Book of Abstracts

Book of abstracts 31st European Crystallographic Meeting 31st European Crystallographic Meeting • Oviedo, Spain 22-27 August Plenary Lectures PL-O2 A tale in two parts: how a search for antivirulence compounds led to the PL-O1 discovery of a shapeshifting copper Crystallography in the 21st century: the age resistance protein of electron? Jennifer Martin1 Lukáš Palatinus1 1. Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia 1. Department of Structure Analysis, Institute of Physics of the CAS, Prague, Czech Republic email: jlm@griffith.edu.au email: palat@fzu.cz Protein disulfide bonds are covalent links formed be- tween sulfurs of cysteine sidechains. There is now over- Crystallography as a scientific discipline has a history reaching whelming evidence to show that these inter-residue bonds at least four hundred years in the past. However, only in the are critical for Gram negative bacterial virulence [1]. 19thcentury it became a systematically studied field. In these This presentation describes how the structures of the bacte- early times, crystals were studied mostly by visible light. This rial machinery components that introduce disulfide bonds “age of light” ended abruptly with the discovery of the diffrac- into folding proteins [2] have been used in the search for tion of X-rays by crystals, starting the “age of x-rays” and the inhibitors [3,4,5]; and outlines the serendipitous discovery dramatic development of structural crystallography. of a shape-shifting foldase [6] that is potentially useful for Electron microscopy and electron diffraction have long been plug-and-play bionanotechnology. considered useful, but mainly supplementary crystallograph- References: ic techniques. However, we have been witnessing a number of important developments in the field of electron crystallog- [1] Heras et al (2009) “DSB proteins and bacterial pathogenicity”, raphy over the last decade that have changed the situation. Nature Rev Micro, 7:215 - 225. First, it is the wide-spread availability of aberration-corrected [2] Shouldice et al (2011) “Structure and function of DsbA, a key transmission electron microscopes now allows a routine ob- oxidative folding catalyst”, Antioxid Redox Signal 14:1729-60 servation of – mostly inorganic – crystals at atomic resolu- [3] Duprez et al (2015) “Peptide inhibitors of the Escherichia coli tion, including atomic-level chemical analysis. This gives an DsbA oxidative machinery essential for bacterial virulence”, J Med unprecedented insight into the structural arrangements at the Chem 58:577-87 smallest possible scale. Second, the development of the Cryo- [4] Adams*, Sharma* et al (2015) “Application of fragment-based EM technique for the reconstruction of molecular structures screening to the design of inhibitors of Escherichia coli DsbA”, by high-resolution single-particle imaging brought a qualita- Angew Chem Int Ed Engl 54:2179-84 tive leap forward in our ability to understand the structures of [5] Halili*, Bachu*, Lindahl* et al (2015) “Small molecule inhibitors biologically relevant molecular systems. of disulfide bond formation by the bacterial DsbA-DsbB dual enzyme system”, ACS Chemical Biology 10:957-64 Somewhat in the shadow of these two ground-breaking de- [6] Furlong et al (2017) “A shape-shifting redox foldase contributes velopments stands another important progress in electron to Proteus mirabilis copper resistance”, Nature Commun, 8:16065. crystallography, namely the ability to solve and refine crystal structures from electron diffraction data. While some ten Keywords: bionanotechnology, anti virulence compounds years ago an ab-initio solution of a crystal structure purely from electron diffraction data was limited only to special cases and was considered a very difficult challenge, today it has become an almost routine procedure. Hundreds of crystal structures have been solved from electron diffraction data, and some of them refined to accuracy comparable to the accuracy of x-ray structure analysis. The examples cover all types of structures, from oxides and metal alloys through minerals, zeolites and other framework materials, to metal-organic frameworks, organometallic compounds or pharmaceutically relevant organic materials, and even macromolecular crystals. This technique opens up a whole new realm of application of single-crystal structure analysis, because electron diffraction techniques are able to analyze crystals down to the size of a few nanometers. There is no doubt that in the coming years x-ray diffraction techniques will remain dominant in the crystallographic research. However, seeing the rapid growth of importance of electron-based techniques, one may indeed ask a question: After the 19thcentury being the age of light and the 20thcentury being the age ofx-rays, is the 21st century going to be the age of electrons? Keywords: electron crystallography, electron microscopy, nanocrystals Acta Cryst. (2018). A74, e1 31st European Crystallographic Meeting • Oviedo, Spain 22-27 August Keynote Lectures KN-2 The Joy of Seeing - in honour of Dorothy Hodgkin KN-1 Eleanor Dodson1 The vocabulary of protein-DNA 1. University of York, York, United Kingdom interactions: Symmetry, degeneracy, email: eleanor.dodson@york.ac.uk modifications To quote Dorothy Hodgkin: The great advantage of X-ray Matthias Bochtler1 analysis as a method of chemical structure analysis is its power to show some totally unexpected and surprising 1. International Institute of Molecular and Cell Biology & Institute structure and to do so with absolute certainty. of Biochemistry and Biophysics, Warsaw, Poland I will show examples of how Fourier analysis using X-ray email: mbochtler@iimcb.gov.pl observations from a crystal, combined with imperfect The basics of protein nucleic acid interactions have been phases, can allow us to boot-strap our way to a satisfactory worked out a long time ago, but new themes are still emerg- structure. Combining these basic principals with the great ing. The vocabulary for the non-degenerate recognition of computing power, and excellent data acquisition facilities DNA bases is well understood, but this is not the case for now available has extended our power to “see” to new lev- semi-degenerate recognition, which may occur “acciden- els. tally”, or be imposed by symmetry. In the first part of my References: talk, I will focus on principles of semi-degenerate readout of DNA sequence, by minor groove readout, base unstack- [1] Hodgkin, D. C. Pickworth, J. Robertson, J. H. Trueblood, K. N. ing, and nucleotide flipping (1). In the second part of my Prosen, R. J. & White, J. G. (1955). Nature, 176 (4477), 325–328. talk, I will concentrate on modification specific DNA bind- [2] Jenkins, H. T. (2018). Acta crystallographica. Section D, ing. How nucleic acid modifications such as methylation Structural biology, 205–214. inhibit DNA binding by steric exclusion is readily under- [3] Rodríguez, D. D. Grosse, C. Himmel, S. González, C. de standable. Whether a predicted clash is biologically relevant Ilarduya, I. M. Becker, S. Sheldrick, G. M. & Usón, I. (2009) Nature depends on whether protein and nucleic acid are sufficiently Methods, 6(9), 651–653. flexible to avoid the steric conflict (2). How nucleic acid conformations become a prerequisite for binding is harder Keywords: Fourier analysis, computing techniques to understand, especially when the dependence on the modification is stringent and when a modifier group (such as a methyl group) offers little opportunity for strong attractive interactions. In my talk, I will focus on several published and unpublished structures from our own work which il- lustrate the modification selective binding of nucleic acids containing 6-methyladenine, 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and glucosyl-5-hydroxymethylcytosine (g5hmC) (3). References: (1) Bochtler, M., Szczepanowski, R.H., Tamulaitis, G., Grazulis, S., Czapinska, H., Manakova, E. and Siksnys, V. (2006) Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J, 25, 2219-2229. (2) Mierzejewska, K., Bochtler, M., Czapinska, H. (2016) On the role of steric clashes in methylation control of restriction endonuclease activity. Nucleic Acids Res, 44, 485-495. (3) Mierzejewska, K., Siwek, W., Czapinska, H., Kaus-Drobek, M., Radlinska, M., Skowronek, K., Bujnicki, J.M., Dadlez, M. and Bochtler, M. (2014) Structural basis of the methylation specificity of R.DpnI. Nucleic Acids Res, 42, 8745-8754. Keywords: Symmetry, degeneracy, modifications Acta Cryst. (2018). A74, e2 31st European Crystallographic Meeting • Oviedo, Spain 22-27 August KN-3 KN-4 Understanding and using likelihood in How CRISPR-Cas RNA-guided structural biology endonucleases cut specific DNA regions for Randy Read1, Robert Oeffner1, Airlie McCoy1 Genome Editing? 1. Department of Haematology, Cambridge Institute for Medical Guillermo Montoya1 Research, University of Cambridge, Cambridge, United Kingdom 1. Novo Nordisk Foundation Center for Protein Research Faculty email: rjr27@cam.ac.uk of Health and Medical Sciences, University of Copenhagen, The principle of maximum likelihood provides an ideal Copenhagen, Denmark way to understand how experiments and prior knowledge email: guillermo.montoya@cpr.ku.dk can be used to inform our understanding of the systems we Since ancestral time mankind has tried to modify plants and study. Likelihood-based methods now pervade all aspects animals to obtain an offspring that could adapt to our needs. of macromolecular

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