Proteins, helical crystallization

Ellenberger, T.E., et al. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted a helices crystal structure of the protein-DNA complex. Cell 71 1223-1237, 1992. 

The existence of electrostatic interactions between oppositely charged residues and hydrogen bonding between side chains agrees with the observations in protein helices that (1) helix probability correlates with the frequency of occurrence of oppositely charged residues spaced i, i + 4 apart in proteins 88 and (2) there is a strong tendency for nearby, oppositely charged, side chains to point toward each other. 89 In the case of C-peptide, the side-chain interactions were also evident in the crystal structure of RNase A. 

Figure 21, Images (a,c) and Fourier transforms (b,d) of helical crystals of streptavidin formed on lipid tubules containing DODA-EOa-biotin (50). (a,c) Stain striations extend along the tubules. Protein densities are particularly visible at tube edges, corresponding to streptavidin molecules viewed edge-on. Scale bar 40 nm. (b,d) Distribution of Fourier transform amplitudes from the tubes shown in (a,c) corresponding to about 1700 streptavidin molecules. The fine spacing between layer lines indicates a helical repeat of 47 nm. Visible diffraction peaks extend up to 1.7 nm (arrowhead in (b)]. Reproduced from ref. 242 (Ringler et al., Chem. Eur. J. 1997, 3, 620) with permission ofWiley-VCH.

Chiral Fibers as Templates for Helical Crystallization of Proteins. 207... 

Wilson-Kubalek et al. also produced specifically and nonspecifically functionalized unilamellar lipid tubules by using mixtures of a tubule-forming galactosylceramide and various charged or derivatized lipids [166]. Thus, nickel-doped lipids allowed the helical crystallization of histidine-tagged proteins. The authors also reproduced the helical crystallization of streptavidin. They even obtained helical arrays of relatively small proteins, such as actin and annexin, as well as large macromolecules, such as RNA polymerase (Fig. 21). 

Possibly the simplest representation for a two-state folding transition of a peptide is the crystallization into helical stmctures. Since most proteins possess hehcal segments, the heluc coil transition is perhaps the most prominent stmcture formation process of proteins. Helices form, if the values of the dihedral angles ijf and (p (see Fig. 1.6) of amino acids adjacent in the sequence lie within a certain section of the Ramachandran map. The boundaries of this section are not well defined, but most amino acids in hehcal state are found with dihedral angles in the intervals (p e (—90°, —30°) and jr e (—77°, —17°) [223]. 

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 ... 

In spite of the absence of the C-terminal domains, the DNA-binding domains of lambda repressor form dimers in the crystals, as a result of interactions between the C-terminal helix number 5 of the two subunits that are somewhat analogous to the interactions of the C-terminal p strand 3 in the Cro protein (Figure 8.7). The two helices pack against each other in the normal way with an inclination of 20° between the helical axes. The structure of the C-terminal domain, which is responsible for the main subunit interactions in the intact repressor, remains unknown. 

Figure 12.3 Two-dimensional crystals of the protein bacteriorhodopsin were used to pioneer three-dimensional high-resolution structure determination from electron micrographs. An electron density map to 7 A resolution (a) was obtained and interpreted in terms of seven transmembrane helices (b).

Figure 26.9 X-ray crystal structure of citrate synthase. Part (a) is a space-filling model and part (b) is a ribbon model, which emphasizes the a-helical segments of the protein chain and indicates that the enzyme is dimeric that is, it consists of two identical chains held together by hydrogen bonds and other intermolecular attractions. Part (cl is a close-up of the active site in which oxaloacetate and an unreactive acetyl CoA mimic are bound.

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