Structure determination

To reach our main goal - uncover the relationship between structure and function of biological molecules, we need to determine the structure of a protein (or protein-ligand complex). For this we mostly use protein crystallography but also small angle X-ray scattering and cryoelectron microscopy (single particle analysis). Various supplementary biophysical and biochemical methods complete the picture of molecular behaviour under given conditions.

Most frequently used techniques and availability of equipment

1. Protein expression in bacteria (in-house and collaborators), LEXSy system (in-house), HEK293 cells (in-house and collaborators), and Aspergillus-based expression (collaborator).

2. Equipment for protein purification, protein concentration measurements, SDS or native gel electrophoresis, various chromatographic methods.

3. Crystallization: manual setup of hanging- or sitting-drop vapour diffusion methods, robotic crystallization setup (CMS, in-house). Automated monitoring of crystallization - Formulatrix RI1000 (CMS, in-house).

4. Crystallization and crystal treatment and manipulation under defined atmosphere (glove box, CMS, in-house).

5. X-ray diffraction experiments: X-ray diffractometer D8 Venture with MetalJet X-ray source (in-house, CMS). Data collection at synchrotrons BessyII, PetraIII, Diamond Light Source, diffraction data processing, various methods of phasing and structure refinement, validation.

6. Structure analysis: graphics workstations, computer simulations, databases, and other in house licenses and computational power for demanding tasks.

7. Low resolution structural studies using SAXS (Small Angle X-ray Scattering): in-house (CMS) SAXSPoint 2.0 with MetalJet X-ray source and Eiger detector.

8. Protein characterization using biophysical techniques available in-house (CMS) and high resolution mass spectrometry analysis to determine protein identity, posttranslational modifications, complex formation and more ..

Fig. 1. Left panel: protein crystals; Middle panel: diffraction pattern created by diffraction of X-rays on protein crystal; Right panel: map of electron density determined from data contained in the diffraction intensities (spots) in the diffraction patterns.

Fig. 2. Animation of diffraction data collection from a protein crystal. As the crystal rotates, individual diffraction images are recorded. Notice the lunes of diffraction spots typical for protein diffraction and changes throughout the data set. Click on the picture to view the animation.

Protein crystallography

Protein crystallography is one of the key techniques of structural biology and is focused on determination of three-dimensional structure of proteins or nucleic acids by the means of single crystal x-ray diffraction. As proteins are both structural and functional units of living organisms the knowledge of their structure helps our understanding of their mechanisms and functionality and also enables targeted modifications with effects on their activity. New information acquired by this technique leads to explanation of the basic principles of functions of living organisms and at the same time to new approaches in fight against diseases such as cancer or AIDS and to many industrial biotechnology-based applications.

Samples of bio-macromolecules

The process of structure determination of a protein begins by production of a protein sample of sufficient amount (milligrams) and quality. The procedure is rather complicated and time-consuming. Some target molecules are produced in our laboratory and other by our collaborators (see above). Protein production requires optimization of the genetic code of the gene of interest, molecular cloning into the desired vector (plasmid, circular DNA), introduction of the vector into the host organism and controlled expression of the protein. This is followed by protein purification procedures which should result in a pure, homogeneous sample of fully functional protein.

Protein crystals are macromolecular crystals with a large solvent content

The next step is protein crystallisation. Compared to inorganic or organic compounds protein crystallisation is much more complicated and is performed in aqueous solutions; a resulting crystal exists in an equilibrium with the “mother” solution and approximately one half of its volume are channels filled by unordered solvent. The process depends on many parameters, e.g. protein and precipitant concentration, temperature, pH, purity and homogeneity of protein sample, crystallisation method and experiment set-up, etc. There is a large number of parameters influencing protein crystallisation and it is practically impossible to forecast the results or simulate the process. This often makes obtaining of a crystal suitable for diffraction experiments time-consuming and experimentally demanding. Search for suitable crystallisation conditions for one project can take several weeks to several years.

Crystal quality

Mere visual evaluation of quality of protein single crystals is insufficient and their suitability for structural studies is always tested properly only by an X-ray diffraction experiment. Frequently the quality of diffraction is not sufficient for structural analysis and varies with crystals. Therefore a large number of crystals of different morphology must be often screened with concurrent optimization of crystal cryo-protection.

Diffraction experiment

Size of unit cell of protein crystals varies between tens and hundreds of Ångström in one direction and together with a relatively higher proportion of unordered atoms results in much weaker intensity of X-ray diffraction patterns when compared for instance with inorganic single crystals. Therefore more intensive sources of X-ray radiation are preferred such as a rotating anode, liquid metal anode or synchrotron radiation sources. To limit the extent of radiation damage to protein single crystals the diffraction experiments are usually carried out at low temperatures (80-120 K). This is achieved by a controlled stream of vapours of liquid nitrogen in majority of the cases. The so called oscillation method is most commonly used for diffraction data collection.

Phase problem

To determine the three-dimensional structure of a given molecule once the diffraction intensities are measured it is necessary to determine or at least estimate initial values of phases of structure factors. In the case of macromolecular crystals two basic approaches are used: either similarity of the studied structure with a known one is exploited (molecular replacement) or a set of initial phases is determined experimentally, for example by the means of anomalous dispersion of heavier atoms present in the molecule (e.g. MAD – Multiple wavelength Anomalous Dispersion).

In some cases structure solution (determination of initial phases) can be a lengthy procedure requiring persistent experimental work (e.g. years of search for suitable crystal form and at the same time heavy atom derivatives of such crystals). Direct incorporation of heavy atoms in native or engineered protein form makes experimental phasing easier. Direct methods of structure solution (computational solution of the phase problem) have been successfully applied with some smaller proteins providing diffraction data to atomic diffraction limits (resolution). There are two reasons why such approach cannot be applied routinely: limited resolution of X-ray diffraction of most protein crystals and mathematical dimensionality of the computational task (thousands to tens of thousands of non-hydrogen atoms forming one asymmetric unit of a crystal).

Protein structure refinement

Refinement of protein structures is carried out computationally and manually with use of specialized software designed for this purpose. Depending on structure complexity and data quality this step takes weeks to months. A finalised crystal structure of a biological macromolecule is validated as for its agreement with experimental data and with expected stereochemical parameters. Then it is deposited (uploaded) together with its experimental data in the international databank of protein structures PDB (Protein Data Bank). Both, structural and experimental data, are publicly accessible.