Other Protein Crystals

Before describing those protein gels whose structures appear to involve three-dimensional networks, it will be useful to review the properties of some simpler network systems formed by the junction of long threadlike or rodlike molecules. 

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FIGURE 30.7 Crystal packing of a human thrombin complex. Twelve unit cells with one layer of molecules are shown. By looking carefully, one can see that the two molecules in each unit cell are rotated 180° with respect to each other. Protein crystals used for X-ray diffraction extend into 3D and consist of many layers of molecules. The next layer of thrombin molecules fits into the holes present in the layer shown. 

Leucine residues 2, 5, 7, 12, 20, and 24 of the motif are invariant in both type A and type B repeats of the ribonuclease inhibitor. An examination of more than 500 tandem repeats from 68 different proteins has shown that residues 20 and 24 can be other hydrophobic residues, whereas the remaining four leucine residues are present in all repeats. On the basis of the crystal structure of the ribonuclease inhibitor and the important structural role of these leucine residues, it has been possible to construct plausible structural models of several other proteins with leucine-rich motifs, such as the extracellular domains of the thyrotropin and gonadotropin receptors. 

Despite considerable efforts very few membrane proteins have yielded crystals that diffract x-rays to high resolution. In fact, only about a dozen such proteins are currently known, among which are porins (which are outer membrane proteins from bacteria), the enzymes cytochrome c oxidase and prostaglandin synthase, and the light-harvesting complexes and photosynthetic reaction centers involved in photosynthesis. In contrast, many other membrane proteins have yielded small crystals that diffract poorly, or not at all, using conventional x-ray sources. However, using the most advanced synchrotron sources (see Chapter 18) it is now possible to determine x-ray structures from protein crystals as small as 20 pm wide which will permit more membrane protein structures to be elucidated. 

Figure 18.4 The hanging-drop method of protein crystallization, (a) About 10 pi of a 10 mg/ml protein solution in a buffer with added precipitant—such as ammonium sulfate, at a concentration below that at which it causes the protein to precipitate—is put on a thin glass plate that is sealed upside down on the top of a small container. In the container there is about 1 ml of concentrated precipitant solution. Equilibrium between the drop and the container is slowly reached through vapor diffusion, the precipitant concentration in the drop is increased by loss of water to the reservoir, and once the saturation point is reached the protein slowly comes out of solution. If other conditions such as pH and temperature are right, protein crystals will occur in the drop, (b) Crystals of recombinant enzyme RuBisCo from Anacystis nidulans formed by the hanging-drop method. (Courtesy of Janet Newman, Uppsala, who produced these crystals.)...

MIR), requires the introduction of new x-ray scatterers into the unit cell of the crystal. These additions should be heavy atoms (so that they make a significant contribution to the diffraction pattern) there should not be too many of them (so that their positions can be located) and they should not change the structure of the molecule or of the crystal cell—in other words, the crystals should be isomorphous. In practice, isomorphous replacement is usually done by diffusing different heavy-metal complexes into the channels of preformed protein crystals. With luck the protein molecules expose side chains in these solvent channels, such as SH groups, that are able to bind heavy metals. It is also possible to replace endogenous light metals in metal-loproteins with heavier ones, e.g., zinc by mercury or calcium by samarium. 

Figure 18.10 The diffracted waves from the protein part (ted) and from the heavy metals (green) interfere with each other in crystals of a heavy-atom derivative. If this interference is positive as illustrated in (a), the intensity of the spot from the heavy-atom derivative (blue) crystal will be stronger than that of the protein (red) alone (larger amplitude). If the interference is negative as in (b). the reverse is true (smaller amplitude).

ITowever, membrane proteins can also be distributed in nonrandom ways across the surface of a membrane. This can occur for several reasons. Some proteins must interact intimately with certain other proteins, forming multisubunit complexes that perform specific functions in the membrane. A few integral membrane proteins are known to self-associate in the membrane, forming large multimeric clusters. Bacteriorhodopsin, a light-driven proton pump protein, forms such clusters, known as purple patches, in the membranes of Halobacterium halobium (Eigure 9.9). The bacteriorhodopsin protein in these purple patches forms highly ordered, two-dimensional crystals. 

Physicochemical Aspects. Other than toxicity toward insects, the protein of the crystals has no unique characteristics not shared by other protein molecules. It contains between 17.5 (15) and 18% (1) nitrogen, present in 17 to 19 amino acids (Table I), none of which are unusual or present in any unusual concentration. The protein is sensitive to heat and when dissolved (0.01N hydroxide) absorbs characteristically at the 280-m/ maximum displayed by aromatic amino acids. 

Once a suitable crystal is obtained and the X-ray diffraction data are collected, the calculation of the electron density map from the data has to overcome a hurdle inherent to X-ray analysis. The X-rays scattered by the electrons in the protein crystal are defined by their amplitudes and phases, but only the amplitude can be calculated from the intensity of the diffraction spot. Different methods have been developed in order to obtain the phase information. Two approaches, commonly applied in protein crystallography, should be mentioned here. In case the structure of a homologous protein or of a major component in a protein complex is already known, the phases can be obtained by molecular replacement. The other possibility requires further experimentation, since crystals and diffraction data of heavy atom derivatives of the native crystals are also needed. Heavy atoms may be introduced by covalent attachment to cystein residues of the protein prior to crystallization, by soaking of heavy metal salts into the crystal, or by incorporation of heavy atoms in amino acids (e.g., Se-methionine) prior to bacterial synthesis of the recombinant protein. Determination of the phases corresponding to the strongly scattering heavy atoms allows successive determination of all phases. This method is called isomorphous replacement. 

There are four other proteins - stellacyanin, rusticyanin, umecyanin and ami-cyanin (Table 3) which have been fairly extensively studied. A crystal structure determination for amicyanin from Thiobacillus versutus is now under way [61]. A number of other type 1 proteins have been identified. These include pseudo-... 

Homologous proteins. Homologous proteins usually crystallize under very different conditions. For example, in our laboratory two homologous proteins crystallize in either 10 mM sodium acetate, pH 3.8, 5 mM DTT, and 50% (v/v) MPD (Weichsel et al, 1996), or 100 mM ammonium sulfate, 30% PEG 6000, and 10 mM DTT (Filson et al, 2003). This technique was first used by Kendrew for solving the structure of sperm whale myoglobin (Kendrew et al., 1954) and has been used in many other structural studies. Currently, this technique is heavily exploited in membrane protein crystallography (Wiener,... 

For protein crystallography, the repository of most protein crystal structures is the PDB hosted at http // www.rcsb.org/pdb/ (Berman et al., 2000). This database contains the 3-D coordinates (and sometimes the structure factor files) for almost all protein crystal structures. Most journals currently require deposition of the coordinates when pubhshing stmcture papers. Each structure is given a unique identification code that will be listed in the paper (see Figure 22-1 for examples of PDB codes). Structures can be accessed using this code, or using various other search criteria. The PDB also contains structural information for NMR structures. 

Several proteins have recently been crystallized, and from the X-ray studies it is expected that much important information on the three-dimensional structure will be forthcoming. Many other proteins can probably be crystallized if suitable preparative procedures and crystallization conditions are found. 

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