CHAPTER2 PARTICLES Learning Objectives On completing this chapter,you should be able to: Understand the reasons why viruses encode the proteins to make particles. Identify the main types of virus particle Explain how the virus capsid interacts with both the host cell and virus genome during replication. THE FUNCTION AND FORMATION OF VIRUS PARTICLES Much of the information about virus structures is highly visual in nature and is difficult to represent adequately in print.It is strongly recommended that the reader view the virus structure resources on the accompanying CDAlso,Figure 2.1 illustrates the approximate shapes and sizes of different families of viruses. Why bother to form a virus particle to contain the genome?In fact,some infectious agents,such as viroids,do not (see Chapter 8);however,the fact tha viruses struggle with the genetic and biochemical burden entailed in encoding and assembling the components of a particle indicates that this strategy must offer some positive benefits.At the simplest level,the function of the outer shells of a virus particle is to protect the fragile nucleic acid genome from physical,chemical,or enzymatic damage.After leaving the host cell,the virus enters a hostile environ- ment that would quickly inactivate the unprotected genome.Nucleic acids are sus- ceptible to physical damage,such as shearing by mechanical forces,and to chemical
PARTICLES CHAPTER 2 Learning Objectives On completing this chapter, you should be able to: ■ Understand the reasons why viruses encode the proteins to make particles. ■ Identify the main structural types of virus particle. ■ Explain how the virus capsid interacts with both the host cell and virus genome during replication. THE FUNCTION AND FORMATION OF VIRUS PARTICLES Much of the information about virus structures is highly visual in nature and is difficult to represent adequately in print. It is strongly recommended that the reader view the virus structure resources on the accompanying CD. Also, Figure 2.1 illustrates the approximate shapes and sizes of different families of viruses. Why bother to form a virus particle to contain the genome? In fact, some infectious agents, such as viroids, do not (see Chapter 8); however, the fact that viruses struggle with the genetic and biochemical burden entailed in encoding and assembling the components of a particle indicates that this strategy must offer some positive benefits. At the simplest level, the function of the outer shells of a virus particle is to protect the fragile nucleic acid genome from physical, chemical, or enzymatic damage. After leaving the host cell, the virus enters a hostile environment that would quickly inactivate the unprotected genome. Nucleic acids are susceptible to physical damage, such as shearing by mechanical forces, and to chemical
26 Principles of Molecular Virology DNA viruses Revers Pupovaviridae Parvoviridae Circoviridae Hepadnaviridae Retrovirida RNA viruses Birnaviridae Rhabdoviridae Filoviridae Orthomyxoviridae Bunyaviridae Arenaviridae (Coronavirus) (Torovirus) Coronaviridae Arteriviridae Picornaviridae Caliciviridae Astroviridae Togaviridae Flaviviridae
26 Principles of Molecular Virology Poxviridae Papovaviridae Reoviridae Orthomyxoviridae Arteriviridae Picornaviridae Caliciviridae Astroviridae Togaviridae Flaviviridae Bunyaviridae Arenaviridae Coronaviridae (Coronavirus) (Torovirus) Birnaviridae Paramyxoviridae Filoviridae Rhabdoviridae Bornaviridae Parvoviridae Circoviridae Hepadnaviridae Retroviridae Asfarviridae DNA viruses Reverse-transcribing viruses RNA viruses Herpesviridae Adenoviridae
Particles27 Figure 2.1 A diagram illustrating the shapes and sizes of viruses of families that include animal,zoonotic,and human pathogens.The virions are drawn to scale, but artistic license has been used in representing their structure.In some,the cross sectional structures of capsid and envelope are shown,with a representation of the genome.For the very small virions,only their size and symmetry are depicted. (Courtesy of EA.Murphy,School of Veterinary Medicine,University of California,Davis.) modification by ultraviolet light(sunlight).The natural environment is heavily laden with nucleases either derived from dead or leaky cells or deliberately secreted by vertebrates as defence against infection.In viruses with single-stranded genomes, the breaking of a single phosphodiester bond or chemical modification of one nucleotide is sufficient to inactivate that virus particle,making replication of the genome impossible.How is protection against this achieved?The protein subunits in a virus capsid are multiplyredundant(i.e.,present in many copies per particle) Damage to one or more subunits may render that particular subunit nonfunctional. but rarely does limited damage destroy the infectivity of the entire particle.This makes the capsid an effective barrier. The protein shells surrounding virus particles are very tough,about as strong as a hard plastic such as Perspex"or Plexiglas",although,of course,they are only a billionth of a metre or so in diameter;however,they are also elastic and are able to deform by up to a third without breaking.This combination of strength,flex- ibility,and small size means that it is physically difficult (although not impossible) to break open virus particles by physical pressure. The outer surface of the virus is also responsible for recognition of and the first interaction with the host cell.Initially,this takes the form of binding of a spe- cific virus-attachment protein to a cellular receptor molecule.However,the capsid also has a role to play in initiating infection by delivering the genome in a form in which it can interact with the host cell.In some cases,this is a simple process that consists only of dumping the genome into the cytoplasm of the cell. In other cases,this stage is much more complex;for example,retroviruses carry out extensive modifications to the virus genome while it is still inside the parti- cle,converting two molecules of single-stranded RNA to one molecule of double- stranded DNA before delivering it to the cell nucleus.Hence,the role of the capsid is vital in allowing viruses to establish an infection. To form infectious particles,viruses must overcome two fundamental problems First,they must assemble the particle utilizing the information available from the components that make up the particle itself.Second,virus particles form regular geometric shapes,even though the proteins from which they are made are irreg ularly shaped.How do these simple organisms solve these difficulties?The solu- tions to both problems lie in the rules of symmetry
modification by ultraviolet light (sunlight).The natural environment is heavily laden with nucleases either derived from dead or leaky cells or deliberately secreted by vertebrates as defence against infection. In viruses with single-stranded genomes, the breaking of a single phosphodiester bond or chemical modification of one nucleotide is sufficient to inactivate that virus particle, making replication of the genome impossible. How is protection against this achieved? The protein subunits in a virus capsid are multiplyredundant (i.e., present in many copies per particle). Damage to one or more subunits may render that particular subunit nonfunctional, but rarely does limited damage destroy the infectivity of the entire particle. This makes the capsid an effective barrier. The protein shells surrounding virus particles are very tough, about as strong as a hard plastic such as Perspex® or Plexiglas®, although, of course, they are only a billionth of a metre or so in diameter; however, they are also elastic and are able to deform by up to a third without breaking. This combination of strength, flexibility, and small size means that it is physically difficult (although not impossible) to break open virus particles by physical pressure. The outer surface of the virus is also responsible for recognition of and the first interaction with the host cell. Initially, this takes the form of binding of a specific virus-attachment protein to a cellular receptor molecule. However, the capsid also has a role to play in initiating infection by delivering the genome in a form in which it can interact with the host cell. In some cases, this is a simple process that consists only of dumping the genome into the cytoplasm of the cell. In other cases, this stage is much more complex; for example, retroviruses carry out extensive modifications to the virus genome while it is still inside the particle, converting two molecules of single-stranded RNA to one molecule of doublestranded DNA before delivering it to the cell nucleus. Hence, the role of the capsid is vital in allowing viruses to establish an infection. To form infectious particles, viruses must overcome two fundamental problems. First, they must assemble the particle utilizing the information available from the components that make up the particle itself. Second, virus particles form regular geometric shapes, even though the proteins from which they are made are irregularly shaped. How do these simple organisms solve these difficulties? The solutions to both problems lie in the rules of symmetry. Particles 27 Figure 2.1 A diagram illustrating the shapes and sizes of viruses of families that include animal, zoonotic, and human pathogens. The virions are drawn to scale, but artistic license has been used in representing their structure. In some, the crosssectional structures of capsid and envelope are shown, with a representation of the genome. For the very small virions, only their size and symmetry are depicted. (Courtesy of F.A. Murphy, School of Veterinary Medicine, University of California, Davis.)
23 Principles of Molecular Virology CAPSID SYMMETRY AND VIRUS ARCHITECTURE It is possible to imagine a virus particle,the outer shell of which(the capsid)con- sists of a single,hollow protein molecule,which,as it folds to assume its mature conformation,traps the virus genome inside.In practice,this arrangement cannot occur,for the following reason.The triplet nature of the genetic code means that three nucleotides (or base pairs,in the case of viruses with double-stranded genomes)are necessary to encode one amino acid.Viruses cannot,of course,utilize an alternative,more economical,genetic code because this could not be deciphered by the host cell.Because the approximate molecular weight of a nucleotide triplet is 1000 and the average molecular weight of a single amino acid is 150,a nucleic acid can only encode a protein that is at most 15%of its own weight;therefore. virus capsids must be made up of multiple protein molecules(subunit construction), and viruses must overcome the problem of how these subunits are arranged. In 1957,Fraenkel-Conrat and Williams showed that,when mixtures of puri- fied tobacco mosaic virus (TMV)RNA and coat protein were incubated together, virus particles formed.The discovery that virus particles could form spontaneously from purified subunits without any extraneous information indicated that the particle was in the free energy minimum state and was therefore the favoured structure of the components.This stability is an important feature of the virus par- ticle.Although some viruses are very fragile and unable to survive outside the pro- tected host cell environment,many are able to persist for long periods,in some cases for years The forces that drive the assembly of virus particles include hydrophobic and electrostatic interactions-only rarely are covalent bonds involved in holding together the multiple subunits.In biological terms,this means that protein-protein, protein-nucleic acid,and protein-lipid interactions are used.It would be fair to say that the sublety of these is not filly understood for the majority of virus structures,but we now have a good understanding of general principles and repeated structural motifs that appear to govern the construction of dive rse,un- related viruses.These are discussed below under the two main classes of virus structures:helical and icosahedral symmetry. Helical Capsids Tobacco mosaic virus is representative of one of the two major structural classes seen in viruses,those with helical symmetry.The simplest way to arrange multiple, identical protein subunits is to use rotational symmetry and to arrange the irreg ularly shaped proteins around the circumference of a circle to form a disk.Multi- ple disks can then be stacked on top of one another to form a cylinder,with the virus genome coated by the protein shell or contained in the hollow centre of
CAPSID SYMMETRY AND VIRUS ARCHITECTURE It is possible to imagine a virus particle, the outer shell of which (the capsid) consists of a single, hollow protein molecule, which, as it folds to assume its mature conformation, traps the virus genome inside. In practice, this arrangement cannot occur, for the following reason. The triplet nature of the genetic code means that three nucleotides (or base pairs, in the case of viruses with double-stranded genomes) are necessary to encode one amino acid.Viruses cannot, of course, utilize an alternative, more economical, genetic code because this could not be deciphered by the host cell. Because the approximate molecular weight of a nucleotide triplet is 1000 and the average molecular weight of a single amino acid is 150, a nucleic acid can only encode a protein that is at most 15% of its own weight; therefore, virus capsids must be made up of multiple protein molecules (subunit construction), and viruses must overcome the problem of how these subunits are arranged. In 1957, Fraenkel-Conrat and Williams showed that, when mixtures of puri- fied tobacco mosaic virus (TMV) RNA and coat protein were incubated together, virus particles formed.The discovery that virus particles could form spontaneously from purified subunits without any extraneous information indicated that the particle was in the free energy minimum state and was therefore the favoured structure of the components.This stability is an important feature of the virus particle. Although some viruses are very fragile and unable to survive outside the protected host cell environment, many are able to persist for long periods, in some cases for years. The forces that drive the assembly of virus particles include hydrophobic and electrostatic interactions—only rarely are covalent bonds involved in holding together the multiple subunits. In biological terms, this means that protein–protein, protein–nucleic acid, and protein–lipid interactions are used. It would be fair to say that the subtlety of these interactions is not fully understood for the majority of virus structures, but we now have a good understanding of general principles and repeated structural motifs that appear to govern the construction of diverse, unrelated viruses. These are discussed below under the two main classes of virus structures: helical and icosahedral symmetry. Helical Capsids Tobacco mosaic virus is representative of one of the two major structural classes seen in viruses, those with helical symmetry.The simplest way to arrange multiple, identical protein subunits is to use rotational symmetry and to arrange the irregularly shaped proteins around the circumference of a circle to form a disk. Multiple disks can then be stacked on top of one another to form a cylinder, with the virus genome coated by the protein shell or contained in the hollow centre of 28 Principles of Molecular Virology
Particles29 the cylinder.Denaturation and phase-transition studies of TMV suggest that this is the form the particle takes (see Chapter 1). Closer exan nation of the TMV particle by x-ray crystallography reveals tha the structure of the capsid actually consists of a helix rather than a pile of stacked disks.A helix can be defined mathematically by two parameters:its amplitude (diameter)and pitch (the distance covered by each complete turn of the helix) (Figure 2.2).Helices are rather simple structures formed by stacking repeated com- nents with a constant relationship (amplitude and pitch)to one another.Note that,if this simple constraint is broken,a spiral forms rather than a helix and thi spiral is quite unsuitable for containing a virus genome.In terms of individual protein subunits,helices are described by the number of subunits per turn of the helix,u,and the axial rise per subunit,p;therefore,the pitch of the helix,P,is equal to: P=μ×P For TMV.16.3 that is,there are 163 coat protein molecules per helix tu and p=0.14 nm.Therefore,the pitch of the TMV helix is 16.3 x 0.14 =2.28 nm. chhei 162 (subunits/helix turn) 王4bun Figure 2.2 Tobacco mosaic virus (TMV)has a capsid consisting of many mole cules of a single-coat protein arranged in a constant relationship,forming a helix with a pitch of 2.28 A
the cylinder. Denaturation and phase-transition studies of TMV suggest that this is the form the particle takes (see Chapter 1). Closer examination of the TMV particle by x-ray crystallography reveals that the structure of the capsid actually consists of a helix rather than a pile of stacked disks. A helix can be defined mathematically by two parameters: its amplitude (diameter) and pitch (the distance covered by each complete turn of the helix) (Figure 2.2). Helices are rather simple structures formed by stacking repeated components with a constant relationship (amplitude and pitch) to one another. Note that, if this simple constraint is broken, a spiral forms rather than a helix and this spiral is quite unsuitable for containing a virus genome. In terms of individual protein subunits, helices are described by the number of subunits per turn of the helix, m, and the axial rise per subunit, p; therefore, the pitch of the helix, P, is equal to: P =m¥ p For TMV, m = 16.3; that is, there are 16.3 coat protein molecules per helix turn, and p = 0.14 nm.Therefore, the pitch of the TMV helix is 16.3 ¥ 0.14 = 2.28 nm. Particles 29 Pitch of helix P 2.28 nm p0.14 nm (axial rise/subunit) m 16.3 (subunits/helix turn) Figure 2.2 Tobacco mosaic virus (TMV) has a capsid consisting of many molecules of a single-coat protein arranged in a constant relationship, forming a helix with a pitch of 2.28 Å