Atomic viral proteins

Today, science has an armoury of powerful probes to study matter at a range of scales from viral proteins to sub-atomic quarks. In spectroscopy, these probes are electromagnetic radiation, whilst in scattering experiments they are particles. Waveparticle duality allows electrons, for example, to be used in either mode. Each probe affords a unique perspective on the nature of the sample under investigation and different probes interact with the sample in different ways. 

Three-dimensional structures of several HRV capsids have been determined to atomic detail by using X-ray crystallography (Rossmann et al., 1985 Kim et al., 1989 Oliveira et al., 1993 Zhao et al., 1996). These structures show the precise arrangement of the different viral proteins in the capsid. In all of them, a 20-A deep depression, or canyon , encircles each five-fold vertex. 

The procedures for solving and refining macromolecular stmctures are similar to those for smaH molecules. The class of macromolecular stmctures solved consists mostly of proteins, some polynucleic acids, and some viral stmctures. These stmctures usuaHy contain thousands of atoms. 

There are three potential methods by which a protein s three-dimensional structure can be visualized X-ray diffraction, NMR and electron microscopy. The latter method reveals structural information at low resolution, giving little or no atomic detail. It is used mainly to obtain the gross three-dimensional shape of very large (multi-polypeptide) proteins, or of protein aggregates such as the outer viral caspid. X-ray diffraction and NMR are the techniques most widely used to obtain high-resolution protein structural information, and details of both the principles and practice of these techniques may be sourced from selected references provided at the end of this chapter. The experimentally determined three-dimensional structures of some polypeptides are presented in Figure 2.8. 

The structure determination proceeded in steps starting with separate structural analyses of the component protein VP7. Information from a 22 A resolution cryo-EM reconstruction of the viral core (Grimes et al., 1997) was then combined with the high-resolution atomic structure for the VP7(T13) trimer (Grimes et al., 1995) to yield a model providing phase information to a higher resolution than the EM reconstruction alone. Infectious BTV-1 crystals (unit cell dimensions a = 796 A,b = 822 A, and c = 753 A), containing half a particle in the asymmetric unit. 

With one exception (Smith et al, 1996), all the studies of complexes of viruses with other proteins are hybrids of cryo-EM for the complex and crystallography for its components. The fitting of atomic models within cryo-EM density maps has revealed the relative positioning of structural components of viruses, and their receptors or antibodies, and has afforded insights into the mechanisms of cell invasion, viral uncoating, and immune recognition. 

A single mechanism will not describe even the "controlled aggregation of proteins in nature. A single viral coat protein, for example, may form several different contacts with itself and other proteins, depending on its final position within the shell structure. Indeed, the original postulate of "quasi-equivalent binding at lattice points in virus capsules was modified to "non-equivalency" when the first structure was solved at atomic dimensions. For example, the coat of Tomato bushy stunt virus consists of 180 identical subunits of a 43 kD protein which self-interact at lattice points in at least three distinct ways k... 

Macromolecular crystallography is a very powerful method used to study complex biological systems. The structures of a wide variety of proteins, nucleic acids and their assemblies have been determined at atomic or near-atomic resolution. As a result, a detailed understanding has been gained of various living processes such as enzyme catalysis, the immune response, the encoding of hereditary information, viral infection and photosynthesis. 

RT and HIV PR is capable of reducing the viral load in blood patients. These enzymes, which exist respectively as a heterodimer and a homodimer for HIV RT and HTV PR, are well-characterized more than 170 structures of HIV PR and its complexes with various inhibitors have been solved by protein crystallography techniques. Thus, a dipalmitoylated derivative of 2,7-naphthalene disulfonic acid demonstrated micromolar activity for both fflV-1 and HIV-2 RT (Fig. 16.14). Symmetrical nature of HTV PR was used in the search for novel anti-HTV drugs that would embody the predicted characteristic of the active site. The design of inhibitors of HIV PR has led to symmetrical compounds, which can be divided into two groups (1) pseudosymmetrical compounds, like derivatives A 74704 ° and L 700,417 which contain asymmetric atoms in close proximity to the inhibitor two-fold axis (2) fully Ca-symmetrical inhibitors like the cyclic urea and the diol derivatives (Fig. 16.14). 

---