Proteins crystallizing

Membrane proteins comprise another important class of protein crystallized in 2D. These proteins perform important functions as membrane channels and recognition sites for cells. Unlike the streptavidin crystals, membrane proteins... 

York, D.M., Wlodawer, A., Pederson, L.G., Darden, T.A. Atomic-level accuracy in simulation of large protein crystals. Proc. Natl Acad. Sci. USA 91 (1994) 8715-8718. 

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

M, A Wlodawer, L G Pedersen and T A Darden 1994. Atomic-level Accuracy in Simulations of irge Protein Crystals. Proceedings of the National Academy of Sciences USA 91 8715-8718. 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

Protein acidulant Protein additives Protein ammo acids a-l-Proteinase inhibitor Protein-based mimetics Protein Ca [42617-41-4] Protein channels Protein chromatography Protein crystal growth... 

Oxford University Press, ISBN 0199636788 (paperback) T.L.Blundell and L.N.Johnson Protein Crystallisation, Academic Press, NY, 1976 A,McPherson Preparation and Analysis of Protein Crystals, J.Wiley Sons, NY, 1982 A.McPherson, Crystallisation of Biological Macromolecules, Cold Spring Harbour Laboratory Press, 2001 ISBN 0879696176.]... 

Martensite transformations are not limited just to metals. Some ceramics, like zirconia, have them and even the obscure system of (argon + 40 atom% nitrogen) forms martensite when it is cooled below 30 K. Helical protein crystals in some bacteria undergo a martensitic transformation and the shape change helps the bacteria to burrow into the skins of animals and people ... 

A3) Bond lengths and bond angles vary in protein crystal structures. 

I Pontius, I Richelle, SI Wodak. Deviations from standard atomic volumes as a quality measure for protein crystal structures. I Mol Biol 264 121-136, 1996. 

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 12.2 (a) Schematic drawing of membrane proteins in a typical membrane and their solubilization by detergents. The hydrophilic surfaces of the membrane proteins are indicated by red. (b) A membrane protein crystallized with detergents bound to its hydrophobic protein surface. The hydrophilic surfaces of the proteins and the symbols for detergents are as in (a). (Adapted from H. Michel, Trends Biochem. Sci. 8 56-59, 1983.)... 

Figure 18.3 Protein crystals contain large channels and holes filled with solvent molecules, as shown in this diagram of the molecular packing in crystals of the enzyme glycolate oxidase. The subunits (colored disks) form octamers of molecular weight around 300 kDa, with a hole in the middle of each of about 15 A diameter. Between the molecules there are channels (white) of around 70 A diameter through the crystal. (Courtesy of Ylva Lindqvist, who determined the structure of this enzyme to 2.0 A resolution in the laboratory of Carl Branden, Uppsala.)...

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. 

How do we find phase differences between diffracted spots from intensity changes following heavy-metal substitution We first use the intensity differences to deduce the positions of the heavy atoms in the crystal unit cell. Fourier summations of these intensity differences give maps of the vectors between the heavy atoms, the so-called Patterson maps (Figure 18.9). From these vector maps it is relatively easy to deduce the atomic arrangement of the heavy atoms, so long as there are not too many of them. From the positions of the heavy metals in the unit cell, one can calculate the amplitudes and phases of their contribution to the diffracted beams of the protein crystals containing heavy metals. 

The amplitudes and the phases of the diffraction data from the protein crystals are used to calculate an electron-density map of the repeating unit of the crystal. This map then has to be interpreted as a polypeptide chain with a particular amino acid sequence. The interpretation of the electron-density map is complicated by several limitations of the data. First of all, the map itself contains errors, mainly due to errors in the phase angles. In addition, the quality of the map depends on the resolution of the diffraction data, which in turn depends on how well-ordered the crystals are. This directly influences the image that can be produced. The resolution is measured in A... 

Crystallization of proteins can be difficult to achieve and usually requires many different experiments varying a number of parameters, such as pH, temperature, protein concentration, and the nature of solvent and precipitant. Protein crystals contain large channels and holes filled with solvents, which can be used for diffusion of heavy metals into the crystals. The addition of heavy metals is necessary for the phase determination of the diffracted beams. 

In NMR the magnetic-spin properties of atomic nuclei within a molecule are used to obtain a list of distance constraints between those atoms in the molecule, from which a three-dimensional structure of the protein molecule can be obtained. The method does not require protein crystals and can be used on protein molecules in concentrated solutions. It is, however, restricted in its use to small protein molecules. 

McPherson, A. The Preparation and Analysis of Protein Crystals. New York Wiley, 1982. 

Several different techniques are used to study the structure of protein molecules Protein crystals are difficult to grow X-ray sources are either monochromatic or polychromatic... 

S. C. Ke, L. J. DeLucas, J. G. Harrison. Computer simulation of protein crystal growth using aggregates as the growth unit. J Phy D 57 1064, 1998. 

A. M. Kierzek, W. M. Wolf, P. Zielenkiewicz. Simulations of nucleation and early growth stages of protein crystals. Biophys J 75 571, 1997. 

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