Data-driven challenges and opportunities in crystallography

Glynn, Calina; Rodríguez, José A.

doi:10.1042/etls20180177

Cited by 7 publications

(5 citation statements)

References 89 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Despite the higher indexing rate, our overall hI/(I)i is lower than that of 5k2d (Table 1), possibly because of background scattering from the helium path between the crystal and the beam stop (Perutz & Rogers, 1946). Furthermore, it has been shown that acquiring more images can improve the signal-to-noise ratio of the dataset (Glynn & Rodriguez, 2019). In our dataset we used fewer images (16 737) compared with 5k2d (72 753).…”

Section: Discussionmentioning

confidence: 88%

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

Lee

Geiger

Ishchenko

et al. 2020

IUCrJ

View full text Add to dashboard Cite

Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.

show abstract

Section: Discussionmentioning

confidence: 88%

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

Lee

Geiger

Ishchenko

et al. 2020

IUCrJ

View full text Add to dashboard Cite

show abstract

“…Such joint analytical strategy would not be effective in early years when far fewer protein structures were determined to atomic resolution. Recent rapid growth in protein crystallography, such as in structural genomics (Berman et al, 2012; Bonvin, 2021; Chandonia and Brenner, 2006) and in serial crystallography (Glynn and Rodriguez, 2019; Schaffer et al, 2021), has supplied the necessarily wide sampling of protein structures for a joint analytical strategy to come of age. The vacancies or gaps in a conformational space between well-populated conformational clusters often correspond to less stable transient states whose conformations are difficult to capture, if not impossible.…”

Section: Methodsmentioning

confidence: 99%

Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin

Ren

2021

Preprint

View full text Add to dashboard Cite

Photoisomerization of retinoids inside a confined protein pocket represents a critical chemical event in many important biological processes from animal vision, non-visual light effects, to bacterial light sensing and harvesting. Light driven proton pumping in bacteriorhodopsin entails exquisite electronic and conformational reconfigurations during its photocycle. However, it has been a major challenge to delineate transient molecular events preceding and following the photoisomerization of the retinal from noisy electron density maps when varying populations of intermediates coexist and evolve as a function of time. Here I report several distinct early photoproducts deconvoluted from the recently observed mixtures in time-resolved serial crystallography. This deconvolution substantially improves the quality of the electron density maps hence demonstrates that the all-trans retinal undergoes extensive isomerization sampling before it proceeds to the productive 13-cis configuration. Upon light absorption, the chromophore attempts to perform trans-to-cis isomerization at every double bond coupled with the stalled anti-to-syn rotations at multiple single bonds along its polyene chain. Such isomerization sampling pushes all seven transmembrane helices to bend outward, resulting in a transient expansion of the retinal binding pocket, and later, a contraction due to recoiling. These ultrafast responses observed at the atomic resolution support that the productive photoreaction in bacteriorhodopsin is initiated by light-induced charge separation in the prosthetic chromophore yet governed by stereoselectivity of its protein pocket. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

show abstract

“…Such joint analytical strategy would not be effective in early years when far fewer protein structures were determined to atomic resolution. Recent rapid growth in protein crystallography, such as in structural genomics (Chandonia andBrenner, 2006, 2012) and in serial crystallography (Glynn and Rodriguez, 2019;Schaffer et al, 2021), has supplied the necessarily wide sampling of protein structures for a joint analytical strategy to come of age. The vacancies or gaps in a conformational space between wellpopulated conformational clusters often correspond to less stable transient states whose conformations are difficult to capture, if not impossible.…”

Section: Meta-analysis Of Protein Structuresmentioning

confidence: 99%

Directional proton conductance in bacteriorhodopsin is driven by concentration gradient, not affinity gradient

Ren

2021

Preprint

View full text Add to dashboard Cite

It is widely spread that microorganisms can harvest energy from sun light to establish electrochemical potential across cell membrane by pumping protons outward. Light driven proton pumping against a transmembrane gradient entails exquisite electronic and conformational reconfiguration at fs to ms time scales. However, transient molecular events along the photocycle of bacteriorhodopsin are difficult to comprehend from noisy electron density maps obtained from multiple experiments when the intermediate populations coexist and evolve as a function of 13 decades of time. Here I report an in-depth meta-analysis of the recent time-resolved datasets collected by several consortiums. This analysis deconvolutes the observed mixtures, thus substantially improves the quality of the electron density maps, and provides a clear visualization of the isolated intermediates from I to M. The primary photoproducts revealed here suggest a proton transfer uphill against 15 pH units is accomplished by the same physics that governs the tablecloth trick. While the Schiff base is displaced at the beginning of the photoisomerization within ~30 fs, the proton stays due to its inertia. This affinity-independent early deprotonation builds up a steep proton concentration gradient that drives the directional proton conductance toward the extracellular medium. This mechanism fundamentally deviates from the widely adopted assumption based on equilibrium processes driven by light-induced changes of proton affinities. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

show abstract

Data-driven challenges and opportunities in crystallography

Cited by 7 publications

References 89 publications

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin

Directional proton conductance in bacteriorhodopsin is driven by concentration gradient, not affinity gradient

Contact Info

Product

Resources

About