to image structures resistant to large crystallization, such as membrane proteins, by substituting a large ensemble of easier to build nanocrystals, typically <1 μm, often delivered to the beam via a liquid jet (1)(2)(3)(4)(5)(6) (Fig. 1).…”

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confidence: 99%

“…Furthermore, these techniques only narrow down orientation to a list of possibilities when the diffraction pattern has less symmetry than the lattice, leading to an ambiguity in the image orientation, known as the indexing ambiguity. Current methods of processing the diffraction data are largely based on averaging out the data variance over several images (1)(2)(3)(4)(5)(6)(7)(8). However, if the data are processed without resolving the indexing ambiguity then they will appear to be perfectly twinned, i.e., averaged over multiple orientations.…”

mentioning

confidence: 99%

Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity

Donatelli¹,

Sethian²

2013

Proc. Natl. Acad. Sci. U.S.A.

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X-ray nanocrystallography allows the structure of a macromolecule to be determined from a large ensemble of nanocrystals. However, several parameters, including crystal sizes, orientations, and incident photon flux densities, are initially unknown and images are highly corrupted with noise. Autoindexing techniques, commonly used in conventional crystallography, can determine orientations using Bragg peak patterns, but only up to crystal lattice symmetry. This limitation results in an ambiguity in the orientations, known as the indexing ambiguity, when the diffraction pattern displays less symmetry than the lattice and leads to data that appear twinned if left unresolved. Furthermore, missing phase information must be recovered to determine the imaged object's structure. We present an algorithmic framework to determine crystal size, incident photon flux density, and orientation in the presence of the indexing ambiguity. We show that phase information can be computed from nanocrystallographic diffraction using an iterative phasing algorithm, without extra experimental requirements, atomicity assumptions, or knowledge of similar structures required by current phasing methods. The feasibility of this approach is tested on simulated data with parameters and noise levels common in current experiments.A lthough conventional X-ray crystallography has been used extensively to determine atomic structure, it is limited to objects that can be formed into large crystal samples ð>10 μmÞ. An appealing alternative, made possible by recent advances in light source technology, is X-ray nanocrystallography, which is able to image structures resistant to large crystallization, such as membrane proteins, by substituting a large ensemble of easier to build nanocrystals, typically <1 μm, often delivered to the beam via a liquid jet (1-6) ( Fig. 1). However, the beam power required to retrieve sufficient information destroys the crystal, hence ultrafast pulses (≤70 fs) are required to collect data before damage effects alter the signal. Using nanocrystals introduces several challenges. Due to the small crystal size, Bragg peaks are smeared out, and there is noticeable signal between peaks. Typically, only partial peak reflections are measured, resulting in reduced intensities. Variations in crystal size and incident photon flux density, unknown orientations, shot noise, and background signal from the liquid and detector add additional uncertainty to the data.If crystal orientations were known, noise and variation in the peak measurements could be averaged out, and the data could be inverted to retrieve the object's electron density. Although autoindexing techniques can be used to determine crystal orientation up to lattice symmetry from the location of a sufficient number of Bragg peaks, they typically face difficulties in the presence of partial and non-Bragg reflections common in nanocrystal diffraction images. Furthermore, these techniques only narrow down orientation to a list of possibilities when the diffraction pattern has less ...

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In vivo protein crystallization opens new routes in structural biology

Cited by 197 publications

References 27 publications

Effect of screening by external charges on the atomic orbitals and photoinduced processes within the Hartree-Fock-Slater atom

Effect of screening by external charges on the atomic orbitals and photoinduced processes within the Hartree-Fock-Slater atom

Mesoscopic nucleation theory for confined systems: A one-parameter model

Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity

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