Growing Biological crystals for Neutrons

Transcription

1 European Molecular Biology Laboratory Grenoble Outstation Growing Biological crystals for Neutrons Monika Budayova-Spano UJF EMBL CNRS / ILL

2 Why neutron protein crystallography? Providing evidence on the protonation state of the inhibitor and residues within the active site and on the solvent structure surrounding a protein which cannot be seen by X-ray analysis. Neutron diffraction can be used to directly determine the positions of H-isotopes at medium resolutions (~2.5 Ǻ).

3 The importance of H-atoms Hydrogen atoms mediate structure and function. Identifying the positions of hydrogen atoms in a structure helps us understand how the protein functions. H/D exchange; identification of solvent accessible areas Endothiapepsin Vitamin B12 Enzyme mechanisms; location of H-atoms aids our understanding of catalytic activity Solvent structure; can play an important role in some physiological and enzymatic functions Trypsin 1:1 co-crystal of BPY and thiodiglycolic acid Ligand binding interactions; identification of key hydrogen bonds

4 Neutron protein crystallography Advantages; H/D more readily visualized with neutrons than with X-rays Able to distinguish between hydrogen isotopes Non-destructive probe no radiation damage, thus can collect data at room temperature Limitations: Low flux of neutron beams Large sample size required Long times scales Only a few (<20) high-resolution neutron structures have been solved!

5 X-rays Positions of all non-hydrogen atoms of a protein structure e.g. C, N, O, S. High resolution X-ray data (better than 1.2 Å) required even then only those H-atoms which are extremely well localized can be seen. X-rays Scattered from electrons Scattering proportional to Z H C N O Al Si P Ti D

6 Neutrons Neutrons Scattered by nuclei Scattering not proportional to Z H C N O Al Si P Ti D x10-14 cm Less variation between the elements Large difference in the cross-section among isotopes Neutron diffraction can be used to directly determine the positions of H-isotopes at medium resolutions (~2.5 Ǻ)

7 Why deuteration of a protein sample? Deuteration largely avoids large incoherent scattering of hydrogen which contributes to the background of the diffraction images and enhances the visibility of hydrogen and water positions in the resulting neutron scattering density maps.

8 Hydrogenated and fully deuterated proteins Approx. 50% of a protein structure are hydrogen atoms. H σ incoh = barns Incoherent scattering adds to background on detector, therefore reduces the S/N ratio of the data. H-atoms appear as negative peaks in highresolution neutron Fourier maps, however, at medium resolution, cancellation can occur (Courtesy of T. Forsyth, ILL) A-DNA/H 2 O Fully deuterated proteins; A-DNA/D 2 O D σ incoh = 2.05 barns H to D; incoherent scattering reduced and S/N ratio increased. Exchanging all H for D aids the refinement and interpretation of the structure With D-atoms, no cancellation of density but rather enhancement of positive nuclear density. Smaller crystal volumes needed (~0.1mm 3 ) Can address larger unit-cell problems Aids the success of cryo-cooling the crystal Decreases the spatial overlap problem of reflections

9 The ILL-EMBL Deuteration Laboratory Molecular biology, cloning, expression, purification D, 15 N, 13 C labelling of macromolecules for neutron scattering and NMR Fermentation Crystallogenesis Dedicated P2 facilities Photobioreactors Biopolymer synthesis Proteomics

10 The ILL-EMBL Deuteration Facility Deuterium labelling for neutron scattering experiments Neutron Protein Crystallography Localization of catalytic protons in enzymes Fibre Diffraction Localization of water molecules in DNA LADI Neutron reflectivity Structure of model membranes, and the interaction with peptides, proteins and DNA D19 Solution Scattering (SANS) Observation of conformational changes of single sub-units within a complex Inelastic Neutron Scattering Studies of macromolecular dynamics IN D11 D22 D17 web-site:

11 Why to improve the size and quality of crystals? Large crystals are required to compensate for the weak flux of available neutron beams. X-rays X-rays diffracted μm 3 Neutrons Neutrons diffracted mm 3 X-ray source (ESRF) much more (10 9 x) intense than neutron source (ILL) Diffraction Intensity in Bragg reflections I I 0.F 2 Structure factor.v ( V ) 2 cell sample Incident neutron intensity Illuminated volume of crystal Measured signal is directly proportional to the crystal volume Unit cell volume

12 A methodology and an instrument for the temperature-controlled optimization of crystal growth Budayova-Spano et al., Acta Cryst. D63, 2007, allowing for control of the kinetics of the crystallization process by taking advantage of thermodynamics and generic features of the phase diagram.

13 A methodology for the temperature-controlled optimization of crystal growth Rational physico-chemical approach based on knowledge of the phase diagram Budayova-Spano et al., Acta Cryst. D63, 2007, Solubility measurement f(t) Identifying the favourable zone for ordered crystal growth (metastable zone) thanks to a change in temperature. Promotion of crystal growth by keeping the crystallization solution metastable during the process of crystal growth thanks to a change in temperature.

14 Solubility measurements f(t) Urate oxidase (Uox), involved in catalysis of the oxidation of uric acid to allantoin Budayova-Spano et al., Acta Cryst. D63, 2007, Solution protein concentration by crystallization Time by dissolution Protein solubility is obtained by following the concentration variation of super and under-saturated solutions seeded with small protein crystallites. This is done by removing aliquots and measuring the absorbance at 280nm. The protein concentration in equilibrium crystal/solution is measured and corresponds to the solubility at a given temperature. 5% PEG 8000, 100mM NaCl, Tris-HCl 50mM, ph (pd) 8.5 Protein concentration (mg/ml) Protein concentration (mg/ml) Cs H 2 O (T) Cs D 2 O (T) Cs H 2 O (T) > Cs D 2 O (T) Temperature (ºC) Cs H 2 O (T) = Cs D 2 O (T+7.2 C) Temperature (ºC)

15 Promotion of crystal growth by keeping the crystallization solution metastable: Urate oxidase (Uox), involved in catalysis of the oxidation of uric acid to allantoin (Budayova-Spano et al., Acta Cryst. D63, 2007, ) Improved Large Crystal Growth at 20 C Protein concentration (mg/ml) Improved Large Crystal Growth Direct Solubility Nucleation zone S U P E R S A T U R A T I O N START Metastable zone SOLUBILITY CURVE = SATURATION END U N D E R S A T U R A T I O N μl: 5% PEG 8000, 100mM NaCl, Tris-HCl 50mM, init. prot. conc. 8mg/ml, pd 8.5 Temperature ( C) Crystal growth of the seeds is maintained inside the metastable zone as long as possible thanks to the temperature variations as soon as the equilibrium crystal/solution is reached. Total time 2 days, 1 image per 2 hours

16 Growing large crystals for neutrons Case of recombinant Uox complexed with a purine-type inhibitor (8-AZA) Illustrating the high quality of the neutron Laue diffraction data collected from crystals grown via knowledge of the phase diagram. V final =1.8mm 3 2.1Å resolution on LADI-ILL 0.5mm Neutron scattering density map (2Fo-Fc at 1.5 sigma) superposed with the current model of Uox-8-AZA Clear density for D atoms and orientations of D 2 O molecules Budayova-Spano et al., 2006 Acta Cryst. F62,

17 Growing large crystals for neutrons Case of perdeuterated yeast inorganic pyrophosphatase, model system for studying phosphoryl transfer reactions catalysed by multiple metal ions 200μl: 15% MPD, 1mM MnCl 2, 1mM P i, 30mM MES pd 6.0, prot. conc. 20mg/ml 1. Temperature variation to low temperature values (20 C => 5 C) allows to stabilise and grow the crystalline form of our interest Start 1 month later Budayova-Spano et al., Acta Cryst. D63, 2007, X-ray diffraction to 1.9Å 2. Crystal quality grown by this method appears to be better than that of the seed (centre of the crystal) 2 months later: 0.15mm 3 Diffraction to 3Å resolution on LADI-ILL 2 months later: 0.7mm 3

18 Growing larger better diffracting crystals for X-rays Case of perdeuterated human carbonic anhydrase II involved in catalysis of the hydration of carbon dioxide Transforming the clusters of crystals to the single crystals suitable for X-ray analysis Crystal cluster grown by hanging-drop vapour-diffusion technique at 20 ºC prot. conc. 24mg/ml Seeding at 35ºC Crystallization Batch: 100μl Prot. Quantity: 33μl (800 μg) Diffraction to 2.5Å resolution 50μm (a) 50μm (b) at id29 ESRF Growth at 30ºC t=6 days Growth at 35ºC t=3days Diffraction to 1. 5Å resolution at id29 ESRF 50μm 50μm (c) 1.15M Na citrate, 100mM Tris-DCl pd 7.5 (d) Budayova-Spano et al., 2006 Acta Cryst. F62, 4-9.

19 An instrument for the temperature-controlled optimization of crystal growth Budayova-Spano et al., Acta Cryst. D63, 2007, Investigating the phase diagram, controlling the nucleation and crystal growth of biomacromolecules, manipulating the solubility of seeded H/D labelled crystals as a f(t) Regulating the temperature of the crystallization solution using control parameters determined in situ during the growth process (Novel multi-well crystal growth apparatus) Allowing for in situ observation by optical microscopy and sequential image acquisition, processing and storage Facilitating the convenient extraction of the protein crystals after growth, without causing any mechanical damage to them => using MICROMANIPULATOR

20 Acknowledgements and partners Stephen Cusack (EMBL Grenoble) Peter Timmins (ILL Grenoble) François Dauvergne (EMBL Grenoble) Mechanics Michel Audiffren & Thirou Bactivelane (CINaM CNRS Marseille) Electronics and Software Marie-Thérèse Dauvergne (EMBL Grenoble) Production of perdeuterated material Françoise Bonneté (CINaM CNRS Marseille) Uox neutron Bertrand Castro & Mohamed El Hajji diffraction project (Sanofi-Aventis Montpellier) Adrian Goldman & Esko Oksanen Ppase neutron (University Helsinki, Finland) diffraction project Matthew Blakeley (ILL Grenoble) Data collection on LADI (ILL)