Editing Capsid

{{Short description|Protein shell of a virus}}
{{cs1 config|name-list-style=vanc}}[[Image:CMVschema.svg|thumb|right|Schematic of a [[cytomegalovirus]]]]

[[File:Illustration of the Caspar-Klug model for viruses (or "Goldberg Polyhedra" or "Geodesic domes" or "Fullerenes").gif|thumb|right|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<ref>{{cite journal | vauthors = Asensio MA, Morella NM, Jakobson CM, Hartman EC, Glasgow JE, Sankaran B, Zwart PH, Tullman-Ercek D | display-authors = 6 | title = A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle | journal = Nano Letters | volume = 16 | issue = 9 | pages = 5944–50 | date = September 2016 | pmid = 27549001 | doi = 10.1021/acs.nanolett.6b02948 | url = http://www.escholarship.org/uc/item/0hh6m30h | bibcode = 2016NanoL..16.5944A | osti = 1532201 | s2cid = 16706951 }}</ref>]] 

A '''capsid''' is the protein shell of a [[virus]], enclosing its [[genetic material]]. It consists of several [[oligomer]]ic (repeating) structural subunits made of [[protein]] called [[Protomer (structural biology)|protomer]]s. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called [[capsomere]]s. The proteins making up the capsid are called '''capsid proteins''' or '''viral coat proteins''' ('''VCP'''). The virus genomic component inside the capsid, along with occasionally present [[virus core protein]], is called the '''virus core'''. The capsid and core together are referred to as a '''nucleocapsid''' (cf. also [[virion]]).

Capsids are broadly classified according to their structure.  The majority of the viruses have capsids with either [[Helix|helical]] or [[icosahedral]]<ref>{{cite journal | vauthors = Lidmar J, Mirny L, Nelson DR | s2cid = 6023873 | title = Virus shapes and buckling transitions in spherical shells | journal = Physical Review E | volume = 68 | issue = 5 Pt 1 | pages = 051910 | date = November 2003 | pmid = 14682823 | doi = 10.1103/PhysRevE.68.051910 | arxiv = cond-mat/0306741 | bibcode = 2003PhRvE..68e1910L }}</ref><ref>{{cite journal | vauthors = Vernizzi G, Olvera de la Cruz M | title = Faceting ionic shells into icosahedra via electrostatics | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 47 | pages = 18382–6 | date = November 2007 | pmid = 18003933 | pmc = 2141786 | doi = 10.1073/pnas.0703431104 | bibcode = 2007PNAS..10418382V | doi-access = free }}</ref> structure.  Some viruses, such as [[bacteriophage]]s, have developed more complicated structures due to constraints of elasticity and electrostatics.<ref>{{cite journal | vauthors = Vernizzi G, Sknepnek R, Olvera de la Cruz M | title = Platonic and Archimedean geometries in multicomponent elastic membranes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 11 | pages = 4292–6 | date = March 2011 | pmid = 21368184 | pmc = 3060260 | doi = 10.1073/pnas.1012872108 | bibcode = 2011PNAS..108.4292V | doi-access = free }}</ref>  The icosahedral shape, which has 20 equilateral triangular faces, approximates a [[sphere]], while the helical shape resembles the shape of a [[Spring (device)|spring]], taking the space of a cylinder but not being a cylinder itself.<ref>{{cite book|title=Introduction to Protein Structure| last1 = Branden | first1 = Carl | last2 = Tooze | first2 = John |year=1991|pages=161–162|isbn=978-0-8153-0270-4|publisher=Garland|location=New York}}</ref>  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.<ref>{{cite web|url=http://www.web-books.com/MoBio/Free/Ch1E1.htm|title=Virus Structure (web-books.com)|access-date=2007-07-10|archive-date=2021-02-07|archive-url=https://web.archive.org/web/20210207140236/http://www.web-books.com/MoBio/Free/Ch1E1.htm|url-status=dead}}</ref>

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 apparatus|Golgi]] membrane, and the cell's outer [[cell membrane|membrane]].<ref>{{cite book|title=Molecular Biology of the Cell|url=https://archive.org/details/molecularbiology00albe|url-access=registration|edition=4th|page=[https://archive.org/details/molecularbiology00albe/page/280 280]|year=1994|last1=Alberts|first1=Bruce|last2=Bray|first2=Dennis|last3=Lewis|first3=Julian|last4=Raff|first4=Martin|last5=Roberts|first5=Keith|last6=Watson|first6=James D. |author-link6=James D. Watson}}</ref>

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.<ref name="pmid16051846">{{cite journal | vauthors = Newcomb WW, Homa FL, Brown JC | title = Involvement of the portal at an early step in herpes simplex virus capsid assembly | journal = Journal of Virology | volume = 79 | issue = 16 | pages = 10540–6 | date = August 2005 | pmid = 16051846 | pmc = 1182615 | doi = 10.1128/JVI.79.16.10540-10546.2005 }}</ref>

Structural analyses of major capsid protein (MCP) architectures have been used to categorise viruses into lineages. For example, the bacteriophage PRD1, the algal virus ''[[Chlorovirus|Paramecium bursaria Chlorella virus-1]]'' (PBCV-1), [[mimivirus]] and the mammalian [[Adenoviridae|adenovirus]] have been placed in the same lineage, whereas tailed, double-stranded DNA bacteriophages (''[[Caudovirales]]'') and herpesvirus belong to a second lineage.<ref>{{cite journal | vauthors = Krupovic M, Bamford DH | s2cid = 31542714 | title = Virus evolution: how far does the double beta-barrel viral lineage extend? | journal = Nature Reviews. Microbiology | volume = 6 | issue = 12 | pages = 941–8 | date = December 2008 | pmid = 19008892 | doi = 10.1038/nrmicro2033 }}</ref><ref name="pmid16505372">{{cite journal | vauthors = Forterre P | title = Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 10 | pages = 3669–74 | date = March 2006 | pmid = 16505372 | pmc = 1450140 | doi = 10.1073/pnas.0510333103 | bibcode = 2006PNAS..103.3669F | doi-access = free }}</ref><ref name="pmid16357204">{{cite journal | vauthors = Khayat R, Tang L, Larson ET, Lawrence CM, Young M, Johnson JE | title = Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 52 | pages = 18944–9 | date = December 2005 | pmid = 16357204 | pmc = 1323162 | doi = 10.1073/pnas.0506383102 | doi-access = free }}</ref><ref name="pmid16338410">{{cite journal | vauthors = Laurinmäki PA, Huiskonen JT, Bamford DH, Butcher SJ | title = Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35 | journal = Structure | volume = 13 | issue = 12 | pages = 1819–28 | date = December 2005 | pmid = 16338410 | doi = 10.1016/j.str.2005.08.020 | doi-access = free }}</ref>

==Specific shapes==

===Icosahedral===
[[File:Adenovirus 3D schematic.png|thumb|Icosahedral capsid of an [[Adenoviridae|adenovirus]]]]
[[File:Virus capsid T number.tif|thumb|right|Virus capsid T-numbers]]
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 [[capsomere]]s in an icosahedral capsid can be classified using the "quasi-equivalence principle" proposed by [[Donald Caspar]] and [[Aaron Klug]].<ref name=Caspar1962>{{cite journal | vauthors = Caspar DL, Klug A | title = Physical principles in the construction of regular viruses | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 27 | pages = 1–24 | year = 1962 | pmid = 14019094 | doi = 10.1101/sqb.1962.027.001.005 }}</ref> 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>h \ge 1</math> and <math>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> T = h^2 + h \cdot k + k^2 </math>
In this scheme, icosahedral capsids contain 12 pentamers plus 10(''T''&nbsp;−&nbsp;1) hexamers.<ref>{{cite journal | vauthors = Carrillo-Tripp M, Shepherd CM, Borelli IA, Venkataraman S, Lander G, Natarajan P, Johnson JE, Brooks CL, Reddy VS | display-authors = 6 | title = VIPERdb2: an enhanced and web API enabled relational database for structural virology | journal = Nucleic Acids Research | volume = 37 | issue = Database issue | pages = D436-42 | date = January 2009 | pmid = 18981051 | pmc = 2686430 | doi = 10.1093/nar/gkn840 | url = http://viperdb.scripps.edu/virus.php | access-date = 2011-03-18 | archive-date = 2018-02-11 | archive-url = https://web.archive.org/web/20180211191026/http://viperdb.scripps.edu/virus.php | url-status = dead }}</ref><ref name="Johnson, J. E. and Speir, J.A. 2009 115–123">{{cite book | vauthors = Johnson JE, Speir JA |title=Desk Encyclopedia of General Virology|publisher=Academic Press |location=Boston |year=2009 |pages=115–123 |isbn=978-0-12-375146-1}}</ref> The ''T''-number is representative of the size and complexity of the capsids.<ref>{{cite journal | vauthors = Mannige RV, Brooks CL | title = Periodic table of virus capsids: implications for natural selection and design | journal = PLOS ONE | volume = 5 | issue = 3 | pages = e9423 | date = March 2010 | pmid = 20209096 | pmc = 2831995 | doi = 10.1371/journal.pone.0009423 | bibcode = 2010PLoSO...5.9423M | doi-access = free }}</ref> 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 [[polyomavirus]]es 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 <ref>{{cite web | first = Jean-Yves | last = Sgro | work = Institute for Molecular Virology | publisher = University of Wisconsin-Madison | title=Virusworld | url=http://www.virology.wisc.edu/virusworld/tri_number.php }}</ref>

===Prolate===
[[Image:PhageExterior.svg|thumb|left|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 T<sub>mid</sub>), which can be any positive integer,<ref>{{cite journal | vauthors = Luque A, Reguera D | title = The structure of elongated viral capsids | journal = Biophysical Journal | volume = 98 | issue = 12 | pages = 2993–3003 | date = June 2010 | pmid = 20550912 | pmc = 2884239 | doi = 10.1016/j.bpj.2010.02.051 | bibcode = 2010BpJ....98.2993L }}</ref> 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 T<sub>end</sub>) number.<ref>{{cite book | vauthors = Casjens S |title=Desk Encyclopedia of General Virology|publisher=Academic Press |location=Boston |year=2009 |pages=167–174 |isbn=978-0-12-375146-1}}</ref>{{clear}}

The bacterium ''E. coli'' is the host for [[Escherichia virus T4|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.<ref name = Marusich1998>Marusich EI, Kurochkina LP, Mesyanzhinov VV. Chaperones in bacteriophage T4 assembly. Biochemistry (Mosc). 1998;63(4):399-406</ref> Like GroES, gp31 forms a stable complex with [[GroEL]] [[chaperone (protein)|chaperonin]] that is absolutely necessary for the folding and assembly ''in vivo'' of the bacteriophage T4 major capsid protein gp23.<ref name = Marusich1998/>

===Helical===
[[File:Helical capsid with RNA.png|thumb|left|3D model of a helical capsid structure of a virus]]

Many rod-shaped and filamentous plant viruses have capsids with [[Symmetry (geometry)#Helical symmetry|helical symmetry]].<ref name="autogenerated9">{{cite journal | vauthors = Yamada S, Matsuzawa T, Yamada K, Yoshioka S, Ono S, Hishinuma T | title = Modified inversion recovery method for nuclear magnetic resonance imaging | journal = The Science Reports of the Research Institutes, Tohoku University. Ser. C, Medicine. Tohoku Daigaku | volume = 33 | issue = 1–4 | pages = 9–15 | date = December 1986 | pmid = 3629216 }}</ref> The helical structure can be described as a set of ''n'' 1-D molecular helices related by an ''n''-fold axial symmetry.<ref name="autogenerated84"/> The helical transformation are classified into two categories: one-dimensional and two-dimensional helical systems.<ref name="autogenerated84">{{cite journal | vauthors = Aldrich RA | title = Children in cities--Seattle's KidsPlace program | journal = Acta Paediatrica Japonica | volume = 29 | issue = 1 | pages = 84–90 | date = February 1987 | pmid = 3144854 | doi = 10.1111/j.1442-200x.1987.tb00013.x | s2cid = 33065417 }}</ref> Creating an entire helical structure relies on a set of translational and rotational matrices which are coded in the protein data bank.<ref name="autogenerated84"/> Helical symmetry is given by the formula ''P''&nbsp;=&nbsp;''μ''&nbsp;x&nbsp;''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.<ref name="virology">{{cite book | vauthors = Racaniello VR, Enquist LW |title=Principles of Virology, Vol. 1: Molecular Biology |publisher=ASM Press |location=Washington, D.C. |year=2008 |isbn=978-1-55581-479-3 }}</ref> The most understood helical virus is the tobacco mosaic virus.<ref name="autogenerated9"/> The virus is a single molecule of (+) strand RNA.  Each coat protein on the interior of the helix binds 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,<ref name="autogenerated9"/> while the influenza A virus has a 28 amino acid tail loop.<ref>{{cite journal|vauthors=Ye Q, Guu TS, Mata DA, Kuo RL, Smith B, Krug RM, Tao YJ|date=26 December 2012|title=Biochemical and structural evidence in support of a coherent model for the formation of the double-helical influenza A virus ribonucleoprotein|journal=mBio|volume=4|issue=1|pages=e00467–12|doi=10.1128/mBio.00467-12|pmc=3531806|pmid=23269829}}</ref>

==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 [[enzyme]]s.  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.<ref name=Krupovic2017>{{cite journal | vauthors = Krupovic M, Koonin EV | title = Multiple origins of viral capsid proteins from cellular ancestors | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 114 | issue = 12 | pages = E2401–E2410 | date = March 2017 | pmid = 28265094 | pmc = 5373398 | doi = 10.1073/pnas.1621061114 | bibcode = 2017PNAS..114E2401K | doi-access = free }}</ref> 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).<ref name=Krupovic2017 /><ref name=Krupovic2019 />

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.<ref>{{cite journal | vauthors = Jalasvuori M, Mattila S, Hoikkala V | title = Chasing the Origin of Viruses: Capsid-Forming Genes as a Life-Saving Preadaptation within a Community of Early Replicators | journal = PLOS ONE | volume = 10 | issue = 5 | pages = e0126094 | date = 2015 | pmid = 25955384 | pmc = 4425637 | doi = 10.1371/journal.pone.0126094 | bibcode = 2015PLoSO..1026094J | doi-access = free }}</ref> The displacement of these ancestral genes between cellular organisms could favor the appearance of new viruses during evolution.<ref name=Krupovic2019 >{{cite journal | vauthors = Krupovic M, Dolja VV, Koonin EV | s2cid = 169035711 | title = Origin of viruses: primordial replicators recruiting capsids from hosts | journal = Nature Reviews. Microbiology | volume = 17 | issue = 7 | pages = 449–458 | date = July 2019 | pmid = 31142823 | doi = 10.1038/s41579-019-0205-6 | url = https://hal-pasteur.archives-ouvertes.fr/pasteur-02557191/file/Krupovic_NRMICRO-19-022_MS_v3_clean.pdf }}</ref>

== See also==
{{Portal|Viruses}}
* [[Geodesic polyhedron]]
* [[Goldberg–Coxeter construction]]
* [[Fullerene#Other buckyballs]]

== References ==
{{Reflist}}

== Further reading ==
{{Refbegin}}
* {{cite book |last=Williams |first=Robert |author-link=Robert Williams (geometer) |date=1 June 1979 |title=The Geometrical Foundation of Natural Structure: A Source Book of Design |publisher=Dover Publications |at=pp.&nbsp;142–144, Figures 4-49, 50, 51: Custers of 12 spheres, 42 spheres, 92 spheres |isbn=978-0-486-23729-9}}
* {{cite book |last=Pugh |first=Antony |date=1 September 1976 |title=Polyhedra: A Visual Approach |publisher=University of California Press |at=Chapter 6. The Geodesic Polyhedra of R. Buckminster Fuller and Related Polyhedra |isbn=978-0-520-02926-2}}
* {{cite journal | vauthors = Almansour I, Alhagri M, Alfares R, Alshehri M, Bakhashwain R, Maarouf A | title = IRAM: virus capsid database and analysis resource | journal = Database: The Journal of Biological Databases and Curation | volume = 2019 | date = January 2019 | pmid = 31318422 | pmc = 6637973 | doi = 10.1093/database/baz079 }}
{{Refend}}

== External links ==
* [https://iram.iau.edu.sa/#/ IRAM-Virus Capsid Database and Analysis Resource] {{Webarchive|url=https://web.archive.org/web/20191023183438/https://iram.iau.edu.sa/#/ |date=2019-10-23 }}

{{Commons category}}

{{Virus topics}}
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[[Category:Virology]]
[[Category:Protein complexes]]