Following the solution of the three-dimensional structure of myoglobin by John Kendrew in 1960, x-ray crystallography has revealed the structures of thousands of biologic macro molecules ranging from proteins to oligonucleotides and viruses. For the solution of its structure by x-ray crystallography, a protein is first precipitated under conditions that form well-ordered crystals. To establish appropriate conditions, crystallization trials use a few microliters of protein solution and a matrix of variables (temperature, pH, presence of salts or organic solutes such as polyethylene glycol) to establish optimal conditions for crystal formation. Suitably sized crystals are then irradiated with a beam of x-rays and the pattern formed by those x-rays that are diffracted as a consequence of colliding with atomic nuclei of the protein recorded.

Early crystallographers collected the patterns formed by the diffracted x-rays as a series of spots on film. In order to calculate the position of each atom, the phases of the diffracted x-rays must first be determined. The traditional approach to solving the “phase problem” employs isomorphous displacement, in which an atom with a strong and distinctive x-ray “signature,” such as mercury or uranium, is introduced into a crystal at known positions in the primary structure of the protein. Alternatively, recombinant expression can be used to substitute methionine with selenocysteine, whose selenium atom also possesses a distinct x-ray signature. If the protein being analyzed is homologous to one whose structure has already been solved, one can phase diffraction data without using heavy atoms by performing molecular replacement using the existing structure as a scaffold.

Initially, extrapolating the position of the individual atoms in the protein required manually measuring the position of each spot in the diffraction pattern followed by a series of lengthy hand calculations. Today, the patterns are recorded electronically using an area detector, then analyzed using a mathematical approach termed a Fourier synthesis. Do proteins inside these crystals exist in the same conformation as in free solution? The consensus is yes, a conclusion supported by the capacity of many enzymes retain the ability to catalyze chemical reactions when in the crystalline state.

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