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Schönherr R, Boger J, Lahey-Rudolph JM, Harms M, Kaiser J, Nachtschatt S, Wobbe M, Duden R, König P, Bourenkov G, Schneider TR, Redecke L. A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Nat Commun 2024; 15:1709. [PMID: 38402242 PMCID: PMC10894269 DOI: 10.1038/s41467-024-45985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/02/2024] [Indexed: 02/26/2024] Open
Abstract
With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Juliane Boger
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - J Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Hamburg, Germany
- X-ray technology lab, TH Lübeck - University of Applied Sciences Lübeck, Lübeck, Germany
| | - Mareike Harms
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | | | | | - Marla Wobbe
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Rainer Duden
- Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Peter König
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
- Airway Research Center North (ARCN), University of Lübeck, German Center for Lung Research (DZL), Lübeck, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany.
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
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Mehrabi P, Schulz EC. Sample Preparation for Time-Resolved Serial Crystallography: Practical Considerations. Methods Mol Biol 2023; 2652:361-379. [PMID: 37093487 DOI: 10.1007/978-1-0716-3147-8_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Time-resolved serial crystallography is an emerging method to elucidate the structure-function relationship of biomolecular systems at up to atomic resolution. However, to make this demanding method a success, a number of experimental requirements have to be met. In this chapter, we summarize general guidelines and protocols towards performing time-resolved crystallography experiments, with a particular emphasis on sample requirements and preparation but also a brief excursion into reaction initiation.
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Affiliation(s)
- Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
| | - Eike C Schulz
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
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3
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Saggiomo V. A 3D Printer in the Lab: Not Only a Toy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202610. [PMID: 35831252 PMCID: PMC9507339 DOI: 10.1002/advs.202202610] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Although 3D printers are becoming more common in households, they are still under-represented in many laboratories worldwide and regarded as toys rather than as laboratory equipment. This short review wants to change this conservative point of view. This mini-review focuses on fused deposition modeling printers and what happens after acquiring your first 3D printer. In short, these printers melt plastic filament and deposit it layer by layer to create the final object. They are getting cheaper and easier to use, and nowadays it is not difficult to find good 3D printers for less than €500. At such a price, a 3D printer is one, if not the most, versatile piece of equipment you can have in a laboratory.
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Affiliation(s)
- Vittorio Saggiomo
- Department of BioNanoTechnologyWageningen UniversityBornse Weilanden 9Wageningen6708WGThe Netherlands
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4
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Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging. Structure 2022; 30:763-776.e4. [PMID: 35338852 PMCID: PMC9081212 DOI: 10.1016/j.str.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022]
Abstract
Cataract, a clouding of the eye lens from protein precipitation, affects millions of people every year. The lens proteins, the crystallins, show extensive post-translational modifications (PTMs) in cataractous lenses. The most common PTMs, deamidation and oxidation, promote crystallin aggregation; however, it is not clear precisely how these PTMs contribute to crystallin insolubilization. Here, we report six crystal structures of the lens protein γS-crystallin (γS): one of the wild-type and five of deamidated γS variants, from three to nine deamidation sites, after sample aging. The deamidation mutations do not change the overall fold of γS; however, increasing deamidation leads to accelerated disulfide-bond formation. Addition of deamidated sites progressively destabilized protein structure, and the deamidated variants display an increased propensity for aggregation. These results suggest that the deamidated variants are useful as models for accelerated aging; the structural changes observed provide support for redox activity of γS-crystallin in the lens.
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The reproducible normality of the crystallographic B-factor. Anal Biochem 2022; 645:114594. [DOI: 10.1016/j.ab.2022.114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 11/20/2022]
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Liu J, Zhang CY, Liu Y, Wu XL, Zhang TD, Zhao FZ, Chen LL, Jin XQ, He JL, Yin DC. The dual function of impurity in protein crystallization. CrystEngComm 2022. [DOI: 10.1039/d1ce01535d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein crystallization could be promoted with a low concentration of impurities and inhibited with a high concentration of impurities, and this inhibition can be weakened by an audible sound.
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Affiliation(s)
- Jie Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Yue Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Xiang-Long Wu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Tuo-Di Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Feng-Zhu Zhao
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Liang-Liang Chen
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Xiao-Qian Jin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Jin-Liang He
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
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Schulz EC, Yorke BA, Pearson AR, Mehrabi P. Best practices for time-resolved serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2022; 78:14-29. [PMID: 34981758 PMCID: PMC8725164 DOI: 10.1107/s2059798321011621] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
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Affiliation(s)
- Eike C. Schulz
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Briony A. Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford BD7 1DP, United Kingdom
| | - Arwen R. Pearson
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
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