Protein Crystallization Services: Overview

SARomics Biostructures offers protein crystallization services platform, including protein-ligand complex crystallization and structure determination by X-ray crystallography. Crystallization and crystallography are the oldest methods for three-dimensional structure determination at atomic resolution. After the discovery of X-rays by Conrad Röntgen (Nobel Prize in Physics, 1901), the physical principles of X-ray diffraction were discovered by Max von Laue (Nobel Prize in Physics, 1914), while the foundation for X-ray crystallography was laid by the Braggs father and son (Nobel Prize in Physics, 1915). Apart from X-ray crystallography, currently both NMR spectroscopy and cryo-electron microscopy may provide atomic resolution protein structures. However, the vast majority of entries in the Protein Data Bank (PDB) still originate from X-ray crystallography.

1. Protein expression, purification and characterization

The company’s recombinant protein expression and purification platform (see our catalogue of high purity crystallisation grade proteins) is adapted for obtaining high purity and stable crystallization grade proteins. After cloning, expression and purification, and prior to crystallization, an accurate characterization of the state of the recombinant protein is performed. Probably one of the most important requirements is a monodisperse solution of the protein at a given concentration, which means the solution should not contain aggregated or denatured material. Monodispersity may be assessed using dynamic light scattering (DLS). The protein should also be stable in solution within a certain range of pH and ionic strength. By other words, a proper characterization of the protein, including its solubility, is critical for the success of a crystallization project.

Our services platform is built up around the most advanced biophysical protein characterization methods and includes:

  • DLS
  • CD spectroscopy
  • Differential scanning fluorimetry (DSF, a thermodenaturation shift assay). DSF was first developed at the Structural Genomics Consortium for protein characterization prior to crystallization.
  • Protein NMR spectroscopy is used as required.
NMR spectroscopy may answer questions, like does the construct result in a folded, well-behaved protein? The HSQC fingerprint spectrum of the protein readily shows whether the protein is well-folded, unfolded or ‘molten-globule’ like, and whether parts of the protein are flexible.

2. Crystallization

After protein characterization, conditions for obtaining well-diffracting single crystals need to be identified (if the protein has not been crystallized before). The number of experimental parameters affecting protein crystallization can be very large. Among these one can find:

  • The type of the buffer and the pH of the solution
  • The ionic strength of the buffer
  • The presence of various salts in the buffer
  • The presence of various ligands (co-factors, substrate analogues, inhibitors).
  • The type of precipitant used, which is probably the most central components in the setup.

Among the most popular precipitants used in protein crystallization are polyethylene glycols of various lengths, ammonium sulfate, and some alcohols. To find the right combination of parameters, one needs to screen a large number of different conditions. Several hundreds, and often thousands of different conditions are screened before the protein crystallization conditions can be identified. Commercial screens, like those from Hampton Research or Molecular Dimensions, are initially used. However, we have the facilities to design our own screens, if required (usually done during optimization of the conditions found using the initial screens).

In protein structure determination, for the most efficient identification of the crystallization conditions we use high throughput and high precision screening and imaging robotics. Of the available crystallization methods, the sitting-drop method is the most commonly used with robotics equipment. Using such a robot, 96 different conditions can be screened with as little as 15 microL of protein sample using a Mosquito liquid handling robot. The use of robotics helps in saving both time and precious material. When an initial condition is found, it normally needs to be optimized further to yield crystals more suitable for X-ray crystallography.

3. Structure determination

When suitable crystals are obtained it is time for the first test in an X-ray beam. If the X-ray diffraction from the crystals is of good quality (good resolution and nice X-ray diffraction pattern), data are collected at an X-ray source. Among others, we use MAX IV synchrotron radiation facility, which is located in Lund, or send the crystals to other synchrotrons for remote data collect.

If an experimental structure for the same protein is already available, the method of molecular replacement is used, an electron density map is calculated and interpreted, to identify the position of bound ligands, ligand occupancy, etc. Further refinement of the model will ensure that the fine details of the structure are well visible in the electron density map.
Additional information on protein structure and crystallization can be found on our educational site.

Below you can download a guide to shipping samples and an overview of sample handling at our company.

Crystallization techniques

96-well protein crystallization plate

96-well protein crystallization plate from Hampton Research for the use of sitting-drop vapor diffusion technique.

For the optimization of the crystallization and structure determination pipeline, SARomics Biostructures has developed standard operation procedures (SOP), which allow an efficient use of time and resources, also helping in keeping the operation costs as low as possible for our clients. These include:

• Developments of Freedom evo scripts and excel scripts for optimization of crystallization experiments
• Standard operating procedures (SOPs) for dynamic light scattering evaluation of protein solutions
• Development of SOPs for X-ray data collection
• Standard protocols for fast track structure determination