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

Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å.

[1]  J. Broecker,et al.  Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. , 2017, Structure.

[2]  Craig M. Ogata,et al.  A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals , 2016, Crystal growth & design.

[3]  Garth J. Williams,et al.  Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography , 2016, Nature Communications.

[4]  Su Lin,et al.  Ultrafast Electron Transfer Kinetics in the LM Dimer of Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides. , 2016, The journal of physical chemistry. B.

[5]  F. von Delft,et al.  An overview of heavy-atom derivatization of protein crystals , 2016, Acta crystallographica. Section D, Structural biology.

[6]  D. Yin,et al.  Sensitivity of lysozyme crystallization to temperature variation , 2016 .

[7]  Aidin R. Balo,et al.  Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography , 2015, Structural dynamics.

[8]  Garth J. Williams,et al.  Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography , 2015 .

[9]  Ezequiel Panepucci,et al.  In meso in situ serial X-ray crystallography of soluble and membrane proteins , 2015, Acta crystallographica. Section D, Biological crystallography.

[10]  Ilme Schlichting,et al.  Serial femtosecond crystallography: the first five years , 2015, IUCrJ.

[11]  Manfred Burghammer,et al.  Lipidic cubic phase serial millisecond crystallography using synchrotron radiation , 2015, IUCrJ.

[12]  Martin Caffrey,et al.  A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes , 2015, Acta crystallographica. Section F, Structural biology communications.

[13]  P. Kenis,et al.  X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination , 2014, Crystal growth & design.

[14]  Wei Liu,et al.  Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography , 2014, Nature Protocols.

[15]  Anton Barty,et al.  Fixed-target protein serial microcrystallography with an x-ray free electron laser , 2014, Scientific Reports.

[16]  Uwe Weierstall,et al.  Liquid sample delivery techniques for serial femtosecond crystallography , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[17]  Elspeth F. Garman,et al.  Developments in X-ray Crystallographic Structure Determination of Biological Macromolecules , 2014, Science.

[18]  C. Drummond,et al.  In meso crystallization: compatibility of different lipid bicontinuous cubic mesophases with the cubic crystallization screen in aqueous solution , 2014 .

[19]  Anton Barty,et al.  Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography , 2014, Nature Communications.

[20]  Gwyndaf Evans,et al.  Membrane protein structure determination — The next generation☆☆☆ , 2014, Biochimica et biophysica acta.

[21]  Garth J. Williams,et al.  Serial Femtosecond Crystallography of G Protein–Coupled Receptors , 2013, Science.

[22]  Sudipto Guha,et al.  Fabrication of X-ray compatible microfluidic platforms for protein crystallization. , 2012, Sensors and actuators. B, Chemical.

[23]  D. Yin,et al.  Sensitivity of lysozyme crystallization to minute variations in concentration. , 2012, Acta crystallographica. Section D, Biological crystallography.

[24]  C. Baeken,et al.  Controlled In Meso Phase Crystallization – A Method for the Structural Investigation of Membrane Proteins , 2012, PloS one.

[25]  C. Rienstra,et al.  A rapid and robust method for selective isotope labeling of proteins. , 2011, Methods.

[26]  Nathaniel Echols,et al.  Accessing protein conformational ensembles using room-temperature X-ray crystallography , 2011, Proceedings of the National Academy of Sciences.

[27]  P. Nollert,et al.  Monoolein Lipid Phases as Incorporation and Enrichment Materials for Membrane Protein Crystallization , 2011, PloS one.

[28]  S. Rasmussen,et al.  Crystal Structure of the β2Adrenergic Receptor-Gs protein complex , 2011, Nature.

[29]  R. Johnson,et al.  Behavior of capillary valves in centrifugal microfluidic devices prepared by three-dimensional printing , 2011 .

[30]  P. Nollert,et al.  A plug-based microfluidic system for dispensing lipidic cubic phase (LCP) material validated by crystallizing membrane proteins in lipidic mesophases , 2010, Microfluidics and nanofluidics.

[31]  Sarah L Perry,et al.  Microfluidic Generation of Lipidic Mesophases for Membrane Protein Crystallization. , 2009, Crystal growth & design.

[32]  Wilhelm Pfleging,et al.  Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis. , 2009, Lab on a chip.

[33]  Naomi E Chayen,et al.  Protein crystallization: from purified protein to diffraction-quality crystal , 2008, Nature Methods.

[34]  John P. Overington,et al.  How many drug targets are there? , 2006, Nature Reviews Drug Discovery.

[35]  R. Neutze,et al.  Lipidic sponge phase crystallization of membrane proteins. , 2006, Journal of molecular biology.

[36]  Axel T Brunger,et al.  Refractive index‐based determination of detergent concentration and its application to the study of membrane proteins , 2005, Protein science : a publication of the Protein Society.

[37]  Naomi E Chayen,et al.  Turning protein crystallisation from an art into a science. , 2004, Current opinion in structural biology.

[38]  M. Caffrey,et al.  Detergents destabilize the cubic phase of monoolein: implications for membrane protein crystallization. , 2003, Biophysical journal.

[39]  V. Cherezov,et al.  Crystallization screens: compatibility with the lipidic cubic phase for in meso crystallization of membrane proteins. , 2001, Biophysical journal.

[40]  G. Whitesides,et al.  Generation of Solution and Surface Gradients Using Microfluidic Systems , 2000 .

[41]  M. Caffrey,et al.  A lipid's eye view of membrane protein crystallization in mesophases. , 2000, Current opinion in structural biology.

[42]  S. Quake,et al.  Monolithic microfabricated valves and pumps by multilayer soft lithography. , 2000, Science.

[43]  J. Rosenbusch,et al.  Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Martin Caffrey,et al.  The Temperature-Composition Phase Diagram and Mesophase Structure Characterization of the Monoolein/Water System , 1996 .

[45]  W. Hendrickson Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. , 1991, Science.

[46]  G. Feher,et al.  LM complex of reaction centers from Rhodopseudomonas sphaeroides R-26: characterization and reconstitution with the H subunit , 1985 .

[47]  H. Michel,et al.  Crystallization of membrane proteins. , 1983, Current opinion in structural biology.

[48]  Tina Ritschel,et al.  Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery , 2018 .

[49]  Paul R Jaschke,et al.  Modification of the genome of Rhodobacter sphaeroides and construction of synthetic operons. , 2011, Methods in enzymology.

[50]  V. Cherezov,et al.  Crystallizing membrane proteins using lipidic mesophases , 2009, Nature Protocols.

[51]  Elspeth F Garman,et al.  Cryocooling and radiation damage in macromolecular crystallography. , 2006, Acta crystallographica. Section D, Biological crystallography.

[52]  A. Tehrani,et al.  Effects of Precise Deletions in Rhodobacter sphaeroides Reaction Center Genes on Steady-state Levels of Reaction Center Proteins: A Revised Model for Reaction Center Assembly , 2004, Photosynthesis Research.

[53]  U. Andréasson,et al.  Characterization of a semi-stable, charge-separated state in reaction centers from Rhodobacter sphaeroides , 2004, Photosynthesis Research.

[54]  Vincent B. Chen,et al.  Acta Crystallographica Section D Biological , 2001 .

[55]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[56]  M. Caffrey,et al.  Biological Crystallography Experimental Phasing for Structure Determination Using Membrane-protein Crystals Grown by the Lipid Cubic Phase Method , 2022 .