Proteinase K and Digalacturonic Acid
Amazing AdditivesResearchers at CHTSB have been exploring a new way to grow crystals. They noted that in many cases, crystals are only obtained after particular "additive" molecules are included in the crystallization mixture. These may be small molecules like nucleotides or cofactors that bind in the active site and stabilize the protein. More provocatively, they may be molecules with several functional groups that form links between molecules, stabilizing the proteins in the crystal lattice. Unfortunately, these crystal-inducing additives are often discovered by serendipity, added to the crystallization liquor based on an intuition, or even left over from the process of purification.
Finding a Needle in a HaystackCHTSB researchers are now trying to be systematic about discovery of crystallization additives. They add a mixture of several diverse molecules to the crystallization liquor, improving the chances that one of them is the right shape and size. The trial additives are chosen for their properties: they are typically bristling with hydrogen-bonding, charged, and hydrophobic groups that interact with protein surfaces. In several large tests of proteins, these mixtures of additives have performed quite well, doubling the success rate of obtaining crystals.
Lattice InteractionsOne example of the success of an additive mixture is shown here. Proteinase K was crystallized from a mixture that included three very different small molecules: an antiepileptic drug with two hydrophobic phenyl groups, an acidic sugar, and a nucleotide. The mixture also included the buffer HEPES, which has a several functional groups. The sugar was the winner. It helped coax the protein into a new crystal lattice, forming a bridge between the proteins. The lattice is shown here (PDB entry 3dyb), with the protein in blue and the sugar (digalacturonic acid) in red. The HEPES buffer also bound to the surface of the protein, as shown in green in the figure.
Proteinase K and Digalacturonic Acid (PDB entry 3dyb)
Digalacturonic acid, shown here in red balls-and-sticks, bridges between two proteins, shown in blue, forming hydrogen bonds with serine amino acids on both proteins. Use the buttons below to see a spacefilling representation and to change the colors.
- Larson, S.B., Day, JB., Nguyen, C., Cudney, R., McPherson, A. (2009) High-resolution structure of proteinase K cocrystallized with digalacturonic acid. Acta Cryst. F65, 192-198.
- Larson, S.B., Day, JB., Nguyen, C., Cudney, R., McPherson, A. (2008) Progress in the development of an alternative approach to macromolecular crystallization. Cryst. Growth Design 8, 3038-3052.