Biology:Capsid

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Short description: Protein shell of a virus

Template:Cs1 config

Schematic of a cytomegalovirus
Illustration of geometric model changing between two possible capsids. A similar change of size has been observed as the result of a single amino-acid mutation[1]

A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The proteins making up the capsid are called capsid proteins or viral coat proteins (VCP). The capsid and inner genome is called the nucleocapsid.

Capsids are broadly classified according to their structure. The majority of the viruses have capsids with either helical or icosahedral[2][3] structure. Some viruses, such as bacteriophages, have developed more complicated structures due to constraints of elasticity and electrostatics.[4] The icosahedral shape, which has 20 equilateral triangular faces, approximates a sphere, while the helical shape resembles the shape of a spring, taking the space of a cylinder but not being a cylinder itself.[5] The capsid faces may consist of one or more proteins. For example, the foot-and-mouth disease virus capsid has faces consisting of three proteins named VP1–3.[6]

Some viruses are enveloped, meaning that the capsid is coated with a lipid membrane known as the viral envelope. The envelope is acquired by the capsid from an intracellular membrane in the virus' host; examples include the inner nuclear membrane, the Golgi membrane, and the cell's outer membrane.[7]

Once the virus has infected a cell and begins replicating itself, new capsid subunits are synthesized using the protein biosynthesis mechanism of the cell. In some viruses, including those with helical capsids and especially those with RNA genomes, the capsid proteins co-assemble with their genomes. In other viruses, especially more complex viruses with double-stranded DNA genomes, the capsid proteins assemble into empty precursor procapsids that include a specialized portal structure at one vertex. Through this portal, viral DNA is translocated into the capsid.[8]

Structural analyses of major capsid protein (MCP) architectures have been used to categorise viruses into lineages. For example, the bacteriophage PRD1, the algal virus Paramecium bursaria Chlorella virus-1 (PBCV-1), mimivirus and the mammalian adenovirus have been placed in the same lineage, whereas tailed, double-stranded DNA bacteriophages (Caudovirales) and herpesvirus belong to a second lineage.[9][10][11][12]

Specific shapes

Icosahedral

Icosahedral capsid of an adenovirus

File:Virus capsid T number.tif The icosahedral structure is extremely common among viruses. The icosahedron consists of 20 triangular faces delimited by 12 fivefold vertexes and consists of 60 asymmetric units. Thus, an icosahedral virus is made of 60N protein subunits. The number and arrangement of capsomeres in an icosahedral capsid can be classified using the "quasi-equivalence principle" proposed by Donald Caspar and Aaron Klug.[13] Like the Goldberg polyhedra, an icosahedral structure can be regarded as being constructed from pentamers and hexamers. The structures can be indexed by two integers h and k, with [math]\displaystyle{ h \ge 1 }[/math] and [math]\displaystyle{ k \ge 0 }[/math]; the structure can be thought of as taking h steps from the edge of a pentamer, turning 60 degrees counterclockwise, then taking k steps to get to the next pentamer. The triangulation number T for the capsid is defined as:

[math]\displaystyle{ T = h^2 + h \cdot k + k^2 }[/math]

In this scheme, icosahedral capsids contain 12 pentamers plus 10(T − 1) hexamers.[14][15] The T-number is representative of the size and complexity of the capsids.[16] Geometric examples for many values of h, k, and T can be found at List of geodesic polyhedra and Goldberg polyhedra.

Many exceptions to this rule exist: For example, the polyomaviruses and papillomaviruses have pentamers instead of hexamers in hexavalent positions on a quasi T = 7 lattice. Members of the double-stranded RNA virus lineage, including reovirus, rotavirus and bacteriophage φ6 have capsids built of 120 copies of capsid protein, corresponding to a T = 2 capsid, or arguably a T = 1 capsid with a dimer in the asymmetric unit. Similarly, many small viruses have a pseudo T = 3 (or P = 3) capsid, which is organized according to a T = 3 lattice, but with distinct polypeptides occupying the three quasi-equivalent positions [17]

T-numbers can be represented in different ways, for example T = 1 can only be represented as an icosahedron or a dodecahedron and, depending on the type of quasi-symmetry, T = 3 can be presented as a truncated dodecahedron, an icosidodecahedron, or a truncated icosahedron and their respective duals a triakis icosahedron, a rhombic triacontahedron, or a pentakis dodecahedron.[18][clarification needed]

Prolate

The prolate structure of a typical head on a bacteriophage

An elongated icosahedron is a common shape for the heads of bacteriophages. Such a structure is composed of a cylinder with a cap at either end. The cylinder is composed of 10 elongated triangular faces. The Q number (or Tmid), which can be any positive integer,[19] specifies the number of triangles, composed of asymmetric subunits, that make up the 10 triangles of the cylinder. The caps are classified by the T (or Tend) number.[20]

The bacterium E. coli is the host for bacteriophage T4 that has a prolate head structure. The bacteriophage encoded gp31 protein appears to be functionally homologous to E. coli chaperone protein GroES and able to substitute for it in the assembly of bacteriophage T4 virions during infection.[21] Like GroES, gp31 forms a stable complex with GroEL chaperonin that is absolutely necessary for the folding and assembly in vivo of the bacteriophage T4 major capsid protein gp23.[21]

Helical

3D model of a helical capsid structure of a virus

Many rod-shaped and filamentous plant viruses have capsids with helical symmetry.[22] The helical structure can be described as a set of n 1-D molecular helices related by an n-fold axial symmetry.[23] The helical transformation are classified into two categories: one-dimensional and two-dimensional helical systems.[23] Creating an entire helical structure relies on a set of translational and rotational matrices which are coded in the protein data bank.[23] Helical symmetry is given by the formula P = μ x ρ, where μ is the number of structural units per turn of the helix, ρ is the axial rise per unit and P is the pitch of the helix. The structure is said to be open due to the characteristic that any volume can be enclosed by varying the length of the helix.[24] The most understood helical virus is the tobacco mosaic virus.[22] The virus is a single molecule of (+) strand RNA. Each coat protein on the interior of the helix bind three nucleotides of the RNA genome. Influenza A viruses differ by comprising multiple ribonucleoproteins, the viral NP protein organizes the RNA into a helical structure. The size is also different; the tobacco mosaic virus has a 16.33 protein subunits per helical turn,[22] while the influenza A virus has a 28 amino acid tail loop.[25]

Functions

The functions of the capsid are to:

  • protect the genome,
  • deliver the genome, and
  • interact with the host.

The virus must assemble a stable, protective protein shell to protect the genome from lethal chemical and physical agents. These include extremes of pH or temperature and proteolytic and nucleolytic enzymes. For non-enveloped viruses, the capsid itself may be involved in interaction with receptors on the host cell, leading to penetration of the host cell membrane and internalization of the capsid. Delivery of the genome occurs by subsequent uncoating or disassembly of the capsid and release of the genome into the cytoplasm, or by ejection of the genome through a specialized portal structure directly into the host cell nucleus.

Origin and evolution

It has been suggested that many viral capsid proteins have evolved on multiple occasions from functionally diverse cellular proteins.[26] The recruitment of cellular proteins appears to have occurred at different stages of evolution so that some cellular proteins were captured and refunctionalized prior to the divergence of cellular organisms into the three contemporary domains of life, whereas others were hijacked relatively recently. As a result, some capsid proteins are widespread in viruses infecting distantly related organisms (e.g., capsid proteins with the jelly-roll fold), whereas others are restricted to a particular group of viruses (e.g., capsid proteins of alphaviruses).[26][27]

A computational model (2015) has shown that capsids may have originated before viruses and that they served as a means of horizontal transfer between replicator communities since these communities could not survive if the number of gene parasites increased, with certain genes being responsible for the formation of these structures and those that favored the survival of self-replicating communities.[28] The displacement of these ancestral genes between cellular organisms could favor the appearance of new viruses during evolution.[27]

See also

References

  1. ↑ "A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle". Nano Letters 16 (9): 5944–50. September 2016. doi:10.1021/acs.nanolett.6b02948. PMID 27549001. Bibcode: 2016NanoL..16.5944A. http://www.escholarship.org/uc/item/0hh6m30h. 
  2. ↑ "Virus shapes and buckling transitions in spherical shells". Physical Review E 68 (5 Pt 1): 051910. November 2003. doi:10.1103/PhysRevE.68.051910. PMID 14682823. Bibcode: 2003PhRvE..68e1910L. 
  3. ↑ "Faceting ionic shells into icosahedra via electrostatics". Proceedings of the National Academy of Sciences of the United States of America 104 (47): 18382–6. November 2007. doi:10.1073/pnas.0703431104. PMID 18003933. Bibcode: 2007PNAS..10418382V. 
  4. ↑ "Platonic and Archimedean geometries in multicomponent elastic membranes". Proceedings of the National Academy of Sciences of the United States of America 108 (11): 4292–6. March 2011. doi:10.1073/pnas.1012872108. PMID 21368184. Bibcode: 2011PNAS..108.4292V. 
  5. ↑ Branden, Carl; Tooze, John (1991). Introduction to Protein Structure. New York: Garland. pp. 161–162. ISBN 978-0-8153-0270-4. 
  6. ↑ "Virus Structure (web-books.com)". http://www.web-books.com/MoBio/Free/Ch1E1.htm. 
  7. ↑ Alberts, Bruce; Bray, Dennis; Lewis, Julian; Raff, Martin; Roberts, Keith; Watson, James D. (1994). Molecular Biology of the Cell (4th ed.). p. 280. https://archive.org/details/molecularbiology00albe. 
  8. ↑ "Involvement of the portal at an early step in herpes simplex virus capsid assembly". Journal of Virology 79 (16): 10540–6. August 2005. doi:10.1128/JVI.79.16.10540-10546.2005. PMID 16051846. 
  9. ↑ "Virus evolution: how far does the double beta-barrel viral lineage extend?". Nature Reviews. Microbiology 6 (12): 941–8. December 2008. doi:10.1038/nrmicro2033. PMID 19008892. 
  10. ↑ "Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain". Proceedings of the National Academy of Sciences of the United States of America 103 (10): 3669–74. March 2006. doi:10.1073/pnas.0510333103. PMID 16505372. Bibcode: 2006PNAS..103.3669F. 
  11. ↑ "Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses". Proceedings of the National Academy of Sciences of the United States of America 102 (52): 18944–9. December 2005. doi:10.1073/pnas.0506383102. PMID 16357204. 
  12. ↑ "Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35". Structure 13 (12): 1819–28. December 2005. doi:10.1016/j.str.2005.08.020. PMID 16338410. 
  13. ↑ "Physical principles in the construction of regular viruses". Cold Spring Harbor Symposia on Quantitative Biology 27: 1–24. 1962. doi:10.1101/sqb.1962.027.001.005. PMID 14019094. 
  14. ↑ "VIPERdb2: an enhanced and web API enabled relational database for structural virology". Nucleic Acids Research 37 (Database issue): D436-42. January 2009. doi:10.1093/nar/gkn840. PMID 18981051. PMC 2686430. http://viperdb.scripps.edu/virus.php. Retrieved 2011-03-18. 
  15. ↑ Desk Encyclopedia of General Virology. Boston: Academic Press. 2009. pp. 115–123. ISBN 978-0-12-375146-1. 
  16. ↑ "Periodic table of virus capsids: implications for natural selection and design". PLOS ONE 5 (3): e9423. March 2010. doi:10.1371/journal.pone.0009423. PMID 20209096. Bibcode: 2010PLoSO...5.9423M. 
  17. ↑ Sgro, Jean-Yves. "Virusworld". Institute for Molecular Virology. University of Wisconsin-Madison. http://www.virology.wisc.edu/virusworld/tri_number.php. 
  18. ↑ "A general method to quantify quasi-equivalence in icosahedral viruses". Journal of Molecular Biology 324 (4): 723–37. December 2002. doi:10.1016/S0022-2836(02)01138-5. PMID 12460573. 
  19. ↑ "The structure of elongated viral capsids". Biophysical Journal 98 (12): 2993–3003. June 2010. doi:10.1016/j.bpj.2010.02.051. PMID 20550912. Bibcode: 2010BpJ....98.2993L. 
  20. ↑ Desk Encyclopedia of General Virology. Boston: Academic Press. 2009. pp. 167–174. ISBN 978-0-12-375146-1. 
  21. ↑ 21.0 21.1 Marusich EI, Kurochkina LP, Mesyanzhinov VV. Chaperones in bacteriophage T4 assembly. Biochemistry (Mosc). 1998;63(4):399-406
  22. ↑ 22.0 22.1 22.2 "Modified inversion recovery method for nuclear magnetic resonance imaging". The Science Reports of the Research Institutes, Tohoku University. Ser. C, Medicine. Tohoku Daigaku 33 (1–4): 9–15. December 1986. PMID 3629216. 
  23. ↑ 23.0 23.1 23.2 "Children in cities--Seattle's KidsPlace program". Acta Paediatrica Japonica 29 (1): 84–90. February 1987. doi:10.1111/j.1442-200x.1987.tb00013.x. PMID 3144854. 
  24. ↑ Principles of Virology, Vol. 1: Molecular Biology. Washington, D.C: ASM Press. 2008. ISBN 978-1-55581-479-3. 
  25. ↑ "Biochemical and structural evidence in support of a coherent model for the formation of the double-helical influenza A virus ribonucleoprotein". mBio 4 (1): e00467–12. 26 December 2012. doi:10.1128/mBio.00467-12. PMID 23269829. 
  26. ↑ 26.0 26.1 "Multiple origins of viral capsid proteins from cellular ancestors". Proceedings of the National Academy of Sciences of the United States of America 114 (12): E2401–E2410. March 2017. doi:10.1073/pnas.1621061114. PMID 28265094. Bibcode: 2017PNAS..114E2401K. 
  27. ↑ 27.0 27.1 "Origin of viruses: primordial replicators recruiting capsids from hosts". Nature Reviews. Microbiology 17 (7): 449–458. July 2019. doi:10.1038/s41579-019-0205-6. PMID 31142823. https://hal-pasteur.archives-ouvertes.fr/pasteur-02557191/file/Krupovic_NRMICRO-19-022_MS_v3_clean.pdf. 
  28. ↑ "Chasing the Origin of Viruses: Capsid-Forming Genes as a Life-Saving Preadaptation within a Community of Early Replicators". PLOS ONE 10 (5): e0126094. 2015. doi:10.1371/journal.pone.0126094. PMID 25955384. Bibcode: 2015PLoSO..1026094J. 

Further reading

External links




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