Sticky triangles: New tools for experimental phasing of biological macromolecules

Abstract

X-ray crystallography is the prime method for the elucidation of three-dimensional molecular structures. It enables the structure determination of biological macromolecules such as proteins and nucleic acids. The determination of novel macromolecular structures is hampered by the crystallographic phase problem, i.e. only the intensity of the reflections but not their phase angle can be recorded during the diffraction experiment. Experimental phasing is one technique to solve this phase problem; it usually requires the incorporation of heavy atoms in the protein crystal. Conventional derivatisation with heavy-metal salts often suffers from non-specific binding, resulting in low occupancy of the heavy-atom sites or derivatisation failing completely. In this thesis a new class of compounds was developed that combines heavy atoms for experimental phasing with functional groups for interaction with biological macromolecules. The lead structure is based on a benzene ring that provides a rigid scaffold. The ring is substituted with three functional groups and three heavy atoms, iodine or bromine, respectively. The three functional groups, e.g. carboxyl or amino groups, but also hydroxyl or methoxy moieties, may interact with protein residues and therefore the novel compounds show enhanced binding properties compared to traditional heavy-atom compounds. The three halogen atoms provide a strong anomalous signal and may be used for experimental phasing. The halogen atoms form an equilateral triangle, which is easily recognised in the heavy-atom substructure. So far several novel protein structures have been solved with the iodine triangle compound. The sticky compounds of the current work are readily available and easy to use.