Bacteriophage crystals

Figure 8.4 Cro molecules from bacteriophage lambda form dimers both in solution and in the crystal structure. The main dimer interactions ate between p strands 3 from each subunit. In the diagram one subunit is green and the other is brown. Alpha helices 2 and 3, the helix-turn-helix motifs, are colored blue and red, respectively, in both subunits. (Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.)...

Stummeyer, K., Dickmanns, A., Muhlenhoff, M., Gerardy-Schahn, R., and Ficner, R. (2005). Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. Nat. Struct. Mol. Biol. 12, 90-96. 

More recently, triple /1-spiral repeats have been identified in mammalian reovirus type 3 fiber (Chappell et al., 2002 Fig. 4A), avian reovirus fiber (Guardado Calvo et al., 2005 Fig. 4B), and bacteriophage PRD1 P5 protein (Merckel et al., 2005 Fig. 4C). In the latter two cases, it appears that only two repeats are present, just N-terminal to the head domain. Mammalian reovirus fiber contains eight putative triple /1-spiral repeats, of which three were resolved in the crystal structure (Chappell et al., 2002). 

In a multidomain protein whose domains have fixed orientations relative to each other, a unique alignment tensor will represent the preferred orientation of all the domains in the anisotropic environment. Therefore, structure refinement with dipolar couplings is performed as in one-domain proteins (Sect. 8.4). Several examples are reported in the literature of cases with conformational ambiguity due to the lack of NOE contacts between the domains. One example is the determination of subdomain orientation of the riboso-mal protein S4 z)41 [97]. In this work the lack of NOE contacts between the domains produces an ambiguity in interdomain orientation. The authors use two different anisotropic media to obtain dipolar couplings (DMPC/DHPC bicelles and Pfl filamentous bacteriophages). They conclude that subdomain orientation in solution is similar to the one present in the crystal structure. 

Figure 16.4 A plot showing likely crystal stability with increasing particle size based on the observation that for a given surface roughness (e.g. 10 A) the likely contact area is proportional to the particle radius R, whilst the dispersive force is proportional to (i.e. the particle mass). PPb = glycogen phosphorylase b, FMDV = foot-and-mouth disease virus PRDl = PRDl bacteriophage.

Lysozyme is an enzyme that hydrolyzes some bacterial cell-walls, the bacterium used for the assay being Micrococcus lysodeikticus. Lysozyme is found in a wide variety of species and locations, including bacteriophages, blood, egg white, gastric secretions, milk, nasal mucus, papaya, sputum, and tears. The outstanding achievement in this field has been the elucidation of the crystal structures of some of the lysozyme-substrate complexes. 

In addition to its function in catalysis, zinc often plays an important structural role, e.g., in the zinc finger transcriptional regulators (Fig. 5-38).k Zinc ions bind to insulin and stabilize its hexameric structure (Fig. 7-18)/ Six Zn2+ ions are present in the hexagonal tail plate of the T-even bacteriophage (Box 7-C) and appear to be essential for invasion of bacteria.131 In carnivores, the tapetum, the reflecting layer behind the retina of the eye of many animals, contains crystals of the Zn2+-cysteine complex. 

Both X-ray and neutron fiber diffraction (as well as electron microscopy) techniques have been applied to filamentous viruses, for which the prospect of three-dimensional crystals is poor. By combining neutron and X-ray fiber diffraction, NMR, circular dichroism, and Raman and infrared spectroscopies, an atomic model for the filamentous bacteriophage Pfl has been derived (Liu and Day, 1994). Other studies concerning Pfl have relied on purely X-ray fiber diffraction data, together with molecular modeling, to provide detailed filament structures (Pederson et at, 2001 Welsh et at, 1998a,b, 2000). Eiber diffraction was also used to solve the structure of the rodlike helical tobacco mosaic virus (TMV), where all of the coat protein and three genomic nucleotides... 

More recently the crystal structures of the adenovirus fiber shaft and receptor-binding fiber head (van Raaij et al, 1999) and of the head in complex with the coxsackie-adenovirus receptor molecule (GAR) (Bewley et al, 1999) have been solved. The fiber shaft structure revealed a novel (3-sheet triple spiral fold, which is perhaps particularly suited to forming rigid protein projections for interaction with and penetration through cell membranes by adenovirus the structure of the complex that performs the same function in bacteriophage T4 has been solved, revealing a similar fold (Kanamaru et al, 2002). 

Fig. 4. Adenovirus and bacteriophage PRDl. Top On the left, a density isosurface representation of adenovirus at 25-A resolution is shown. The 5-fold axis, occupied by the protein penton, is marked with a pentagon. A trimer of hexon is marked with a triangle close by arrays of hexon extend outward in all directions from the pentagonal vertex, forming the flat faces of the virus. On the right, a close-up of the 5-fold axis is shown (top) and below that a close-up of the hexon trimer with it crystal structure fitted (Athappilly et at, 1994 Stewart et al, 1991). Bottom The Susl mutant of PRDl is shown...

Valegard, K., Murray, J. B., Stockley, P. G., Stonehouse, N. J., and Liljas, L. (1994). Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature 371, 623-626. 

---