Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves

Guo, Feng; Zhou, Weijie; Li, Peng; Mao, Zhangming; Yennawar, Neela H.; French, Jarrod B.; Huang, Tony Jun

doi:10.1002/smll.201403262

Cited by 51 publications

(38 citation statements)

References 47 publications

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“…Finally, a precise manipulation and patterning of protein crystals for X-ray data collection and screening was demonstrated by using surface acoustic waves (SAW; Guo et al ., 2015). A multi-crystal lysozyme data set was collected using < 20 μm crystals patterned by SAW in a capillary tube.…”

Section: Future Trends and Challengesmentioning

confidence: 99%

Watching proteins function with time-resolved x-ray crystallography

Šrajer

Schmidt

2017

J. Phys. D: Appl. Phys.

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Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron X-ray sources. An expansive database of more than 100,000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al., 2005a; Schmidt 2008; Neutze and Moffat, 2012; Šrajer 2014). In this approach, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron X-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard X-rays (XFELs; 5–20 keV), which provide exceptionally intense, femtosecond X-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al., 2014; Barends et al., 2015; Pande et al., 2016). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.

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Section: Future Trends and Challengesmentioning

confidence: 99%

Watching proteins function with time-resolved x-ray crystallography

Šrajer

Schmidt

2017

J. Phys. D: Appl. Phys.

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“…32–38 It has been used for the handling and processing of various biosamples including the separation of blood components, 39,40 the isolation of circulating tumor cells, 41 the patterning and coculturing of cells, 42–48 and the manipulation of protein crystals. 49 However, most existing acoustofluidic-based manipulation devices are limited to microsized particles because, as the particle size decreases, so does the acoustic radiation force experienced by the particle.…”

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confidence: 99%

Enriching Nanoparticles via Acoustofluidics

et al. 2017

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Focusing and enriching submicrometer and nanometer scale objects is of great importance for many applications in biology, chemistry, engineering, and medicine. Here, we present an acoustofluidic chip that can generate single vortex acoustic streaming inside a glass capillary through using low-power acoustic waves (only 5 V is required). The single vortex acoustic streaming that is generated, in conjunction with the acoustic radiation force, is able to enrich submicrometer- and nanometersized particles in a small volume. Numerical simulations were used to elucidate the mechanism of the single vortex formation and were verified experimentally, demonstrating the focusing of silica and polystyrene particles ranging in diameter from 80 to 500 nm. Moreover, the acoustofluidic chip was used to conduct an immunoassay in which nanoparticles that captured fluorescently labeled biomarkers were concentrated to enhance the emitted signal. With its advantages in simplicity, functionality, and power consumption, the acoustofluidic chip we present here is promising for many point-of-care applications.

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“…The merged data were phased by molecular replacement in MOLREP (Vagin & Teplyakov, 1997) using PDB ID 4woc (Guo et al, 2015) The SA composite omit map at 1.75 Å resolution is contoured at 1.0 above the mean and shows a hole in the center of the tyrosine side chain. The figures were generated using PyMol (Schrö dinger, 2014).…”

Section: I¼1mentioning

confidence: 99%

Modeling truncated pixel values of faint reflections in MicroED images

Hattne

Shi

Cruz³

et al. 2016

J Appl Crystallogr

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The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected microelectron diffraction (MicroED) images.

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Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves

Cited by 51 publications

References 47 publications

Watching proteins function with time-resolved x-ray crystallography

Watching proteins function with time-resolved x-ray crystallography

Enriching Nanoparticles via Acoustofluidics

Modeling truncated pixel values of faint reflections in MicroED images

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