Literature DB >> 35916224

Data collection from crystals grown in microfluidic droplets.

Gyorgy Babnigg1, Darren Sherrell2, Youngchang Kim2, Jessica L Johnson1, Boguslaw Nocek1, Kemin Tan2, Danny Axford3, Hui Li1, Lance Bigelow1, Lukas Welk1, Michael Endres2, Robin L Owen3, Andrzej Joachimiak2.   

Abstract

Protein crystals grown in microfluidic droplets have been shown to be an effective and robust platform for storage, transport and serial crystallography data collection with a minimal impact on diffraction quality. Single macromolecular microcrystals grown in nanolitre-sized droplets allow the very efficient use of protein samples and can produce large quantities of high-quality samples for data collection. However, there are challenges not only in growing crystals in microfluidic droplets, but also in delivering the droplets into X-ray beams, including the physical arrangement, beamline and timing constraints and ease of use. Here, the crystallization of two human gut microbial hydrolases in microfluidic droplets is described: a sample-transport and data-collection approach that is inexpensive, is convenient, requires small amounts of protein and is forgiving. It is shown that crystals can be grown in 50-500 pl droplets when the crystallization conditions are compatible with the droplet environment. Local and remote data-collection methods are described and it is shown that crystals grown in microfluidics droplets and housed as an emulsion in an Eppendorf tube can be shipped from the US to the UK using a FedEx envelope, and data can be collected successfully. Details of how crystals were delivered to the X-ray beam by depositing an emulsion of droplets onto a silicon fixed-target serial device are provided. After three months of storage at 4°C, the crystals endured and diffracted well, showing only a slight decrease in diffracting power, demonstrating a suitable way to grow crystals, and to store and collect the droplets with crystals for data collection. This sample-delivery and data-collection strategy allows crystal droplets to be shipped and set aside until beamtime is available.

Entities:  

Keywords:  X-ray data collection; emulsions; fixed targets; fucosidases; hydrolases; low dose; microfluidic droplets; serial crystallography; sialate O-acetylesterase; α–β fold

Mesh:

Substances:

Year:  2022        PMID: 35916224      PMCID: PMC9344473          DOI: 10.1107/S2059798322004661

Source DB:  PubMed          Journal:  Acta Crystallogr D Struct Biol        ISSN: 2059-7983            Impact factor:   5.699


  48 in total

1.  Formation of droplets of alternating composition in microfluidic channels and applications to indexing of concentrations in droplet-based assays.

Authors:  Bo Zheng; Joshua D Tice; Rustem F Ismagilov
Journal:  Anal Chem       Date:  2004-09-01       Impact factor: 6.986

2.  HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.

Authors:  Wladek Minor; Marcin Cymborowski; Zbyszek Otwinowski; Maksymilian Chruszcz
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-07-18

3.  New vectors for co-expression of proteins: structure of Bacillus subtilis ScoAB obtained by high-throughput protocols.

Authors:  Lucy Stols; Min Zhou; William H Eschenfeldt; Cynthia Sanville Millard; James Abdullah; Frank R Collart; Youngchang Kim; Mark I Donnelly
Journal:  Protein Expr Purif       Date:  2007-02-06       Impact factor: 1.650

Review 4.  High-throughput protein purification and quality assessment for crystallization.

Authors:  Youngchang Kim; Gyorgy Babnigg; Robert Jedrzejczak; William H Eschenfeldt; Hui Li; Natalia Maltseva; Catherine Hatzos-Skintges; Minyi Gu; Magdalena Makowska-Grzyska; Ruiying Wu; Hao An; Gekleng Chhor; Andrzej Joachimiak
Journal:  Methods       Date:  2011-08-31       Impact factor: 3.608

5.  Fixed Target Serial Data Collection at Diamond Light Source.

Authors:  Sam Horrell; Danny Axford; Nicholas E Devenish; Ali Ebrahim; Michael A Hough; Darren A Sherrell; Selina L S Storm; Ivo Tews; Jonathan A R Worrall; Robin L Owen
Journal:  J Vis Exp       Date:  2021-02-26       Impact factor: 1.355

6.  Linking crystallographic model and data quality.

Authors:  P Andrew Karplus; Kay Diederichs
Journal:  Science       Date:  2012-05-25       Impact factor: 47.728

7.  Probing the coordination behavior of Hg2+, CH3Hg+, and Cd2+ towards mixtures of two biological thiols by HPLC-ICP-AES.

Authors:  Katie L Pei; Melani Sooriyaarachchi; Darren A Sherrell; Graham N George; Jürgen Gailer
Journal:  J Inorg Biochem       Date:  2010-12-07       Impact factor: 4.155

8.  Overview of the CCP4 suite and current developments.

Authors:  Martyn D Winn; Charles C Ballard; Kevin D Cowtan; Eleanor J Dodson; Paul Emsley; Phil R Evans; Ronan M Keegan; Eugene B Krissinel; Andrew G W Leslie; Airlie McCoy; Stuart J McNicholas; Garib N Murshudov; Navraj S Pannu; Elizabeth A Potterton; Harold R Powell; Randy J Read; Alexei Vagin; Keith S Wilson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

9.  Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array.

Authors:  Artem Y Lyubimov; Thomas D Murray; Antoine Koehl; Ismail Emre Araci; Monarin Uervirojnangkoorn; Oliver B Zeldin; Aina E Cohen; S Michael Soltis; Elizabeth L Baxter; Aaron S Brewster; Nicholas K Sauter; Axel T Brunger; James M Berger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-03-27

10.  MolProbity: all-atom structure validation for macromolecular crystallography.

Authors:  Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21
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  1 in total

1.  Fixed-target serial crystallography at the Structural Biology Center.

Authors:  Darren A Sherrell; Alex Lavens; Mateusz Wilamowski; Youngchang Kim; Ryan Chard; Krzysztof Lazarski; Gerold Rosenbaum; Rafael Vescovi; Jessica L Johnson; Chase Akins; Changsoo Chang; Karolina Michalska; Gyorgy Babnigg; Ian Foster; Andrzej Joachimiak
Journal:  J Synchrotron Radiat       Date:  2022-08-17       Impact factor: 2.557

  1 in total

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