Characterizing Biological Macromolecules by SAXS Detlef Beckers, Jörg Bolze, Bram Schierbeek, PANalytical B.V., Almelo, The Netherlands

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1 Characterizing Biological Macromolecules by SAXS Detlef Beckers, Jörg Bolze, Bram Schierbeek, PANalytical B.V., Almelo, The Netherlands

2 This document was presented at PPXRD - Pharmaceutical Powder X-ray Diffraction Symposium Sponsored by The International Centre for Diffraction Data This presentation is provided by the International Centre for Diffraction Data in cooperation with the authors and presenters of the PPXRD symposia for the express purpose of educating the scientific community. All copyrights for the presentation are retained by the original authors. The ICDD has received permission from the authors to post this material on our website and make the material available for viewing. Usage is restricted for the purposes of education and scientific research. PPXRD Website ICDD Website -

3 Empyrean Nano edition SAXS / WAXS Ultra-SAXS Bio-SAXS GISAXS v v Transmission diffraction Atomic PDF analysis Powder diffraction

4 Empyrean Nano edition 160

5 Protein powder screening and purity Tetragonal P Crystal system: Tetragonal a (Å) (3) c (Å) (1) V (Å 3 ) (6) Monoclinic P (*) Crystal system: Monoclinic a (Å) 28.20(2) b (Å) 54.50(1) c (Å) 71.68(4) ( o ) (3) V (Å 3 ) (60) (*) Highest probability acc. ExtSym Pawley fit within HighScore Plus

6 X-ray source The scattering process The X-rays interact with the electrons in the sample. Thomson scattering Electrons oscillate in the electric field of the X-rays λ 1 λ 2 λ 1 = λ 2 They emit secondary, coherent waves that interfere with each other For X-rays, all electrons can be treated as free electrons (cf. light scattering: only outer electrons scatter). Image taken from Glatter & Kratky, "Small Angle X-ray Scattering", Academic Press, 1982 The interference pattern is measured at small angles 2θ, very close to the direct beam. Image taken from Glatter & Kratky, "Small Angle X-ray Scattering", Academic Press, 1982

7 SAXS from spheres of different size 10 0 Particle Radius [nm] P(q) = I(q) / I(q=0) I(q) / I(q=0) Particle form factor P(q) R = 10 nm R = 20 nm 10-6 R = 40 nm q [nm -1 ] Scattering vector q [nm -1 ]

8 Trimodal particle size distribution Background-corrected data Particle size distribution Data analysis was done without any assumptions about the shape or modality of the size distribution curve.

9 p(r) p(r) p(r) Pair distance distribution function p(r) for different particle shapes 1.00 Model calculations Model Calculation p(r) functions 1.00 Model Calculation p(r) functions p(r) p(r) p(r) 1.00 Model Calculation p(r) functions D max D max D max Intraparticle distance r [nm] r [nm] Intraparticle distance r [nm] r [nm] Intraparticle distance r [nm] r [nm] D max D max D max Overall spherical Elongated Hollow

10 Log Intensity I BioSAXS data analysis experimental SAXS data q 4 sin λ 2θ wavelength of X-rays scattering angle scattering vector q [nm -1 ] ln(i) I(0) Mw R g Guinier plot Radius of gyration q 2 [nm -2 ] Iq 2 Kratky plot compactness folding/unfolding q [nm -1 ] Small-Angle Scattering Biological Data Bank, Valentini et al., Nucl Acids Res (2014) 43, D357 FT FT -1 p(r) Pair distance distribution fct. overall shape & max. dimension D max intraparticle distance r [nm]

11 SAXS setup Evacuated beam path X-ray mirror WAXS X-ray tube Sample Area detector

12 Advantages of SAXS on proteins Protein characterization can be done in situ, with the proteins in solution and under near physiological conditions. Effects of e.g. ph, salt concentration, temperature, added ligand can be systematically studied. Easy sample preparation as compared to e.g. cryo-em or SC-XRD. Also applicable in case protein doesn t crystallize!

13 Information obtainable from Bio-SAXS experiments (I) Radius of gyration R g : overall size parameter Molecular weight: differentiate between oligomeric forms Overall shape: e.g. overall spherical vs. elongated 3D envelope shape D max : maximum dimension DAMMIN, DAMMIF

14 Information obtainable from Bio-SAXS experiments (II) Validation of atomic structures - Protein in crystal vs. in solution CRYSOL Degree of compactness / flexibility - Protein folding / unfolding folded unfolded Protein stability - Detect protein aggregation - Differentiate repulsive and attractive protein-protein interactions Protein dynamics - Time-resolved measurements

15 Intensity [counts] Protein size shape and structure Apoferritin (12 mg/ml) An iron storage protein sample buffer differential measurement time: 60 min Scattering vector q [nm -1 ]

16 Intensity [counts] ln I Apoferritin - Guinier plot 10 5 ln I R g = 5.9 nm Scattering vector q [nm -1 ] No aggregates Scattering vector q 2 [nm -2 ]

17 Intensity [counts] Apoferritin - Pair distance distribution function p(r) p(r) R g = 5.3 nm D max 13nm experimental data back-transform of p(r) Intraparticle distance r [nm] The characteristic shape of the p(r) function points to an object with a hollow structure Scattering vector q [nm -1 ]

18 Intensity [a.u.] Intensity [counts] Apoferritin - hollow sphere model (*) PM Harrison, The structure of apoferritin: molecular size, shape and symmetry from x-ray data, J. Molec. Biol. 6 (1963), From the X-ray data apoferritin molecules have a molecular weight of 480,000 and a form approximating on the average at a resolution of 26 Å to a spherical shell having an external radius of 61 ± 3 Å and internal to external radius ratio about hollow sphere Hollow sphere model (*) : R core = 37 Å d shell = 24 Å 10 3 solid sphere Scattering vector q [nm -1 ] q [nm -1 ]

19 3D protein shape reconstruction (ab initio) start DAMMIF / DAMMIN* end (*) D. Franke, D.I. Svergun et al., J. Appl. Cryst. 50, (2017)z front view cross-sectional structure Inverse cross-sectional structure. Beads indicate the location of the buffer

20 Intensity [counts] Protein structure in crystal form vs. in solution Calculation of SAXS data from published atomic coordinates CRYSOL 10 5 experimental data simulated from atomic model PDB 1IER atomic structure low-resolution structure hydration layer added 10 2 R g = 5.3 nm (experiment) R g = 5.4 nm (atomic model) Scattering vector q [nm -1 ] The crystal structure of the protein is similar to its structure in solution.

21 Intensity [a.u.] Glucose isomerase (11 mg/ml) Int. [a.u.] protein solution pure buffer differential Enzyme produced by microorganisms (bacteria) Catalyzes the conversion of glucose to fructose ScatterX 78 t = 60 min 100 mm Tris, 1 mm MgCl 2, ph = q [nm -1 ]

22 Glucose isomerase Guinier plot Pair distance distribution function no aggregation overall symmetrical protein shape D max Empyrean Nano (60 min) Empyrean Nano (10 min) Synchrotron R g : radius of gyration D max : maximum dimension of protein

23 Simulation of SAXS data from SC-XRD data and comparison with experimental data Glucose isomerase CRYSOL software 1 Conclusion: In solution the protein is forming a tetramer. The structures in the crystal and in solution are similar. 1 Svergun D.I., Barberato C. and Koch M.H.J. (1995) CRYSOL - a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates J. Appl. Cryst., 28,

24 Intensity [a.u.] Oligomeric mixtures Bovine Serum Albumin (BSA) BSA in Hepes 10mg/ml Bovine serum albumin (BSA), 10 mg/ml in 50 mm Hepes, 50 mm NaCl, ph = 7.5, T = 20 C SAXS data for monomer and dimer were simulated from the published atomic structures (using CRYSOL) Experimental data 100% monomer 100% dimer 50% monomer, 50% dimer Protein Data Bank PDB 4F5S measurement time: 60 min Scattering vector q [nm -1 ] q

25 Protein folding / unfolding - BSA in Hepes buffer SAXS measurements were done without and with added urea (known to be a denaturant). Iq 2 4x10 5 Kratky plot (Iq 2 vs. q) no urea 9M urea Int. prop. q -4 Int. prop. q -2 In pure buffer (no urea): folded, globular particle folded In buffer with 9M urea: unfolded, dissolved polymer chain unfolded 2x Scattering vector q [nm -1 ] Confirmed by R g determination

26 Liposomes Model biomembrane, can be further functionalized and structure / properties can systematically be studied Use as drug carrier Uni-lamellar vesicle Multi-lamellar vesicle

27 Lipid phase transition temperature Lipid bilayer structure Alkyl chain ordering temperature fully extended, closely packed, slightly tilted alkyl chains solid phase ("gel phase") phase transition temperature T m randomly oriented, fluid alkyl chains fluid phase

28 SAXS / WAXS on liposomes Test sample: Phospholipid DPPC (25 mg/ml in a PBS buffer), before extrusion. - Forming multilamellar vesicles. The SAXS signal contains information about the lipid bilayer structure and stacking. From the WAXS signal information about the alkyl chain packing can be deduced. Melting temperature of DPPC = 41 C

29 Summary Structural studies on proteins were performed to determine: Overall size and shape (simulation and ab-initio determination) Folding / unfolding (tertiary structure) Stability and complex formation (quaternary structure) Oligomeric state and oligomeric mixture Molecular weight

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