Crystal Contact Database

Crystal Contact Database

SUPERVISORS: Trevor Sewell and Gwen Nneji

The development of a database of crystal intermolecular contacts and its verification as a useful tool in crystallization studies

Proposal

Construct a database of intermolecular contacts that occur in protein crystals, with a view to understanding crystallization and hence improving the chances of obtaining crystals from "uncrystallizable" proteins.

Why create a database for crystal contacts?

A better understanding of biological macromolecular interactions can lead to an improvement the crystallisation success rate by providing an insight into the functional groups involved in the interactions:

  1. This can be achieved by collating information from the protein database (pdb).
    1. Since crystal formation depends on the geometric arrangement of interactions, the degree of specificity of the interaction and strength of the interaction, data on crystal contacts from the pdb can be classified with respect to these criteria.
    2. This information can then be applied to the crystallisation of novel proteins, where initial analysis of the primary structure would lead to information about the number of potential crystal contacts in the protein and the likelihood of getting crystals.
  2. To enable the design or re-design of protein molecules in order to get improved diffraction, taking into account the amino acids involved in forming crystal contacts.
    1. A greater number of contacts, as well as increase the likelihood of crystal formation, may result in tighter packing and the reduced mobility of component residues, in this way improving the resolution in X-ray diffraction.
  3. Investigate the rates of dissolution of crystals to explore their potential in terms of drug delivery. This aspect would rely on the information defining the type of interaction involved and its likely behaviour in different solution environments.

How to go about construction of the database

Computer based project:

Construct a database derived from the pdb listing the intermolecular contacts for every protein. This will involve writing code to automatically extract this information. Thought will have to be given to presenting the data to a user of the database – this may entail writing software to interface the database as well.

Practical work involved:

  1. To explore the formation of crystal contacts in different solution environments by assessing trials of different conditions and using electron microscopy/dynamic light scattering to determine extent of aggregation before crystal formation is apparent.
    1. How does the solution environment influence the nature of the contacts?
    2. Do the number of contacts required relate to the size or shape of the molecule?
  2. To determine if there is a relationship between the nature of a crystal contact and the solvent environment, pH, temperature etc.
    1. For example which solvents enhance and reduce interactions?
    2. Bulky molecules may have problems with the geometry and the number of interaction what effect would temperature, gels, nucleants have?
  3. What can you do to improve crystallisation in molecules with low strength interactions?
    1. Explore the use of nucleants, channels or pores that may align/orient the molecules possibly providing a foundation for growth.
  4. Testing the models - obtain information about the crystal contacts in a novel protein and use this to design a crystallisation strategy. In effect design a practical method to use the information from such a crystal contact database to reproducibly crystallise novel proteins.