Lipidico Injection Protocol for Serial Crystallography Measurements at the Australian Synchrotron

Podsumowanie

The goal of this protocol is to demonstrate how to prepare serial crystallography samples for data collection on a high viscous injector, Lipidico, recently commissioned at the Australian synchrotron.

Streszczenie

A facility for performing serial crystallography measurements has been developed at the Australian synchrotron. This facility incorporates a purpose built high viscous injector, Lipidico, as part of the macromolecular crystallography (MX2) beamline to measure large numbers of small crystals at room temperature. The goal of this technique is to enable crystals to be grown/transferred to glass syringes to be used directly in the injector for serial crystallography data collection. The advantages of this injector include the ability to respond rapidly to changes in the flow rate without interruption of the stream. Several limitations for this high viscosity injector (HVI) exist which include a restriction on the allowed sample viscosities to >10 Pa.s. Stream stability can also potentially be an issue depending on the specific properties of the sample. A detailed protocol for how to set up samples and operate the injector for serial crystallography measurements at the Australian synchrotron is presented here. The method demonstrates preparation of the sample, including the transfer of lysozyme crystals into a high viscous media (silicone grease), and the operation of the injector for data collection at MX2.

Wprowadzenie

Serial crystallography (SX) is a technique that was developed initially in the context of X-ray Free Electron Lasers (XFELs)^1,2,3,4. Though fixed target approaches can be used for SX^5,6,7, typically, injector systems are employed to deliver crystals in a continuous stream to the X-ray beam. Because it combines data from a large number of crystals, SX avoids the need for any crystal alignment during the experiment, and enables data to be collected at room temperature^8,9. With the aid of a suitable injector, the crystals are streamed one-by-one into the X-ray interaction area and the resulting diffraction data is collected on an area detector^9,10. To date, SX has been successful in solving a number of protein structures^1,11,12,13 including crystals too small to measure using conventional crystallography. It has also provided new insights into time-resolved molecular dynamics by exploiting the femtosecond pulse duration of the XFEL. By initiating pump-probe reactions with optical laser sources, in-depth studies have been carried out on photosystem II^14,15, photoactive yellow protein^16,17, cytochrome C oxidase¹⁸, as well as bacteriorhodopsin^19,20,21. These studies have probed the electron transfer dynamics that occur following light activation demonstrating the significant potential of serial crystallography for understanding time-resolved biological processes.

Development of serial crystallography is also becoming increasingly prevalent at synchrotron sources^{9,12,20,22,23,24}. Synchrotron based SX allows for large numbers of individual crystals to be measured efficiently at room temperature using an appropriate injector system. This approach is suitable for smaller crystals hence, in addition to requiring a fast frame-rate detector to collect the data, a micro-focused beam is also required. Compared to conventional crystallography, SX does not involve the mounting and alignment of individual crystals in the X-ray beam. Because data from a large number of individual crystals is merged, the radiation dose received by each crystal can be substantially reduced compared to conventional crystallography. Synchrotron SX can also be applied to the study of time-resolved reactions, even down to the millisecond regime, provided a detector with a sufficiently high frame rate is available (e.g., 100 Hz or more). Several serial crystallography experiments have been carried out at the synchrotron using injectors that were initially developed at XFEL sources^20,22,23. The two most common types of injector are the Gas Dynamic Virtual Nozzle (GDVN)²⁵ and High Viscous Injector (HVI)^{9,24,26,27,28}. The GDVN is ideal for injecting low viscosity, liquid samples, but requires high flow rates to achieve stable streams, which in turn leads to high sample consumption rates. By contrast, HVI’s are suitable for high viscosity samples which allows generation of a stable stream at much lower flow rates, leading to much lower sample consumption. The HVI injector, therefore, favors delivery of samples where a viscous carrier is preferable (e.g., lipid-based for membrane proteins) and/or large quantities of sample are not available. SX injectors are generally challenging to use and require extensive training to operate. They also involve lengthy sample transfer protocols, as the sample needs to be loaded into a specialized reservoir, this generally has a high risk associated with it of sample being lost either in the ‘dead volume’ or via leakages in the connections. Therefore, it is desirable to optimize the injector design to mitigate any losses prior to the sample reaching the X-ray beam.

Recently, the first SX results were published using Lipidico²³ with a lysozyme target, using an Eiger 16M detector. This injector design limits sample wastage by minimizing the number of steps involved in going from initial crystallization to the transfer of crystals into the injector followed by the delivery of sample to the X-ray beam. This manuscript describes and demonstrates the sample transfer procedure starting from sample preparation, moving on to the injection process, and finally data collection, using the same crystallization vessel. The operation of the injector is also described.

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Protokół

1. Preparation of crystals in a high viscous media using glass syringes

1. Centrifuge the crystal solution gently (~1,000 x g, ~10 min at 22 °C) to form a soft crystal pellet and remove the excess buffer. This will result in a high concentration of crystals in the pellet which can be used for data collection.
   NOTE: To prevent dilution of the viscous media increase the crystal concentration at this step. Optimize the ratio of viscous media to crystal volume for each sample to obtain a high concentration of crystals whilst maintaining a high viscosity for the media. Centrifuge the crystal solution to form a pellet and remove excess buffer to increase the crystal concentration in the solution, as described in Darmanin et. al.²⁹.
2. Set up two 100 µL syringes with a coupler.
3. Fasten the coupler to the end of the first syringe and add 28 µL of crystal solution to the top of the syringe. Slowly, insert the plunger into the top of the syringe and gently push the solution down to the end of the coupler tip, removing any air bubbles that form. Do this by following one of the two methods discussed below.
   NOTE: The volume of crystals to be added to the high viscous media can be varied if it does not significantly change the viscosity of the overall sample.
   1. First method: Use rapid pressure changes to burst the air bubbles.
      1. Carefully place one gloved finger on the top of the blunted coupler needle point and (very gently) apply pressure to create a seal. Do not apply too much pressure as this may result in a needle stick injury.
      2. Now pull the plunger back to draw the solution away from the needle point, this will generate a buildup of pressure in the syringe.
      3. Quickly release the pressure at the top of the syringe by removing the gloved finger from the blunted needle tip. Be careful, if the sample is too close to the tip when the finger is removed it may spray out resulting in loss of sample. The rapid change in pressure within the syringe will burst the air bubbles. Repeat until all bubbles have been removed.
   2. Second method: Using the ‘human centrifuge’ to remove air bubbles.
      1. Place the syringe in one hand with the needle facing upwards and the plunger wedged between two fingers, so that it cannot move.
      2. Quickly rotate the arm holding the syringe in one direction 2–3 times, the resulting centrifugal force on the sample will force any air bubbles out of the syringe. Be careful, if done too slowly sample can be lost.
      3. Inspect the syringe for air bubbles, if bubbles remain, repeat steps 1.3.2.1 – 1.3.2.2 until all the air bubbles are removed.
4. Using a fine spatula, add ~42 µL of high vacuum silicone grease directly to the top of the second syringe. Push the plunger all the way down to the end, removing all the air bubbles and ensuring that there is no air gap in the end of the syringe.
   NOTE: The precise composition of the silicone grease is not critical as it is acting as an inert carrier. A viscosity value of >10 Pa.s or ratio of approximately 60:40 silicone grease to crystal solution is optimal for injection, however, it is possible this may vary depending on the exact characteristics of the sample. Adjust the volume of crystal solution added to the silicone grease to optimize the crystal concentration in the mixture, as outlined in the discussion. High-viscous media other than silicone grease can be used as long as they are compatible with the sample^30,31,32,33.
5. Ensure there are no air bubbles in either of the two syringes and attach the syringes together using the coupler. Hold the syringes vertically by griping just the end of the syringe as warming up the syringe due to the heat generated from fingers can affect the sample.
6. Mix the sample together by gently depressing the plunger on the crystal solution side so that it mixes into the silicone grease and then push the plunger on the silicone grease side, so that it pushes the sample back towards the crystal solution side. Gently, repeat this process 50 to 100 times so that the sample is mixed thoroughly and looks homogeneous.
   NOTE: If the crystals are grown directly in highly viscous media (e.g., lipidic cubic phase, LCP), steps 1.1–1.6 are not required. Protocols for growing crystals within the syringes can be found in Liu et.al.^34,35. Follow this protocol up to sample consolidation, step 10, where all the sample is now contained in one syringe and the crystallization buffer is removed. The addition of 7.9MAG is not required for this protocol. Instead, remove all excess liquid from the syringe by gently pushing the plunger down in the sample until no more liquid remains in the syringe.
7. Visualize the crystals under an optical microscope either through the syringe or, for best results, extract a small amount (~1 µL) on to a glass slide and place a cover slip on the top.
8. Check crystal concentration.
   1. Determine the crystal concentration in the silicone grease by counting the number of crystals in a specific area using the optical microscope images. For best results, a high density of crystals uniformly dispensed throughout the media is ideal (>10⁶ crystals/mL) in order to obtain a high crystal-hit rate.
   2. Adjust the crystal concentration in the syringe by changing the ratio of crystals to viscous media in steps 1.3 and 1.4.
      1. To decrease the crystal concentration, dilute the crystals in the syringe by increasing the amount of silicone grease/HV media at step 1.4 or by diluting the crystal pellet in solution with the crystallization buffer prior to setting up the syringes in step 1.1.
      2. To increase the crystal concentration, decrease the amount of silicone grease in step 1.4 but be mindful not to reduce the viscosity below 10 Pa.s.
         NOTE: The crystal concentration reported here was optimized for this specific sample and crystal size. However, the ideal crystal concentration will depend on the crystal size, beam size, the needle Internal Diameter (I.D.), and the incident X-ray flux. This can be determined from the hit rate with an optimal hit rate of ~30% considered as 'good'. In practice, the crystal concentration must be optimized for different samples during beam time to obtain the desired hit rate. Start with a high concentration of crystals, 10⁹ crystals/mL. The procedure for adjusting the crystal concentration is given in Liu et.al.³⁵.
   3. The protocol can be paused here until the injector is ready for data collection.
      1. If the crystals are grown in LCP, then seal them and let them remain in syringes for up to a few days at room temperature.
      2. If the crystals have been transferred to a different high viscous media (e.g., silicone grease), then a stability test of the crystals over time should be carried out prior to the measurement. This will determine how long the crystals are stable in the inert media (ideally > 8 h) and the time limit for data collection. Here, lysozyme crystals were stable for days in silicone grease and did not show signs of dissolving when inspected using an optical microscope.
9. Move all the sample into one syringe prior to disconnecting the coupler. Disconnect the coupler from the syringe and attach the injection needle. Screw the needle firmly into the base of the syringe and ensure that it is fastened tightly to prevent any leakages. A 108 µm I.D. needle (needle length 13 mm, point style 3) was used for this experiment. Depending on the crystal size and the beam size attach either a 51 µm or 108 µm I.D. needle.
   NOTE: Pre-testing of the sample stream prior to beam time is required to be able to select the correct injector needle size. Depending on the sample characteristics (i.e., viscosity, charging, buffer composition) and the needle I.D., the samples will flow differently. Therefore, it is recommended to test a variety of needle sizes to produce the most stable stream with the smallest possible I.D. needle to maximize the signal-to-noise ratio during data collection.
10. If the injector is already mounted and aligned on the beam line move to section 3 and mount the sample syringe directly onto the injector.
    NOTE: The protocol can be paused here.

2. Injector mounting and control

1. Mount the injector onto the beamline. Remove the cryogenic nozzle on the MX2 beamline and replaced it with the injector. Loosen the clamping screw that holds the cryogenic nozzle and attach it to the bracket located next to the motorized stage.
2. Lift the injector up from its trolley by holding the black handle and place it on the motorized stage.
   1. To fasten the injector to the motorized stage; hand tighten the black clamping screw knob.
3. Mount an empty syringe onto the injector
   1. In the injector computer control interface (i.e., EPOS position control software), select Homing Mode under Tools in the software menu. Then select Negative Limit Switch, and Start Homing, let the software run until the screw is retracted sufficiently for the syringe to fit under the screw. If left to run unsupervised the limit switch stops the screw automatically.
   2. Mount an empty (‘dummy’) syringe onto the injector by inserting the needle through the slit in the syringe holder. Line up the syringe against the bracket.
   3. Fasten the syringe with two O-rings.
      1. Wrap the first O-ring across the mid-section of the syringe attaching it to the hooks on either side of the syringe.
      2. Loop the second O-ring around the hooks on the upper section of the syringe and then put one part of the O-ring on the top of the glass syringe as shown in the demonstration and Figure 1B.
4. Align the injector to X-ray beam
   1. Move the motorized stage with the injector towards the X-ray interaction point via the beamline control software. This can be visualized using the inline camera. The size and position of the beam is denoted by a red cross on the screen and the motorized stage can be moved to align the needle with the X-ray interaction region.
   2. Adjust the x and y position of the stage to align the needle with the red cross.
   3. Adjust the z position until the needle tip comes into focus.
   4. Verify alignment of the needle tip and X-ray beam visually by checking that the syringe tip meets the crosshairs which are visible in the optical microscope image generated by the beamline camera.
   5. Once the needle tip is aligned move the tip above the cross hairs ~100 µm. This eliminates x-ray scatter from the needle tip.
      NOTE: Mounting and aligning the injector on the MX2 beamline at the synchrotron must be carried out by the beamline scientists and can be completed in less than 30 min.

3. Mounting the sample syringe

1. Replace the empty syringe with the sample syringe by following step 2.3.
2. Place the injector cap on the sample syringe plunger head.
3. Move the drive screw to the top of the cap.
4. In the injector control software select Velocity Mode.
5. Input 3000 rpm (~115 nL/s) as the Setting Value and press Apply Setting Value.
6. When the drive screw touches the cap on the syringe plunger head, stop the motor.
   1. Set the rpm value to zero in the injector control software by changing the Setting Value to ‘0’ as the screw approaches the cap.
   2. Once contact is made, activate the preset value by pressing Apply Setting Value to stop the screw instantly.
7. Gently wiggle the cap to make sure that it is firmly held in place.
   NOTE: Whenever a new set value is entered in the Setting Value box in the control software it is only activated after pressing Apply Setting Value.

4. Running the injector

1. After the cap drive screw has made firm contact with the top of the plunger change the rpm Setting Value to 100. This is equivalent to ~ 4 nL/s.
2. Visually inspect the needle tip when the sample first comes out or look at the beamline camera image of the needle to observe when the sample starts to extrude from the needle tip.
3. Perform a search of the hutch, close the hutch door, and turn on the X-ray beam. From this point the injector must be operated remotely from outside of the hutch.
4. Tune the rpm until a stable stream is generated.
   1. Decrease the rpm Setting Value to 90.
   2. Repeat step 4.4.1, decreasing the rpm Setting Value in increments of 10, to slow down the stream but still maintain a stable stream. For silicone grease a value of 30 rpm was used.
      NOTE: The typical rpm range varies between 30 – 100 rpm (1 – 4 nL/s) depending on the sample characteristics and X-ray exposure time. In general, the rpm should be tuned to produce the slowest flow rate (to minimize sample consumption) whilst maintaining a stable stream.
5. Managing a sample stream that does not flow well.
   1. Keep increasing the rpm Setting Value in increments of 10 until the stream gets straighter. If the stream does not stabilize, even after increasing the rpm Setting Value to the maximum value of 100 rpm try to improve the stability by implementing one of the two methods described below.
      1. First method: Insert a polystyrene sample catcher underneath the sample stream to help guide the sample. This method works well for highly charged sample streams.
      2. Second method: Insert a venturi suction funnel to the sample catcher. To supply air to the funnel, connect it to the air outlet tube located in the hutch. This method can aid in directing and stabilizing the sample flow independent of the charge of the stream.
6. Once a constant and steady stream is achieved, start data collection, and optimize the detector distance as per a normal X-ray crystallography experiment.
   NOTE: The rpm is converted to flow rate using the supplied conversion table in the Supplementary Information, ‘Lipidico Device Calculator’. Enter the rpm value, needle diameters, and syringe volumes to calculate the flow rate using this calculator.

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Wyniki

Lipidico is an HVI built as an alternative delivery system for use on MX2 (Figure 1). It is ideally suited for SX where crystals are either grown in lipidic cubic phase or transferred to a high viscous inert media.

To demonstrate the injector application silicone grease mixed with lysozyme crystals was used to collect SX data at the MX2 beamline at the Australian synchrotron. To mount the injector on the MX2 beamline the cryogenic nozzle is removed and replaced by...

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Dyskusje

An alternative HVI has been developed, ideal for carrying out SX experiments at synchrotron sources. It has two key advantages over existing HVIs. First, it is easy to install on the beamline allowing rapid switching between conventional crystallography and SX, just ~30 minutes is required for installation and alignment on MX2. Second, the sample syringes used to grow crystals can be directly used as the reservoirs for injection, limiting wastage during sample transfer. The protocol for changing samples has been des...

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Materiały

Name	Company	Catalog Number	Comments
Hen eggwhite lysozyme	Sigma-Aldrich	L6876	Used to grow crystals for testing the injector and the crystals are transferred into silicon grease. https://www.sigmaaldrich.com/
High vacuum silicon grease	Dow Corning	Z273554-1EA	Used for testing of injector. https://www.sigmaaldrich.com/
Injector needle (108 µm ID)	Hamilton	part No: 7803-05	www.hamiltoncompany.com
Glass gas-tight syringes, 100 µl	Hamilton	part no: 7656-01	Syringes used for sample injection. www.hamiltoncompany.com
LCP syringe coupler	Formulatrix	209526	Syringe coupler to mix the samples
Lipidico injector	La Trobe Univerity/ANSTO		This is a specific piece of equipment that can be accessed through La Trobe University / ANSTO Australian Synchrotron Facility