Interactions of Biological Macromolecules Visualized by X-ray Crystallography

Abstract

Abstract Biologically important macromolecules, which principally include proteins and nucleic acids, are polymers of small building block molecules. These are amino acids for proteins, of which there are twenty, and nucleotides, four in number, for nucleic acids. Proteins comprise the major classes of enzymes that catalyze and regulate metabolism, movement and development while nucleic acids, DNA and RNA serve as the reservoir of genetic material as well as provide a means for its expression. In order to completely understand the chemical and physical mechanisms by which these strategic cellular components function, a description of their structure at the atomic level is essential. The only technique currently available for visualizing the structures of macromolecules is X-ray diffraction analysis of single crystals of proteins and nucleic acids. Application of the technique requires the measurement of hundreds of thousands of diffraction intensities from both native and heavy atom modified crystals, their correlation and their incorporation into a Fourier synthesis. The Fourier synthesis, or electron density map, serves as a three-dimensional image of the electron density distribution over the volume in space occupied by the macromolecule. From this distribution and available chemical information, the crystallographer can deduce, and later refine, a detailed atomic model of the protein or nucleic acid. A unique feature of macromolecular crystals is that they have a very high solvent content, which allows the investigator to diffuse various substrates, inhibitors, coenzymes or other ligands directly into the crystals. The ligands, in general, freely complex with the macromolecules even as they are constrained to their lattice positions. By application of a second diffraction procedure, known as a difference Fourier analysis which utilizes the diffraction intensities from the complex crystals, an image of the macromolecule-ligand association can be obtained. From images of such complexes, the means by which specific binding is established, the mechanisms of enzyme catalysis, and the manner by which effectors or drugs regulate macromolecular behavior can be elucidated. In a sense. protein and nucleic acid crystals can be thought of as ligand binding laboratories that offer the X-ray crystallographer the opportunity to see at the molecular level the atomic interactions that mediate and control the vital processes of living tissues.