Gijs van der Schot
Uppsala University
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Publication
Featured researches published by Gijs van der Schot.
Nature Communications | 2015
Gijs van der Schot; Martin Svenda; Filipe R. N. C. Maia; Max F. Hantke; Daniel P. DePonte; M. Marvin Seibert; Andrew Aquila; Joachim Schulz; Richard A. Kirian; Mengning Liang; Francesco Stellato; Bianca Iwan; Jakob Andreasson; Nicusor Timneanu; Daniel Westphal; F. Nunes Almeida; Duško Odić; Dirk Hasse; Gunilla H. Carlsson; Daniel S. D. Larsson; Anton Barty; Andrew V. Martin; S. Schorb; Christoph Bostedt; John D. Bozek; Daniel Rolles; Artem Rudenko; Sascha W. Epp; Lutz Foucar; Benedikt Rudek
There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.
Nature Methods | 2009
Antonio Rosato; Anurag Bagaria; David Baker; Benjamin Bardiaux; Andrea Cavalli; Jurgen F. Doreleijers; Andrea Giachetti; Paul Guerry; Peter Güntert; Torsten Herrmann; Yuanpeng J. Huang; Hendrik R. A. Jonker; Binchen Mao; Thérèse E. Malliavin; Gaetano T. Montelione; Michael Nilges; Srivatsan Raman; Gijs van der Schot; Wim F. Vranken; Geerten W. Vuister; Alexandre M. J. J. Bonvin
We report the completion of the first comparison of automated NMR protein structure calculation methods and announce its continuation in the form of an ongoing, community-wide experiment: CASD-NMR (Critical Assessment of Automated Structure Determination of Proteins by NMR). CASD-NMR is open for any laboratory to participate and/or to submit targets. NMR spectroscopy is the only technique for the determination of the solution structure of biological macromolecules. This typically requires both the assignment of resonances and a labor-intensive analysis of multidimensional NOESY spectra, where peaks are matched to assigned resonances. Software tools for the full automation of the NOESY assignment and the structure calculation steps have the potential to boost the efficiency, reproducibility and reliability of NMR structures. Within the e-NMR project (www.e-nmr.eu), which is funded by the European Commission (Project number 213010), we are developing an approach to assess whether such automated methods can indeed produce structures that closely match those manually refined using the same experimental data (the “reference structures”). The concept closely resembles that of other community-wide experiments, such as CASP, the Critical Assessment of Techniques for Protein Structure Prediction1, and CAPRI, the Critical Assessment of Prediction of Interactions2. At variance with both CASP and CAPRI, CASD-NMR is entirely based on experimental data, presenting special issues in assembling, organizing, and distributing these data among participants. We provided seven research teams in the field with ten experimental data sets for various protein systems of known structure and two sets for protein structures not yet publicly available (“blind tests”), courtesy of the NorthEast Structural Genomics consortium (NESG). We then met in Florence, Italy on May 4–6, 2009 to analyze the structures generated (Fig. 1), by comparison to the reference structures and by using software tools for structure validation. This first experiment indicated that while most submissions had correct overall folds, on certain targets some programs failed to calculate accurate packing and length of secondary structure elements. The root mean square deviations (RMSDs) of the backbone coordinates from the manually-solved structures were typically in the 1–2 A range, but reached values as high as 9 A in some cases. Figure 1 Performance of various automated structure calculation methods
Scientific Data | 2016
Anna Munke; Jakob Andreasson; Andrew Aquila; Salah Awel; Kartik Ayyer; Anton Barty; Richard Bean; Peter Berntsen; Johan Bielecki; Sébastien Boutet; Maximilian Bucher; Henry N. Chapman; Benedikt J. Daurer; Hasan Demirci; Veit Elser; Petra Fromme; Janos Hajdu; Max F. Hantke; Akifumi Higashiura; Brenda G. Hogue; Ahmad Hosseinizadeh; Yoonhee Kim; Richard A. Kirian; Hemanth K. N. Reddy; Ti Yen Lan; Daniel S. D. Larsson; Haiguang Liu; N. Duane Loh; Filipe R. N. C. Maia; Adrian P. Mancuso
Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.
Scientific Data | 2017
Hemanth K. N. Reddy; Chun Hong Yoon; Andrew Aquila; Salah Awel; Kartik Ayyer; Anton Barty; Peter Berntsen; Johan Bielecki; Sergey Bobkov; Maximilian Bucher; Gabriella Carini; Sebastian Carron; Henry N. Chapman; Benedikt J. Daurer; Hasan Demirci; Tomas Ekeberg; Petra Fromme; Janos Hajdu; Max Felix Hanke; Philip Hart; Brenda G. Hogue; Ahmad Hosseinizadeh; Yoonhee Kim; Richard A. Kirian; Ruslan Kurta; Daniel S. D. Larsson; N. Duane Loh; Filipe R. N. C. Maia; Adrian P. Mancuso; Kerstin Mühlig
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.
IUCrJ | 2017
Benedikt J. Daurer; Kenta Okamoto; Johan Bielecki; Filipe R. N. C. Maia; Kerstin Mühlig; M. Marvin Seibert; Max F. Hantke; Carl Nettelblad; W. Henry Benner; Martin Svenda; Nicusor Timneanu; Tomas Ekeberg; N. Duane Loh; Alberto Pietrini; Alessandro Zani; Asawari D. Rath; Daniel Westphal; Richard A. Kirian; Salah Awel; Max O. Wiedorn; Gijs van der Schot; Gunilla H. Carlsson; Dirk Hasse; Jonas A. Sellberg; Anton Barty; Jakob Andreasson; Sebastian Boutet; Garth J. Williams; Jason E. Koglin; Inger Andersson
Facilitating the very short and intense pulses from an X-ray laser for the purpose of imaging small bioparticles carries the potential for structure determination at atomic resolution without the need for crystallization. In this study, experimental strategies for this idea are explored based on data collected at the Linac Coherent Light Source from 40 nm virus particles injected into a hard X-ray beam.
Journal of Biomolecular NMR | 2015
Gijs van der Schot; Alexandre M. J. J. Bonvin
Abstract We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi:10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi:10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.
Scientific Data | 2016
Max F. Hantke; Dirk Hasse; Tomas Ekeberg; Katja John; Martin Svenda; Duane Loh; Andrew V. Martin; Nicusor Timneanu; Daniel S. D. Larsson; Gijs van der Schot; Gunilla H. Carlsson; Margareta Ingelman; Jakob Andreasson; Daniel Westphal; Bianca Iwan; Charlotte Uetrecht; Johan Bielecki; Mengning Liang; Francesco Stellato; Daniel P. DePonte; Sadia Bari; Robert Hartmann; Nils Kimmel; Richard A. Kirian; M. Marvin Seibert; Kerstin Mühlig; Sebastian Schorb; Ken R. Ferguson; Christoph Bostedt; Sebastian Carron
Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
Scientific Data | 2016
Gijs van der Schot; Martin Svenda; Filipe R. N. C. Maia; Max F. Hantke; Daniel P. DePonte; M. Marvin Seibert; Andrew Aquila; Joachim Schulz; Richard A. Kirian; Mengning Liang; Francesco Stellato; Sadia Bari; Bianca Iwan; Jakob Andreasson; Nicusor Timneanu; Johan Bielecki; Daniel Westphal; Francisca Nunes de Almeida; Duško Odić; Dirk Hasse; Gunilla H. Carlsson; Daniel S. D. Larsson; Anton Barty; Andrew V. Martin; Sebastian Schorb; Christoph Bostedt; John D. Bozek; Sebastian Carron; Ken R. Ferguson; Daniel Rolles
Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.
Nature Photonics | 2018
Tais Gorkhover; Anatoli Ulmer; Ken R. Ferguson; Max Bucher; Filipe R. N. C. Maia; Johan Bielecki; Tomas Ekeberg; Max F. Hantke; Benedikt J. Daurer; Carl Nettelblad; Jakob Andreasson; Anton Barty; Petr Bruza; Sebastian Carron; Dirk Hasse; J. Krzywinski; Daniel S. D. Larsson; Andrew J. Morgan; Kerstin Mühlig; Maria Müller; Kenta Okamoto; Alberto Pietrini; Daniela Rupp; Mario Sauppe; Gijs van der Schot; M. Marvin Seibert; Jonas A. Sellberg; Martin Svenda; M. Swiggers; Nicusor Timneanu
Ultrafast X-ray imaging on individual fragile specimens such as aerosols1, metastable particles2, superfluid quantum systems3 and live biospecimens4 provides high-resolution information that is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely defined4,5. Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lateral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond timescale.Femtosecond X-ray Fourier holography imaging with record-high lateral resolution below 20 nm is demonstrated. Phase information is encoded into the interference of the diffraction patterns of a reference particle with a measurement sample.
bioRxiv | 2018
Johan Bielecki; Max F. Hantke; Benedikt J. Daurer; Hemanth K. N. Reddy; Dirk Hasse; Daniel S. D. Larsson; Laura H. Gunn; Martin Svenda; Anna Munke; Jonas A. Sellberg; Leonie Flueckiger; Alberto Pietrini; Carl Nettelblad; Ida V. Lundholm; Gunilla H. Carlsson; Kenta Okamoto; Nicusor Timneanu; Daniel Westphal; Olena Kulyk; Akifumi Higashiura; Gijs van der Schot; Duane Loh; Taylor E. Wysong; Christoph Bostedt; Tais Gorkhover; Bianca Iwan; M. Marvin Seibert; T. Osipov; Peter Walter; P. Hart
The possibility of imaging single proteins constitutes an exciting challenge for X-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available X-ray lasers and, as we demonstrate here, contamination of the aerosolised molecules by non-volatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet-size during aerosolisation. Here we show that with our electrospray injector we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next generation X-ray lasers, constitute an important stepping stone towards the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.