Virus coats

Viruses are parasitic nucleoprotein complexes. They often consist of only a single nucleic acid molecule (DNA or RNA, never both) and a protein coat. Viruses have no metabolism of their own, and can therefore only replicate themselves with the help of host cells. They are therefore not regarded as independent organisms. Viruses that damage the host cell when they replicate are pathogens. Diseases caused by viruses include AIDS, rabies, poliomyelitis, measles, German measles, smallpox, influenza, and the common cold. 

These substances do not kill bacterial spores, mycobacterium (TB), or all viruses. Low-level disinfectants can kill vegetative bacteria, fungi, and some lipid-coated viruses such as HIV. Use low-level disinfectants such as QACs on floors, countertops, furniture, and plastic or metal housing of machines. QAC disinfectants contain their active ingredients as n-alkyl dimethyl ethylbenzyl... 

Lauricidin can be characterized as a nonionic emulsifier with antimicrobial properties. There is no difference in the antimicrobial activity of both isomeric monoglycerides. Lauricidin s antibacterial activity is restricted to gram-positive bacteria (MIC 5000mg/l) MIC s for Gram-negative bacteria are beyond 10000 mg/1. However the activity against molds and yeasts and also against lipid-coated viruses is remarkable. It is recommended to applicate Lauricidin in combination with other microbicides (Parabens, etc.) to achieve a sufficiently broad spectrum of effectiveness, e.g. for the in-can protection of cosmetic and pharmaceutical products. Addition rates 0.5-1% optimum pH 6 7.5. 

Antiparallel beta (P) structures comprise the second large group of protein domain structures. Functionally, this group is the most diverse it includes enzymes, transport proteins, antibodies, cell surface proteins, and virus coat proteins. The cores of these domains are built up by p strands that can vary in number from four or five to over ten. The P strands are arranged in a predominantly antiparallel fashion and usually in such a way that they form two P sheets that are joined together and packed against each other. 

Figure 16.2 The icosahedron (top) and dodecahedron (bottom) have identical symmetries but different shapes. Protein subunits of spherical viruses form a coat around the nucleic acid with the same symmetry arrangement as these geometrical objects. Electron micrographs of these viruses have shown that their shapes are often well represented by icosahedra. One each of the twofold, threefold, and fivefold symmetry axes is indicated by an ellipse, triangle, and pentagon, respectively.

Very few self-sufficient viruses have only 60 protein chains in their shells. The satellite viruses do not themselves encode all of the functions required for their replication and are therefore not self-sufficient. The first satellite virus to be discovered, satellite tobacco necrosis virus, which is also one of the smallest known with a diameter of 180 A, has a protein shell of 60 subunits. This virus cannot replicate on its own inside a tobacco cell but needs a helper virus, tobacco necrosis virus, to supply the functions it does not encode. The RNA genome of the satellite virus has only 1120 nucleotides, which code for the viral coat protein of 195 amino acids but no other protein. With this minimal genome the satellite viruses are obligate parasites of the viruses that parasitize cells. 

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

The coat proteins of many different spherical plant and animal viruses have similar jelly roll barrel structures, indicating an evolutionary relationship... 

One of the most striking results that has emerged from the high-resolution crystallographic studies of these icosahedral viruses is that their coat proteins have the same basic core structure, that of a jelly roll barrel, which was discussed in Chapter 5. This is true of plant, insect, and mammalian viruses. In the case of the picornaviruses, VPl, VP2, and VP3 all have the same jelly roll structure as the subunits of satellite tobacco necrosis virus, tomato bushy stunt virus, and the other T = 3 plant viruses. Not every spherical virus has subunit structures of the jelly roll type. As we will see, the subunits of the RNA bacteriophage, MS2, and those of alphavirus cores have quite different structures, although they do form regular icosahedral shells. 

The canonical jelly roll barrel is schematically illustrated in Figure 16.13. Superposition of the structures of coat proteins from different viruses show that the eight p strands of the jelly roll barrel form a conserved core. This is illustrated in Figure 16.14, which shows structural diagrams of three different coat proteins. These diagrams also show that the p strands are clearly arranged in two sheets of four strands each P strands 1, 8, 3, and 6 form one sheet and strands 2, 7, 4, and 5 form the second sheet. Hydrophobic residues from these sheets pack inside the barrel. 

In all jelly roll barrels the polypeptide chain enters and leaves the barrel at the same end, the base of the barrel. In the viral coat proteins a fairly large number of amino acids at the termini of the polypeptide chain usually lie outside the actual barrel structure. These regions vary considerably both in size and conformation between different coat proteins. In addition, there are three loop regions at this end of the barrel that usually are quite long and that also show considerable variation in size in the plant viruses and the... 

Figure 16.14 Schematic diagrams of three different viral coat proteins, viewed in approximately the same direction. Beta strands I through 8 form the common jelly roll barrel core, (a) Satellite tobacco necrosis virus coat protein, (b) Subunit VPl from poliovirus.

The cleft where this drug binds is inside the jelly roll barrel of subunit VPl. Most spherical viruses of known structure have the tip of one type of subunit close to the fivefold symmetry axes (Figure 16.15a). In all the picor-naviruses this position is, as we have described, occupied by the VPl subunit. Two of the four loop regions at the tip are considerably longer in VPl than in the other viral coat proteins. These long loops at the tips of VPl subunits protrude from the surface of the virus shell around its 12 fivefold axes (Figure 16.15b). 

Since all members of this family of RNA phages have homologous coat proteins, their subunits are expected to have the same three-dimensional structure. It remains to be seen if the MS2 fold is also present in any other unrelated viruses. The fold is so far unique for the MS2 subunit, but similar structures have been observed in other proteins such as the major histocompatibility antigen, HLA, which was discussed in Chapter 15. 

Figure 16.17 The subunit structure of the bacteriophage MS2 coat protein is different from those of other sphericai viruses. The 129 amino acid polypeptide chain is folded into an up-and-down antiparallei P sheet of five strands, P3-P7, with a hairpin at the amino end and two C-terminai a helices. (Adapted from a diagram provided by L. Liijas.)...

Figure 16.21 Structure of one subunit of the core protein of Slndbls virus. The protein has a similar fold to chymotrypsin and other serine proteases, comprising two Greek key motifs separated by an active site cleft. The C-terminus of the protein is bound in the catalytic site, making the coat protein inactive (Adapted from S. Lee et al., Structure 4 531-541, 1996.)...

Vibrio (i) Curved, rod-shaped bacterial cell, (ii) Bacterium of the genus Vibrio. Virion Virus particle the virus nucleic acid surrounded by protein coat and in some cases other material. 

Virus Any of a large group of submicroscopic infective agents that typically contain a protein coat sunounding a nucleic acid core and are capable of growth only in a living cell. 

FIGURE 1.25 The virus life cycle. Viruses are mobile bits of genetic iuformatiou encapsulated in a protein coat. The genetic material can be either DNA or RNA. Once this genetic material gains entry to its host cell, it takes over the host machinery for macromolecular synthesis and subverts it to the synthesis of viral-specific nucleic acids and proteins. These virus components are then assembled into mature virus particles that are released from the cell. Often, this parasitic cycle of virus infection leads to cell death and disease. 

Tannic acid is a strong inhibitor of virus particles in vitro. It inactivated both TMV and TMV-RNA by forming noninfectious complexes (1). TMV-RNA was much more sensitive to inactivation than was whole TMV. It would thus appear that tannic acid could possibly inactivate TMV by reacting with either the protein coat or the RNA core. 

---