Non-Standard Sample Environments Martin A. Schroer SAXS group - - PowerPoint PPT Presentation

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Non-Standard Sample Environments Martin A. Schroer SAXS group - - PowerPoint PPT Presentation

Non-Standard Sample Environments Martin A. Schroer SAXS group Non-standard sample environments options at P12 Disclaimer Might not work for all samples Might not make sense for all samples You will likely need more sample


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SLIDE 1

Non-Standard Sample Environments

Martin A. Schroer SAXS group

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SLIDE 2

Non-standard sample environments options at P12

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Disclaimer

  • Might not work for all samples
  • Might not make sense for all samples
  • You will likely need more sample solution

however

  • can give fundamental new insights
  • In situ
  • Time-resolved
  • demand a synchrotron source
  • Photon flux: weak signals, temporal resolution
  • Small beam sizes: spatial resolution
  • Energy tunability: Penetration

Contact the beamline scientists! See “Satellite: Designing Non- Standard Experiments” In yellow boxes: Advice to the users!

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SLIDE 3

Types of sample environments

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Robotic sample changer SEC-SAXS/MALS

  • Capillary holder
  • Temperature cell

Stopped Flow Microfluidics (e.g. for THz) Laser excitation

28/02/2020

  • in vacuum capillary
  • continuous flow
  • Online purification and

detection system

  • Cryo chamber (P12)

User setups:

  • High pressure cells
  • Rheological cells
  • Heating stages

User setups: Need proper planning!

  • Infrastructure
  • X-ray parameters
  • ....

 Contact in advance (when writing the proposal)

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SLIDE 4

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  • Heating
  • Stopped Flow
  • Laser light
  • Scanning SAXS
  • Collaborative project: THz-radiation

Non-standard sample environments at P12

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SLIDE 5

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  • Removing in-vacuum capillary / sample changer
  • Two sealing windows

 Air gap

  • Place sample cell

 Higher X-ray absorption by air  Higher background signal (air + windows + sample cell)

In vacuum:

  • Quarz capillary

In air

  • Polystyrene cell
  • Air
  • Kapton windows

Try to reduce the air gap as much as possible! Use proper window material!

In air operation

+ BSA + buffer + buffer + BSA + buffer + buffer

Do you really need in-air or better sample changer? Maybe two proposals?

  • > Contact & discuss in advance!
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SLIDE 6

Heating stages (at P12)

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Sample changer temperature range

  • 5 – 60°C (80°C): with new sample unit (>2020)
  • Can Keep samples stored at different T (4 - ~40°C)
  • slow
  • for radiation sensitive samples
  • Proper buffer measurements
  • Lower background

A good choice for:

  • Water-based samples
  • Moderate temperatures
  • Short notice temperature tests
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SLIDE 7

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Temperature controlled capillary holder

  • Peltier element
  • Quartz capillaries -> 1.5 mm diameter
  • different T range
  • fast T changes
  • highly viscous samples
  • tricky samples (toxic, corrosive, dirty,..)
  • Apolar solvent
  • Samples expierence same history
  • Background is different
  • Exposure of similar spots (radiation

damage)

  • > observation holes have been widened

Heating stages (at P12)

  • > New options for heating gel samples

A good choice for:

  • Non-water samples
  • Large range temperature (phase diagram)
  • Strongly scattering samples
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SLIDE 8

Temperature SAXS studies

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  • F. A. Facchini et al. J. Med. Chem. 61, 2895 (2018).

Examples:

  • Biological relevant lipids:

Têmp.-induced melting of lamellar structures

  • Ferro-nematics (liq crystal + nanoparticles)

Phase transition

  • V. Gdovinova, M.A. Schroer et al. Soft Matter 13, 7890 (2017).
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SLIDE 9

Time-resolved: Stopped Flow - Mixer

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Principle:

  • Mix to liquids rapidly
  • Observe the changing signal
  • Example: pH induced dissociation of

apoferritin Dead time: ca. 7 ms load volume: (400 µl)...2-10 ml volume per shot: 100µl

  • Know that there is a reaction -> pre-testing
  • Have enough sample -> repeat & check
  • Explore the power of SAXS -> beyond simple kinetic
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  • Reaction of MsbA Nucleotide binding domain with

ATP

  • 35 ms frames collected
  • Expected: Monomer – dimer transition

Why do I need so much sample? -> An example

Josts et al, Structure 28, 348 (2020).

  • H. Tidow
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SLIDE 11

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  • Start reaction and directly probe

 Continuous change of Rg

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SLIDE 12

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  • Start reaction and directly probe

 Continuous change of Rg

  • Start reaction, wait (delay time), then probe

 Continuous change of Rg But NOT overlapping  Radiation Damage

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  • Start reaction and directly probe

 Continuous change of Rg

  • Start reaction, wait (delay time), then probe

 Continuous change of Rg But NOT overlapping  Radiation Damage

  • Actually only the first frames can be used

 Pump – probe scheme

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SLIDE 14

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  • Start reaction and directly probe

 Continuous change of Rg

  • Start reaction, wait (delay time), then probe

 Continuous change of Rg But NOT overlapping  Radiation Damage

  • Actually only the first frames can be used

 Pump – probe scheme

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SLIDE 15

Pump – probe approach

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  • Mix/pump
  • Wait for time
  • Probe (use only first frame)

 No unneeded exposure of sample Example:

  • Monomer -> Dimer -> Monomer formation
  • Fully corrupted by RD otherwise

+ Allows to determine the kinetics/reaction

  • High sample consumption:
  • Crucial for biological samples
  • Good planning needed!
  • However, already standard ‘non-standard’ experiment.
  • Alternative option:

Stroboscopic mode user P12 chopper!

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SLIDE 16

P12 – laser system

  • Tuneable Nd:YAG – laser (Ekspla, Lithuania)
  • Wave lengths:
  • 335 – 500 nm & 1065 – 2500 nm

(fibre port to P12 hutch experiments)

  • Repetiton rate: 10 Hz
  • Pulse length: 6 ns

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To fibre Direct

Energy per pulse [mJ]

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SLIDE 17

1st laser triggered reactions

19/01/2018 17

0.5 1 1.5 2

q[nm-1]

104 105 106

I(q) [arb. u.]

0 s 30 s 60 s 120 s

  • Reaction of nucleotide binding domain

with caged ATP

  • Excite @355 nm releases ATP
  • Monomer-dimer-monomer reaction
  • Reaction can be initalized after different

number of pulses (here: 300, i.e. 30 s)  Triggering and synchronization works  Laser power via fiber too low for single pulse excitation  Checking options for optimization

50 100 150

delay time [s]

0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

volume fraction

Monomer Dimer

  • Under commissioning
  • Looking for collaborative projects
  • H. Tidow
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SLIDE 18

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Scanning SAXS

  • Scan samples with a small X-ray beam

 Real space maps of SAXS patterns

  • Allows to reveal the spatial distribution on nanometer-

sized structures (shape, size) and orientation

  • Applications:
  • Heterogenuous samples
  • Hierarchical materials: e.g. Bones, wood,

tissue,...

  • Critical parameters (defining the resolution)
  • beam size, steps size, beam divergence
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SLIDE 19

Scanning SAXS @ P12

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Moderate µm focus -> low real space resolution Low divergence

  • > high reciprocal space resolution

 Eiger 4M at large detector distance: e.g. collagen Old mirrors + cutting the beam

  • Beam size: ~ 75 x 75 µm2 (hor x vert)

New mirrors (without cutting)

  • beam size: 200 x 25 µm2 (hor x vert)

Example: Mineral particle distribution within a swordfish sword

From 2021: New SEU - piezo stage

  • Moderate field-of-view scanning SAXS
  • Screening of more specimen -> more (clinical) impact
  • Resolution of large structures
  • F. Schmidt et al. Adv. Sci. 6, 1900287 (2019).
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SLIDE 20

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Collaborative experiment: Studying the effect of THz- radiation on proteins

THz radiation

  • Electromagnetic radiation
  • Sensitive to large molecular vibrations (collective) / low in energy -> THz spectroscopy
  • Strong absorption in water
  • Non-ionizing but thermal & athermal effects
  • > possible risks are discussed in literature
  • L. Wei et al. Frontiers in Laboratory Medicine (2019).

Different steps of an experiments

  • Concept
  • Design
  • Conduction
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THz-excitation of proteins

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Fröhlich‘s prediction

  • THz-radiation can excite collective motions within biological macromolecules by coupling to their dipole

moment (Fröhlich condensation) Such collective vibrations (normal modes) may lead to long-range conformational changes. Such changes can be probed by SAXS.  THz excitation & SAXS probe

  • A. Panjkovich, D.I. Svergun. PCCP 18, 5707 (2016).
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SLIDE 22

THz-SAXS - Experiment

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Such a noval type of experiment needs

  • THz sources (cw + pulsed): complementary spectra
  • > Excite the sample
  • Dedicated microfluidic cell
  • > small channel width
  • Sample delievery system
  • Small, asymmetric X-ray beam:

(80 x 120 µm2) & smaller now!

  • Precise positioning (sub-micron) (hexapod)
  • Synchronization (data collection)

Setup I Setup II

  • M. Roessle (TH Lübeck)
  • G. Katona (U Gothenburg)
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SLIDE 23

THz-SAXS - microfluidic cell

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Combined THz-SAXS measurements demand dedicated sample environment

  • Microfluidic chips:
  • Flowing of sample → reduce radiation damage
  • Transparent for THz → enough sample excitation
  • Narrow channel (500 µm) as THz absorption in water is strong → enough

sample excitation

  • Low X-ray background → record SAXS signal
  • S. Schewa, M.A. Schroer, et al., Rev. Sci. Instrum. 91, 084101 (2020).

 3D printed Polystyrene cell with mylar X-ray windows W = 0.2 mm <-> optimized for THz T = 2 mm <-> optimized for X-rays

  • S. Schewa, M. Roessle et al.

(TH Lübeck)

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SLIDE 24

10/10/2018 24

  • THz-absorption in PS:

Low as PS apolar

  • THz-spectra of PS:

No absorption lines

  • SAXS from proteins:

Access to proteins of different molecular weight

THz-SAXS cell: Properties

  • S. Schewa, M.A. Schroer, et al., Rev. Sci. Instrum. 91, 084101 (2020).
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SLIDE 25

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X-ray THz Noval cell design:

  • THz-excitation / SAXS probing
  • Combined THz-spectroscopy / SAXS
  • Not limited to proteins -> e.g. soft matter, nanoparticles

Setup installed at P12

  • THz beam passes set of mirrors
  • THz can be detected by receiver
  • THz beam & X-ray beam are perpendicular

 The same stop of the sample is illuminated

  • Long-time project with several steps of development
  • Several beamtimes

 Sometimes long breath & creativity

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SLIDE 26

Summary

  • P12 offers several options of performing exciting bioSAXS

experiments

  • Long time experience to deal with challenging problems
  • Looking forward for new interesting experiments
  • Happy to discuss with you:
  • Now
  • During breaks & posters session
  • Satellite meeting of User Meeting (18.11.2020)
  • Always

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SLIDE 27

Acknowledgements

  • All members of the SAXS group, EMBL-HH
  • EMBL-Instrumentation group
  • I. Josts, H. Tidow (U Hamburg)
  • S. Schewa, M. Rößle et al. (TH Lübeck); G. Katona et al. (U Gothenburg)
  • User groups
  • Funding:
  • Röntgen-Angström cluster project „TT-SAS“ (BMBF project number 05K16YEA)
  • DFG
  • Horizion 2020: iNEXT

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