X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds

Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; Varel, Michael J.; Guha, Sudipto; Astrauskaite, Ieva; Gennis, Robert B.; Kenis, Paul J.  A.

doi:10.1039/C7LC01141E

X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds

Journal Article · Sat Feb 17 23:00:00 EST 2018 · Lab on a Chip

DOI:https://doi.org/10.1039/C7LC01141E· OSTI ID:1599433

Schieferstein, Jeremy M. ^[1]; ^[1]; Varel, Michael J. ^[1]; Guha, Sudipto ^[1]; Astrauskaite, Ieva ^[1]; Gennis, Robert B. ^[1]; ^[1]

Univ. of Illinois at Urbana-Champaign, IL (United States)

Crystallization of membrane proteins is a critical step for uncovering atomic resolution 3-D structures and elucidating structure–function relationships. Microseeding, the process of transferring sub-microscopic crystal nuclei from initial screens into new crystallization experiments, is an effective, yet underutilized approach to grow crystals suitable for X-ray crystallography. In this work, we report simplified methods for crystallization of membrane proteins that utilize microseeding in X-ray transparent microfluidic chips. First, a microfluidic method for introduction of microseed dilutions into metastable crystallization experiments is demonstrated for photoactive yellow protein and cytochrome bo3 oxidase. As microseed concentration decreased, the number of crystals decreased while the average size increased. Second, we demonstrate a microfluidic chip for microseed screening, where many crystallization conditions were formulated on-chip prior to mixing with microseeds. Crystallization composition, crystal size, and diffraction data were collected and mapped on phase diagrams, which revealed that crystals of similar diffraction quality and size typically grow in distinct regions of the phase diagram.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC); National Cancer Institute (NCI); National Institute of General Medical Sciences (NIGMS)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1599433

Journal Information:: Lab on a Chip, Journal Name: Lab on a Chip Journal Issue: 6 Vol. 18; ISSN LCAHAM; ISSN 1473-0197

Publisher:: Royal Society of ChemistryCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (63)

Soft Lithography Xia, Younan; Whitesides, George M. Angewandte Chemie International Edition, Vol. 37, Issue 5, p. 550-575 https://doi.org/10.1002/(SICI)1521-3773(19980316)37:5<550::AID-ANIE550>3.0.CO;2-G	journal	March 1998
Soft Lithography Xia, Younan; Whitesides, George M. Angewandte Chemie International Edition, Vol. 37, Issue 5 https://doi.org/10.1002/(sici)1521-3773(19980316)37:5<550::aid-anie550>3.3.co;2-7	journal	March 1998
A Droplet-Based, Composite PDMS/Glass Capillary Microfluidic System for Evaluating Protein Crystallization Conditions by Microbatch and Vapor-Diffusion Methods with On-Chip X-Ray Diffraction Zheng, Bo; Tice, Joshua D.; Roach, L. Spencer Angewandte Chemie, Vol. 116, Issue 19 https://doi.org/10.1002/ange.200453974	journal	May 2004
Time-Controlled Microfluidic Seeding in nL-Volume Droplets To Separate Nucleation and Growth Stages of Protein Crystallization Gerdts, Cory J.; Tereshko, Valentina; Yadav, Maneesh K. Angewandte Chemie, Vol. 118, Issue 48 https://doi.org/10.1002/ange.200602946	journal	December 2006
A Droplet-Based, Composite PDMS/Glass Capillary Microfluidic System for Evaluating Protein Crystallization Conditions by Microbatch and Vapor-Diffusion Methods with On-Chip X-Ray Diffraction Zheng, Bo; Tice, Joshua D.; Roach, L. Spencer Angewandte Chemie International Edition, Vol. 43, Issue 19 https://doi.org/10.1002/anie.200453974	journal	May 2004
Time-Controlled Microfluidic Seeding in nL-Volume Droplets To Separate Nucleation and Growth Stages of Protein Crystallization Gerdts, Cory J.; Tereshko, Valentina; Yadav, Maneesh K. Angewandte Chemie International Edition, Vol. 45, Issue 48 https://doi.org/10.1002/anie.200602946	journal	December 2006
Uncertainties in crystallization of hen-egg white lysozyme: reproducibility issue Yin, Da-Chuan; Wakayama, Nobuko I.; Lu, Hui-Meng Crystal Research and Technology, Vol. 43, Issue 4 https://doi.org/10.1002/crat.200710998	journal	April 2008
The xanthopsins: a new family of eubacterial blue-light photoreceptors. Kort, R.; Hoff, W. D.; Van West, M. The EMBO Journal, Vol. 15, Issue 13 https://doi.org/10.1002/j.1460-2075.1996.tb00685.x	journal	July 1996
Large-scale crystallization of proteins for purification and formulation Hekmat, Dariusch Bioprocess and Biosystems Engineering, Vol. 38, Issue 7 https://doi.org/10.1007/s00449-015-1374-y	journal	February 2015
A plug-based microfluidic system for dispensing lipidic cubic phase (LCP) material validated by crystallizing membrane proteins in lipidic mesophases Li, Liang; Fu, Qiang; Kors, Christopher A. Microfluidics and Nanofluidics, Vol. 8, Issue 6 https://doi.org/10.1007/s10404-009-0512-8	journal	October 2009
Development of a continuous reactor for the electro-reduction of carbon dioxide to formate – Part 1: Process variables Li, Hui; Oloman, Colin Journal of Applied Electrochemistry, Vol. 36, Issue 10, p. 1105-1115 https://doi.org/10.1007/s10800-006-9194-z	journal	August 2006
Understanding protein crystallization on the basis of the phase diagram Haas, C.; Drenth, J. Journal of Crystal Growth, Vol. 196, Issue 2-4 https://doi.org/10.1016/S0022-0248(98)00831-8	journal	January 1999
The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli Yap, Lai Lai; Lin, Myat T.; Ouyang, Hanlin Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1797, Issue 12 https://doi.org/10.1016/j.bbabio.2010.04.011	journal	December 2010
Heterogeneous nucleants for crystallogenesis and bioseparation Shah, Umang V.; Amberg, Christian; Diao, Ying Current Opinion in Chemical Engineering, Vol. 8 https://doi.org/10.1016/j.coche.2015.03.002	journal	May 2015
Structure-guided studies of the SHP-1/JAK1 interaction provide new insights into phosphatase catalytic domain substrate recognition Alicea-Velázquez, Nilda L.; Jakoncic, Jean; Boggon, Titus J. Journal of Structural Biology, Vol. 181, Issue 3 https://doi.org/10.1016/j.jsb.2012.12.009	journal	March 2013
Methods for separating nucleation and growth in protein crystallisation Chayen, N. Progress in Biophysics and Molecular Biology, Vol. 88, Issue 3 https://doi.org/10.1016/j.pbiomolbio.2004.07.007	journal	July 2005
Turning protein crystallisation from an art into a science Chayen, Naomi E. Current Opinion in Structural Biology, Vol. 14, Issue 5 https://doi.org/10.1016/j.sbi.2004.08.002	journal	October 2004
Fabrication of X-ray compatible microfluidic platforms for protein crystallization Guha, Sudipto; Perry, Sarah L.; Pawate, Ashtamurthy S. Sensors and Actuators B: Chemical, Vol. 174 https://doi.org/10.1016/j.snb.2012.08.048	journal	November 2012
From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography Dods, Robert; Båth, Petra; Arnlund, David Structure, Vol. 25, Issue 9 https://doi.org/10.1016/j.str.2017.07.002	journal	September 2017
Protein crystallization and phase diagrams Asherie, N. Methods, Vol. 34, Issue 3 https://doi.org/10.1016/j.ymeth.2004.03.028	journal	November 2004
Rapid Prototyping of Microfluidic Systems in Poly(dimethylsiloxane) Duffy, David C.; McDonald, J. Cooper; Schueller, Olivier J. A. Analytical Chemistry, Vol. 70, Issue 23, p. 4974-4984 https://doi.org/10.1021/ac980656z	journal	October 1998
1.4 .ANG. Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore Borgstahl, Gloria E. O.; Williams, DeWight R.; Getzoff, Elizabeth D. Biochemistry, Vol. 34, Issue 19 https://doi.org/10.1021/bi00019a004	journal	May 1995
Combining Counter-Diffusion and Microseeding to Increase the Success Rate in Protein Crystallization Gavira, Jose A.; Hernandez-Hernandez, M. A.; Gonzalez-Ramirez, Luis A. Crystal Growth & Design, Vol. 11, Issue 6 https://doi.org/10.1021/cg101380j	journal	June 2011
Random Microseeding: A Theoretical and Practical Exploration of Seed Stability and Seeding Techniques for Successful Protein Crystallization Shaw Stewart, Patrick D.; Kolek, Stefan A.; Briggs, Richard A. Crystal Growth & Design, Vol. 11, Issue 8 https://doi.org/10.1021/cg2001442	journal	August 2011
Spatially Precise, Soft Microseeding of Single Protein Crystals by Femtosecond Laser Ablation Yoshikawa, Hiroshi Y.; Hosokawa, Yoichiroh; Murai, Ryota Crystal Growth & Design, Vol. 12, Issue 9 https://doi.org/10.1021/cg300018t	journal	July 2012
ChipX: A Novel Microfluidic Chip for Counter-Diffusion Crystallization of Biomolecules and in Situ Crystal Analysis at Room Temperature Pinker, Franziska; Brun, Mathieu; Morin, Pierre Crystal Growth & Design, Vol. 13, Issue 8 https://doi.org/10.1021/cg301757g	journal	July 2013
Heterogeneous Crystallization of Proteins: Is it a Prenucleation Clusters Mediated Process? Fermani, Simona; Vettraino, Chiara; Bonacini, Irene Crystal Growth & Design, Vol. 13, Issue 7 https://doi.org/10.1021/cg400501f	journal	May 2013
X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S. Crystal Growth & Design, Vol. 14, Issue 10 https://doi.org/10.1021/cg5011488	journal	September 2014
Crystallization Optimization of Pharmaceutical Solid Forms with X-ray Compatible Microfluidic Platforms Horstman, Elizabeth M.; Goyal, Sachit; Pawate, Ashtamurthy Crystal Growth & Design, Vol. 15, Issue 3 https://doi.org/10.1021/cg5016065	journal	February 2015
Control and Measurement of the Phase Behavior of Aqueous Solutions Using Microfluidics Shim, Jung-uk; Cristobal, Galder; Link, Darren R. Journal of the American Chemical Society, Vol. 129, Issue 28 https://doi.org/10.1021/ja071820f	journal	July 2007
Diffusion in Aqueous Solutions of Poly(ethylene glycol) at Low Concentrations Waggoner, R. Allen; Blum, Frank D.; Lang, John C. Macromolecules, Vol. 28, Issue 8 https://doi.org/10.1021/ma00112a010	journal	April 1995
Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography Liu, Wei; Ishchenko, Andrii; Cherezov, Vadim Nature Protocols, Vol. 9, Issue 9 https://doi.org/10.1038/nprot.2014.141	journal	August 2014
Graphene-based microfluidics for serial crystallography Sui, Shuo; Wang, Yuxi; Kolewe, Kristopher W. Lab on a Chip, Vol. 16, Issue 16 https://doi.org/10.1039/C6LC00451B	journal	January 2016
Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis Dhouib, Kaouthar; Khan Malek, Chantal; Pfleging, Wilhelm Lab on a Chip, Vol. 9, Issue 10 https://doi.org/10.1039/b819362b	journal	January 2009
X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; Sun, Chang Biomicrofluidics, Vol. 11, Issue 2 https://doi.org/10.1063/1.4981818	journal	March 2017
A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion Hansen, C. L.; Skordalakes, E.; Berger, J. M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 26 https://doi.org/10.1073/pnas.262485199	journal	December 2002
Combining in-situ proteolysis and microseed matrix screening to promote crystallization of PrPc-nanobody complexes Abskharon, R. N. N.; Soror, S. H.; Pardon, E. Protein Engineering Design and Selection, Vol. 24, Issue 9 https://doi.org/10.1093/protein/gzr017	journal	May 2011
Purification, crystallization and preliminary crystallographic studies of an integral membrane protein, cytochrome bo ₃ ubiquinol oxidase from Escherichia coli Abramson, Jeff; Larsson, Gisela; Byrne, Bernadette Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 8 https://doi.org/10.1107/S0907444900007605	journal	August 2000
Separating nucleation and growth in protein crystallization using dynamic light scattering Saridakis, Emmanuel; Dierks, Karsten; Moreno, Abel Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 10 https://doi.org/10.1107/S0907444902014348	journal	September 2002
Microseed matrix screening to improve crystals of yeast cytosine deaminase Ireton, Gregory C.; Stoddard, Barry L. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 3 https://doi.org/10.1107/S0907444903029664	journal	February 2004
An automated microseed matrix-screening method for protein crystallization D'Arcy, Allan; Villard, Frederic; Marsh, May Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 4 https://doi.org/10.1107/S0907444907007652	journal	March 2007
The role of bias in crystallization conditions in automated microseeding St John, Franz J.; Feng, Bo; Pozharski, Edwin Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 12 https://doi.org/10.1107/S0907444908031302	journal	November 2008
Acoustic matrix microseeding: improving protein crystal growth with minimal chemical bias Villaseñor, Armando G.; Wong, April; Shao, Ada Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 5 https://doi.org/10.1107/S0907444910005512	journal	April 2010
Promoting crystallization of antibody–antigen complexes via microseed matrix screening Obmolova, Galina; Malia, Thomas J.; Teplyakov, Alexey Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 8 https://doi.org/10.1107/S0907444910026041	journal	July 2010
Sensitivity of lysozyme crystallization to minute variations in concentration Chen, Rui-Qing; Yin, Da-Chuan; Lu, Qin-Qin Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 5 https://doi.org/10.1107/S0907444912006427	journal	April 2012
Structure of arylamine N -acetyltransferase from Mycobacterium tuberculosis determined by cross-seeding with the homologous protein from M. marinum : triumph over adversity Abuhammad, Areej; Lowe, Edward D.; McDonough, Michael A. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 8 https://doi.org/10.1107/S0907444913015126	journal	July 2013
Crystallization of wild-type and mutant ferricytochromes c at low ionic strength: seeding technique and X-ray diffraction analysis Sanishvili, R. G.; Margoliash, E.; Westbrook, M. L. Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5 https://doi.org/10.1107/S0907444994002568	journal	September 1994
Nucleation in Protein Crystallization Drenth, J.; Haas, C. Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5 https://doi.org/10.1107/S0907444998002297	journal	September 1998
A method to produce microseed stock for use in the crystallization of biological macromolecules Luft, Joseph R.; DeTitta, George T. Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 5 https://doi.org/10.1107/S0907444999002085	journal	May 1999
Low- Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography Feld, Geoffrey K.; Heymann, Michael; Benner, W. Henry Journal of Applied Crystallography, Vol. 48, Issue 4 https://doi.org/10.1107/S1600576715010493	journal	June 2015
Semi-automated microseeding of nanolitre crystallization experiments Walter, Thomas S.; Mancini, Erika J.; Kadlec, Jan Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 64, Issue 1 https://doi.org/10.1107/S1744309107057260	journal	December 2007
Crystallization and preliminary X-ray crystallographic analysis of sterol transcription factor Upc2 from Saccharomyces cerevisiae Ha, Subin; Tong, Junsen; Yang, Huiseon Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 2 https://doi.org/10.1107/S1744309112051597	journal	January 2013
New crystal forms of NTPDase1 from the bacterium Legionella pneumophila Zebisch, Matthias; Schäfer, Petra; Lauble, Peter Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 3 https://doi.org/10.1107/S1744309113001504	journal	February 2013
Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase Sartmatova, Darika; Nash, Taishayla; Schormann, Norbert Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 3 https://doi.org/10.1107/S1744309113002716	journal	February 2013
Approaches to automated protein crystal harvesting Deller, Marc C.; Rupp, Bernhard Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 2 https://doi.org/10.1107/S2053230X14000387	journal	January 2014
Protein crystallization with microseed matrix screening: application to human germline antibody Fabs Obmolova, Galina; Malia, Thomas J.; Teplyakov, Alexey Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 8 https://doi.org/10.1107/S2053230X14012552	journal	July 2014
Microseed matrix screening for optimization in protein crystallization: what have we learned? D'Arcy, Allan; Bergfors, Terese; Cowan-Jacob, Sandra W. Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 9 https://doi.org/10.1107/S2053230X14015507	journal	August 2014
Micromachining applications of a high resolution ultrathick photoresist Lee, K. Y. Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures, Vol. 13, Issue 6 https://doi.org/10.1116/1.588297	journal	November 1995
Monolithic Microfabricated Valves and Pumps by Multilayer Soft Lithography Unger, M. A. Science, Vol. 288, Issue 5463 https://doi.org/10.1126/science.288.5463.113	journal	April 2000
Soft Lithography Xia, Younan; Whitesides, George M. Annual Review of Materials Science, Vol. 28, Issue 1, p. 153-184 https://doi.org/10.1146/annurev.matsci.28.1.153	journal	August 1998
Protein crystals for the delivery of biopharmaceuticals Basu, Sujit K.; Govardhan, Chandrika P.; Jung, Chu W. Expert Opinion on Biological Therapy, Vol. 4, Issue 3 https://doi.org/10.1517/14712598.4.3.301	journal	March 2004
Preparation of Large Crystals of Photoactive Yellow Protein for Neutron Diffraction and High Resolution Crystal Structure Analysis†: Photochemistry and Photobiology, 2007, 83 Yamaguchi, Shigeo; Kamikubo, Hironari; Shimizu, Nobutaka Photochemistry and Photobiology, Vol. 83, Issue 2 https://doi.org/10.1562/2006-07-23-RA-977	journal	February 2007
Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates Oswald, Christine; Smits, Sander; Bremer, Erhard International Journal of Molecular Sciences, Vol. 9, Issue 7 https://doi.org/10.3390/ijms9071131	journal	July 2008

Cited By (4)

Droplet Microfluidics XRD Identifies Effective Nucleating Agents for Calcium Carbonate Levenstein, Mark A.; Anduix‐Canto, Clara; Kim, Yi‐Yeoun Advanced Functional Materials, Vol. 29, Issue 19 https://doi.org/10.1002/adfm.201808172	journal	March 2019
Crystal-on-crystal chips for in situ serial diffraction at room temperature Ren, Zhong; Ayhan, Medine; Bandara, Sepalika Lab on a Chip, Vol. 18, Issue 15 https://doi.org/10.1039/c8lc00489g	journal	January 2018
Polymeric microfluidic continuous flow mixer combined with hyperspectral FT-IR imaging for studying rapid biomolecular events Jang, Hyukjin; Pawate, Ashtamurthy S.; Bhargava, Rohit Lab on a Chip, Vol. 19, Issue 15 https://doi.org/10.1039/c9lc00182d	journal	January 2019
A microfluidic device for both on-chip dialysis protein crystallization and in situ X-ray diffraction Junius, Niels; Jaho, Sofia; Sallaz-Damaz, Yoann Lab on a Chip, Vol. 20, Issue 2 https://doi.org/10.1039/c9lc00651f	journal	January 2020

Similar Records

X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization

Journal Article · Mon Apr 24 00:00:00 EDT 2017 · Biomicrofluidics · OSTI ID:1355039

X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination

Journal Article · Wed Oct 01 00:00:00 EDT 2014 · Crystal Growth and Design · OSTI ID:1393969

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES

X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds

Citation Formats

References (63)

Cited By (4)

Similar Records

Related Subjects