Chapter 6 tertiary structure.docx

Chapter 6 part 2: **Protein Crystals: Azidomet myohemerythrin** Tertiary structure of the protein describes the folding of its secondary structural elements and specifies the positions of each atom in the protein, including those of its side chains. The common features of protein tertiary structu...

Chapter 6 part 2: **Protein Crystals: Azidomet myohemerythrin** Tertiary structure of the protein describes the folding of its secondary structural elements and specifies the positions of each atom in the protein, including those of its side chains. The common features of protein tertiary structures reveal much about the biological functions of proteins and their evolutionary origin. X-ray crystallography is a technique that directly images molecules. A crystal of molecule to be imaged is exposed to a collimated beam of X-rays and the resulting diffraction pattern , which arises from the regularly repeating positions of atoms in the crystal , is recorded by a radiation detector or a photographic film. This is protein crystal of lamprey hemoglobin. These crystals are colored because the [proteins contains light-absorbing groups]; proteins are colorless in the absence of such groups. This is an X-ray diffraction photograph of a crystal of sperm [whale myoglobin]. The intensity of each diffraction peak (the [darkness of each spot]) is a function of the crystal's electron density; that is of the positions of all of its atoms. This photograph represents a two-dimensional slice through a 3-dimensional diffraction pattern, which consists of \~25000 diffraction peaks. **Electron Density Map** X-rays interact almost exclusively with the electrons in matter, not the nuclei. An X-ray structure is therefore an image of the electron density of the object under study. Such electron density maps are usually represented with the aid of computer graphics as one or more set of contours. Figure: A thin section through a 1.5 A◦ resolution electron density map of a protein that is contoured in 3-dimensions. Only a single contour level (cyan) is shown, together with a ball stick model of the corresponding polypeptide segment colored according to atom type with C yellow, N blue, O red. A water molecule is represented by a red sphere. This is electron density maps of diketopiperazine at different resolution levels. At 6 A◦ resolution, the presence of a molecule the size of diketopiperazine is difficult to discern. At 2 A◦ resolution, its individual atoms cannot yet be distinguished, although its molecular shape has become reasonably evident. At 1.5 A◦ resolution, which roughly corresponds to a bond distance, individual atoms become partially resolved. At 1.1 A◦ resolution, atoms are clearly visible. Hydrogen atoms are not visible in these maps because of their low electron density. **NOESY Spectrum of a Protein** Protein structures can be determined by Nuclear magnetic resonance (NMR). The basis is that, certain atomic nuclei including ^1^H, ^2^H, ^13^C, ^15^N, and ^31^P, when placed in a magnetic field, absorb radio-frequency radiation at frequencies that vary with each type of nucleus, its electronic environment, and its interactions with nearby nuclei. So NMR made it possible to determine the three-dimensional structures of globular proteins in aqueous solution. The diagonal represents the conventional one-dimensional NMR spectrum presented as a contour plot. Note that this is too crowded with peaks to be directly interpretable (even a small protein has hundreds of protons). The cross (off-diagonal) peaks each arise from the interaction of two protons that are \