Biochemistry - Chemical Reactions in the Living Cell, Volume 1 - D. Metzler 1980

How molecules join together
Macromolecular packing
Oligomers with cubic symmetry (polyhedra)

If symmetrical structures possess more than one axis of Symmetry of an order higher than two, they are said to exhibit cubic symmetry. The simplest example of such a Structure is a tetrahedron, which has four 3-fold axes of symmetry passing through the vertices and the centers of the faces, and three 2-fold axes of symmetry passing through the midpoints of the six edges. Because protein subunits are always asymmetric, a tetrameric protein cannot possess cubic symmetry¹. However, a heterologous trimer with a 3-fold axis of symmetry can form a face of a tetrahedron containing a total of 12 asymmetric subunits (Fig. 4-10). A second type of heterologous trimer involving bk-contacts is formed around each vertex, while pairs of subunits at the 2-fold axis form an isologous cl-contact [43].

The interaction of 24 subunits can produce a cube in which three 4-fold axes of symmetry pass through the centers of the faces, four 3-fold axes pass through the vertices, and six 2-fold axes pass through the edges (Fig. 8-17). The largest structure possessing cubic symmetry that can be constructed is the icosahedron (a 20-faced figure)—a symmetrical shape with 20 triangular faces. Its construction requires 60 subunits, which form heterologous pentamers at each of the vertices. As in the case of the tetrahedron, each face contains a heterologous trimer, and interactions across the edges yield isologous dimers.

Class="center">

FIG. 4-10. Arrangement of subunits According to the cubic symmetry type. A tetrahedron constructed from 12 identical, symmetrically arranged subunits. The 3-fold and 2-fold axes of symmetry are indicated. Binding sites are designated by the same letters as in Fig. 4-9. (See also Fig. 8-17.)

¹ As we have already seen, tetrameric Proteins possess dihedral symmetry. Consequently, many theoretical schemes published in the current literature that predict The behavior of four subunits based on their tetrahedral arrangement are not entirely correct.

Addendum 4-B

Viruses^a-c

Nucleoprotein particles known as viruses "attack" A wide variety of living organisms, ranging from the smallest mycoplasma to humans. They lack their own METABOLISM and only "come to life" when the nucleic acid they contain penetrates a living Cell. Viruses attract considerable attention not only because they are pathogenic agents, but also because they are widely used in molecular biological research. A mature viral particle, or virion, consists of one or more nucleic acid molecules and a protein coat—the capsid—which typically has a helical or icosahedral shape. The capsid is built from "morphological subunits," or capsomeres, which are sometimes clearly visible under an Electron microscope. Capsomeres, in turn, consist of A large number of smaller protein subunits. Some large Viral Particles possess a membrane-like envelope. Others, such as the T-even Bacteriophages that infect E. coli, are very unusual in shape (Addendum 4-D).

The Genome of most viruses is represented either by double-stranded DNA or single-stranded RNA, although in some small viruses the DNA is single-stranded, and others contain double-stranded RNA. The number of NUCLEOTIDES in a viral genome ranges from a few thousand to several hundred thousand, and the number of genes ranges from 3 to 200 or more. Sometimes the nucleic acid molecules in a virion form a closed circle, while in other cases they are linear.

The table below characterizes some of the known virus types and A number of individual viruses. The shape of the viral particles is designated by the letters I (icosahedral), H (helical), and C (complex). For some helical and complex viruses, the particle length is given in nm. The length of the nucleic acid molecule is also indicated in thousands of bases (for single-stranded DNA or RNA) or in thousands of nucleotide pairs (for double-stranded Nucleic Acids). The number of genes contained in a viral particle sometimes slightly exceeds this number.

Among the multitude of very small viruses are helical bacteriophages, such as fd, fl, and M-13 (Fig. 4-8), which resemble bacterial pili. These viruses, containing single-stranded circular DNA molecules with a Molecular Weight of ~2·10⁶, attach to the sex pili of "male" Bacteria (e.g., E. coli) and can inject their DNA into the bacterium through them (Ch. 15, Sec. A.1). Bacteriophage —X174 is an icosahedral DNA-containing virus with a diameter of 25 nm, which is only three times thicker than the thinnest cell membrane^d. Its single-stranded DNA consists of only ~5000 nucleotides; the number of genes apparently does not exceed 9^d. Interestingly, such a tiny virus is capable of disrupting normal Metabolic control in a bacterial cell and directionally altering its metabolism toward the synthesis of new viral particles. Clearly, in doing so, the virus utilizes not only its own genes but also many genes and Other components of the infected cell.

Table to Addendum 4-B

A large group of animal viruses, the parvoviruses, are similar in Size and Structure to bacteriophage —X174. Some viruses in this group are unable to replicate in a cell unless that cell is infected with an adenovirus, which has a larger particle size.

Among the icosahedral double-stranded DNA viruses are the so-called papovaviruses, certain species of which cause warts and even malignant tumors. Simian virus 40 (SV40), which is capable of inducing tumors in some other species as well, has been the most thoroughly studied by biochemists. Another tumor virus is the mouse polyoma virus. Papillomaviruses are somewhat larger; one member of this group causes warts in humans. Adenoviruses are even larger (70 nm in diameter); among them, 32 species cause various infectious diseases in humans. Herpesviruses are very large viruses surrounded by a lipid-containing membrane, and the largest of the icosahedral viruses are those causing polyhedrosis in insects. One of these, which infects Tipula flies, has a diameter of 130 nm. Another group of large Introduction/6.html">DNA-containing viruses consists of tailed bacteriophages (which include, in particular, the T-even phages; Addendum 4-D).

The smallest of the RNA-containing Viruses are bacteriophages R17, MS2, and Qß, whose nucleic acids contain 3,500–4,500 nucleotides and possess only three genes. Their nucleotide sequence has been completely elucidated (Ch. 15, Sec. B.2.I)¹.

Somewhat larger are the picornaviruses (from "PicoRNA," indicating a very low RNA content). Among these small icosahedral viruses, 15–30 nm in diameter, are quite a few that cause infectious diseases in humans. These include, in particular, enteroviruses—a group comprising polioviruses, Coxsackie viruses, and some of the ECHO viruses. Another group of picornaviruses includes rhinoviruses, which are responsible for the common cold. Approximately 200 Different types of such viruses are currently known. Many RNA-containing viruses infect plants; an example is turnip yellow mosaic virus (virion diameter 28–30 nm).

Large viruses 80–100 nm in diameter, possessing 8–10 spikes at the vertices of the icosahedron, cause influenza, mumps, and certain other acute infections. The Internal Structure of such viruses appears to be very complex. RNA accounts for only 1% of the total mass of the virus and consists of several fragments of relatively low molecular weight (~0.5·10⁶).

¹ The DNA nucleotide sequences of bacteriophage —X174 and virus SV40, as well as several other viruses, have recently been elucidated. — Trans.

The helical RNA-containing tobacco mosaic virus is the best studied (Sec. G.2)^c. Viruses whose virions resemble a bullet in shape have a more complex structure; an example is the rabies virus, which has a diameter of 65–90 nm and a length of 120–500 nm. Inside the particle of such viruses, the nucleoprotein is coiled into a helix.

The genome of certain viruses, such as reoviruses, is represented by double-stranded RNA, which is relatively rare in nature. In an infected cell, reovirus RNA is fragmented into approximately 10 segments.

Certain plant diseases, including potato spindle tuber, are caused by very small supercoiled RNA molecules with a molecular weight of 120,000 or even less. The protein encoded by such an RNA would have to contain no more than 100 amino acid residues. Therefore, it is unlikely that the virus (or viroid, as it is frequently called) carries a Gene specifying any protein. Whatever Genetic information is introduced by the viroid, it forces The plant cell to reproduce a large number of copies of the RNA molecule, which can then be transmitted to other plants by aphids or by humans via agricultural tools.

^a Horne R. W., Sci. Am., 208, 48–56 (Jan. 1963).

^b Maramorosch K., Kurstak E. (eds.), Comparative Virology, Academic Press, New York, 1971.

^c Knight C. A., Chemistry of Viruses, 2nd ed., Springer Publ., New York, 1975.

^г Benbow R. M, Mayol R. F., Picchi J. C., Sinsheimer R. L, J Virol, 10, 99—114 (1972)

^д Fraenkel-Conrat H., Sсi. Am., 211, 47—54 (Oct. 1964).

^e Marx J. L., Science, 178, 734 (1972).