Recent progress in robot-based systems for crystallography and their contribution to drug discovery

Introduction: X-ray crystallography is the main tool for macromolecular structure solution at atomic resolution. It provides key information for the understanding of protein function, opening opportunities for the modulation of enzymatic mechanisms, and protein–ligand interactions. As a consequence, macromolecular crystallography plays an essential role in drug design, as well as in the a posteriori validation of drug mechanisms. Areas covered: The demand for method developments and also tools for macromolecular crystallography has significantly increased over the past 10 years. As a consequence, access to the facilities required for these investigations, such as synchrotron beamlines, became more difficult and significant efforts were dedicated to the automation of the experimental setup in laboratories. In this article, the authors describe how this was accomplished and how robot-based systems contribute to the enhancement of the macromolecular structure solution pipeline. Expert opinion: The evolution in robot technology, together with progress in X-ray beam performance and software developments, contributes to a new era in macromolecular X-ray crystallography. Highly integrated experimental environments open new possibilities for crystallography experiments. It is likely that it will also change the way this technique will be used in the future, opening the field to a larger community.

[1]  Philippe Carpentier,et al.  A new highly integrated sample environment for protein crystallography. , 2004, Acta crystallographica. Section D, Biological crystallography.

[2]  G. Labesse,et al.  In-plate protein crystallization, in situ ligand soaking and X-ray diffraction. , 2011, Acta crystallographica. Section D, Biological crystallography.

[3]  Didier Nurizzo,et al.  MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments , 2010, Journal of synchrotron radiation.

[4]  Olof Svensson,et al.  EDNA: a framework for plugin-based applications applied to X-ray experiment online data analysis. , 2009, Journal of synchrotron radiation.

[5]  Xia Hong,et al.  Ligand–receptor binding revealed by the TNF family member TALL-1 , 2003, Nature.

[6]  Carl A. Morris,et al.  A structural state of the myosin V motor without bound nucleotide , 2003, Nature.

[7]  Igor Jurisica,et al.  Intelligent decision support for protein crystal growth , 2001, IBM Syst. J..

[8]  H. Eickhoff,et al.  Development of a technology for automation and miniaturization of protein crystallization. , 2001, Journal of biotechnology.

[9]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[10]  M. Bowler,et al.  Direct cryocooling of naked crystals: are cryoprotection agents always necessary? , 2011, Acta crystallographica. Section D, Biological crystallography.

[11]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[12]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[13]  Peter Kuhn,et al.  The genesis of high-throughput structure-based drug discovery using protein crystallography. , 2002, Current opinion in chemical biology.

[14]  Timothy McPhillips,et al.  New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection , 2008, Acta crystallographica. Section D, Biological crystallography.

[15]  Wolfgang Kabsch,et al.  Integration, scaling, space-group assignment and post-refinement , 2010, Acta crystallographica. Section D, Biological crystallography.

[16]  Harren Jhoti,et al.  High-throughput crystallography for lead discovery in drug design , 2002, Nature Reviews Drug Discovery.

[17]  Didier Nurizzo,et al.  The ID23-1 structural biology beamline at the ESRF. , 2006, Journal of synchrotron radiation.

[18]  D. Stuart,et al.  The atomic structure of the bluetongue virus core , 1998, Nature.

[19]  Jean-Luc Ferrer,et al.  REACH: Robotic Equipment for Automated Crystal Harvesting using a six-axis robot arm and a micro-gripper. , 2013, Acta crystallographica. Section D, Biological crystallography.

[20]  Sebastien Petitdemange,et al.  Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection. , 2010, Acta crystallographica. Section D, Biological crystallography.

[21]  Konrad Büssow,et al.  Automated technologies and novel techniques to accelerate protein crystallography for structural genomics , 2008, Proteomics.

[22]  R. Dawson,et al.  Structure of a bacterial multidrug ABC transporter , 2006, Nature.

[23]  Joseph D Ng,et al.  Protein crystallization by capillary counterdiffusion for applied crystallographic structure determination. , 2003, Journal of structural biology.

[24]  S Michael Soltis,et al.  Diffraction-based automated crystal centering. , 2007, Journal of synchrotron radiation.

[25]  A Beteva,et al.  High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline. , 2006, Acta crystallographica. Section D, Biological crystallography.

[26]  Philippe Carpentier,et al.  Automated analysis of vapor diffusion crystallization drops with an X-ray beam. , 2004, Structure.

[27]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[28]  Garth J Simpson,et al.  Nonlinear optical imaging of integral membrane protein crystals in lipidic mesophases. , 2010, Analytical chemistry.

[29]  Takashi Kumasaka,et al.  Upgrade of automated sample exchanger SPACE , 2012 .

[30]  Petra Fromme,et al.  Crystal structure of photosystem II from Synechococcus elongatus at 3.8 Å resolution , 2001, Nature.

[31]  E. Fanchon,et al.  FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments. , 2002, Acta crystallographica. Section D, Biological crystallography.

[32]  Avinash Peddi,et al.  Electronic Reprint Biological Crystallography a Robotic System for Crystallizing Membrane and Soluble Proteins in Lipidic Mesophases Biological Crystallography a Robotic System for Crystallizing Membrane and Soluble Proteins in Lipidic Mesophases , 2022 .

[33]  L Jacquamet,et al.  Upgrade of the CATS sample changer on FIP-BM30A at the ESRF: towards a commercialized standard. , 2009, Journal of synchrotron radiation.

[34]  Aled Edwards,et al.  High-throughput protein crystallization. , 2003, Journal of structural biology.

[35]  Robert Viola,et al.  First experiences with semi-autonomous robotic harvesting of protein crystals , 2011, Journal of Structural and Functional Genomics.

[36]  G. Sheldrick A short history of SHELX. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[37]  Martin Caffrey,et al.  Picolitre‐scale crystallization of membrane proteins , 2006 .

[38]  R. Huber,et al.  Structure of 20S proteasome from yeast at 2.4Å resolution , 1997, Nature.

[39]  Clemens Vonrhein,et al.  Data processing and analysis with the autoPROC toolbox , 2011, Acta crystallographica. Section D, Biological crystallography.

[40]  Nathan Nelson,et al.  Crystal structure of plant photosystem I , 2003, Nature.

[41]  Igor Jurisica,et al.  Macromolecular crystallization in a high throughput laboratory—the search phase , 2001 .

[42]  Earl W. Cornell,et al.  An approach to rapid protein crystallization using nanodroplets , 2002 .

[43]  Gwyndaf Evans,et al.  In situ macromolecular crystallography using microbeams , 2012, Acta crystallographica. Section D, Biological crystallography.

[44]  F Cipriani,et al.  Automation of sample mounting for macromolecular crystallography. , 2006, Acta crystallographica. Section D, Biological crystallography.

[45]  F Cipriani,et al.  Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13. , 1999, Acta crystallographica. Section D, Biological crystallography.

[46]  M. Selmer,et al.  Structure of the 70S Ribosome Complexed with mRNA and tRNA , 2006, Science.

[47]  Aina E Cohen,et al.  An automated system to mount cryo-cooled protein crystals on a synchrotron beam line, using compact sample cassettes and a small-scale robot. , 2002, Journal of applied crystallography.

[48]  Olof Svensson,et al.  ISPyB: an information management system for synchrotron macromolecular crystallography , 2011, Bioinform..

[49]  Graeme Winter,et al.  xia2: an expert system for macromolecular crystallography data reduction , 2010 .

[50]  Jose Cosme,et al.  Crystal structure of human cytochrome P450 2C9 with bound warfarin , 2003, Nature.

[51]  G. Bourenkov,et al.  Automated mounting, centering and screening of crystals for high-throughput protein crystallography. , 2002, Acta crystallographica. Section D, Biological crystallography.

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

[53]  U Heinemann,et al.  The Berlin "protein structure factory" initiative: a technology-oriented approach to structural genomics. , 2001, Ernst Schering Research Foundation workshop.

[54]  James Barber,et al.  Architecture of the Photosynthetic Oxygen-Evolving Center , 2004, Science.

[55]  P. Evans,et al.  Scaling and assessment of data quality. , 2006, Acta crystallographica. Section D, Biological crystallography.

[56]  Victor S Lamzin,et al.  Automated detection and centring of cryocooled protein crystals. , 2006, Acta crystallographica. Section D, Biological crystallography.

[57]  John E Walker,et al.  ATP Synthesis by Rotary Catalysis (Nobel lecture). , 1998, Angewandte Chemie.

[58]  Florent Cipriani,et al.  C3D: a program for the automated centring of cryocooled crystals. , 2006, Acta crystallographica. Section D, Biological crystallography.

[59]  K. Palczewski,et al.  Imaging of protein crystals with two-photon microscopy. , 2012, Biochemistry.

[60]  Thomas Earnest,et al.  Automation of X-ray crystallography , 2000, Nature Structural Biology.

[61]  Raymond C. Stevens,et al.  High-throughput x-ray crystallography for structure-based drug design , 2001 .

[62]  Philippe Carpentier,et al.  CATS: a Cryogenic Automated Transfer System installed on the beamline FIP at ESRF , 2004 .

[63]  Gyorgy Snell,et al.  The TB structural genomics consortium crystallization facility: towards automation from protein to electron density. , 2002, Acta crystallographica. Section D, Biological crystallography.

[64]  Jose Cosme,et al.  Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone , 2004, Science.

[65]  D. Stuart,et al.  Membrane structure and interactions with protein and DNA in bacteriophage PRD1 , 2004, Nature.

[66]  Anastassis Perrakis,et al.  Automated protein model building combined with iterative structure refinement , 1999, Nature Structural Biology.

[67]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[68]  Florent Cipriani,et al.  CrystalDirect: a new method for automated crystal harvesting based on laser-induced photoablation of thin films. , 2012, Acta crystallographica. Section D, Biological crystallography.

[69]  Tom Alber,et al.  Automated protein crystal structure determination using ELVES. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[70]  Gordon A Leonard,et al.  ID29: a high-intensity highly automated ESRF beamline for macromolecular crystallography experiments exploiting anomalous scattering. , 2012, Journal of synchrotron radiation.