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Capsid

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.

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

Capsids are broadly classified according to their structure. The majority of the viruses have capsids with either helical or icosahedral structure. Some viruses, such as bacteriophages, have developed more complicated structures due to constraints of elasticity and electrostatics. 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. 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.

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.

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 includes a specialized portal structure at one vertex. Through this portal, viral DNA is translocated into the capsid.

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.

Contents

Icosahedral

Icosahedral capsid of an adenovirus
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 capsomeres in an icosahedral capsid can be classified using the "quasi-equivalence principle" proposed by Donald Caspar and Aaron Klug. 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 h 1 {\displaystyle h\geq 1} and k 0 {\displaystyle k\geq 0} ; 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:

T = h 2 + h k + k 2 {\displaystyle T=h^{2}+h\cdot k+k^{2}}

In this scheme, icosahedral capsids contain 12 pentamers plus 10(T − 1) hexamers. The T-number is representative of the size and complexity of the capsids. 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

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.[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, 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.

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 chaparone protein GroES and able to substitute for it in the assembly of bacteriophage T4 virions during infection. 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.

Helical

3D model of a helical capsid structure of a virus

Many rod-shaped and filamentous plant viruses have capsids with helical symmetry. The helical structure can be described as a set of n 1-D molecular helices related by an n-fold axial symmetry. The helical transformation are classified into two categories: one-dimensional and two-dimensional helical systems. Creating an entire helical structure relies on a set of translational and rotational matrices which are coded in the protein data bank. 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. The most understood helical virus is the tobacco mosaic virus. 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, while the influenza A virus has a 28 amino acid tail loop.

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 forms of natural radiation, 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.

It has been suggested that many viral capsid proteins have evolved on multiple occasions from functionally diverse cellular proteins. 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).

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. The displacement of these ancestral genes between cellular organisms could favor the appearance of new viruses during evolution.

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Capsid
Capsid Language Watch Edit 160 160 Redirected from Virus capsids 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 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 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 includes 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 Contents 1 Specific shapes 1 1 Icosahedral 1 2 Prolate 1 3 Helical 2 Functions 3 Origin and evolution 4 See also 5 References 6 Further reading 7 External linksSpecific shapes EditIcosahedral Edit Icosahedral capsid of an adenovirus 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 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 h 1 displaystyle h geq 1 and k 0 displaystyle k geq 0 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 T h 2 h k k 2 displaystyle T h 2 h cdot k k 2 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 f6 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 Edit 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 chaparone 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 Edit 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 m x r where m is the number of structural units per turn of the helix r 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 EditThe 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 forms of natural radiation 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 EditIt 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 Edit Viruses portal Geodesic polyhedron Goldberg Coxeter construction Fullerene Other buckyballsReferences Edit Asensio MA Morella NM Jakobson CM Hartman EC Glasgow JE Sankaran B et al September 2016 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 Bibcode 2016NanoL 16 5944A doi 10 1021 acs nanolett 6b02948 OSTI 1532201 PMID 27549001 Lidmar J Mirny L Nelson DR November 2003 Virus shapes and buckling transitions in spherical shells Physical Review E 68 5 Pt 1 051910 arXiv cond mat 0306741 Bibcode 2003PhRvE 68e1910L doi 10 1103 PhysRevE 68 051910 PMID 14682823 S2CID 6023873 Vernizzi G Olvera de la Cruz M November 2007 Faceting ionic shells into icosahedra via electrostatics Proceedings of the National Academy of Sciences of the United States of America 104 47 18382 6 Bibcode 2007PNAS 10418382V doi 10 1073 pnas 0703431104 PMC 2141786 PMID 18003933 Vernizzi G Sknepnek R Olvera de la Cruz M March 2011 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 Bibcode 2011PNAS 108 4292V doi 10 1073 pnas 1012872108 PMC 3060260 PMID 21368184 Branden C Tooze J 1991 Introduction to Protein Structure New York Garland pp 161 162 ISBN 978 0 8153 0270 4 Virus Structure web books com Alberts B Bray D Lewis J Raff M Roberts K Watson JD 1994 Molecular Biology of the Cell 4th ed p 280 Newcomb WW Homa FL Brown JC August 2005 Involvement of the portal at an early step in herpes simplex virus capsid assembly Journal of Virology 79 16 10540 6 doi 10 1128 JVI 79 16 10540 10546 2005 PMC 1182615 PMID 16051846 Krupovic M Bamford DH December 2008 Virus evolution how far does the double beta barrel viral lineage extend Nature Reviews Microbiology 6 12 941 8 doi 10 1038 nrmicro2033 PMID 19008892 S2CID 31542714 Forterre P March 2006 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 Bibcode 2006PNAS 103 3669F doi 10 1073 pnas 0510333103 PMC 1450140 PMID 16505372 Khayat R Tang L Larson ET Lawrence CM Young M Johnson JE December 2005 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 doi 10 1073 pnas 0506383102 PMC 1323162 PMID 16357204 Laurinmaki PA Huiskonen JT Bamford DH Butcher SJ December 2005 Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35 Structure 13 12 1819 28 doi 10 1016 j str 2005 08 020 PMID 16338410 Caspar DL Klug A 1962 Physical principles in the construction of regular viruses Cold Spring Harbor Symposia on Quantitative Biology 27 1 24 doi 10 1101 sqb 1962 027 001 005 PMID 14019094 Carrillo Tripp M Shepherd CM Borelli IA Venkataraman S Lander G Natarajan P et al January 2009 VIPERdb2 an enhanced and web API enabled relational database for structural virology Nucleic Acids Research 37 Database issue D436 42 doi 10 1093 nar gkn840 PMC 2686430 PMID 18981051 Archived from the original on 2018 02 11 Retrieved 2011 03 18 Johnson JE Speir JA 2009 Desk Encyclopedia of General Virology Boston Academic Press pp 115 123 ISBN 978 0 12 375146 1 Mannige RV Brooks CL March 2010 Periodic table of virus capsids implications for natural selection and design PLOS ONE 5 3 e9423 Bibcode 2010PLoSO 5 9423M doi 10 1371 journal pone 0009423 PMC 2831995 PMID 20209096 Sgro J Virusworld Institute for Molecular Virology University of Wisconsin Madison Damodaran KV Reddy VS Johnson JE Brooks CL December 2002 A general method to quantify quasi equivalence in icosahedral viruses Journal of Molecular Biology 324 4 723 37 doi 10 1016 S0022 2836 02 01138 5 PMID 12460573 Luque A Reguera D June 2010 The structure of elongated viral capsids Biophysical Journal 98 12 2993 3003 Bibcode 2010BpJ 98 2993L doi 10 1016 j bpj 2010 02 051 PMC 2884239 PMID 20550912 Casjens S 2009 Desk Encyclopedia of General Virology Boston Academic Press pp 167 174 ISBN 978 0 12 375146 1 a b Marusich EI Kurochkina LP Mesyanzhinov VV Chaperones in bacteriophage T4 assembly Biochemistry Mosc 1998 63 4 399 406 a b c Yamada S Matsuzawa T Yamada K Yoshioka S Ono S Hishinuma T December 1986 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 PMID 3629216 a b c Aldrich RA February 1987 Children in cities Seattle s KidsPlace program Acta Paediatrica Japonica 29 1 84 90 doi 10 1111 j 1442 200x 1987 tb00013 x PMID 3144854 S2CID 33065417 Racaniello VR Enquist LW 2008 Principles of Virology Vol 1 Molecular Biology Washington D C ASM Press ISBN 978 1 55581 479 3 Ye Q Guu TS Mata DA Kuo RL Smith B Krug RM Tao YJ 26 December 2012 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 doi 10 1128 mBio 00467 12 PMC 3531806 PMID 23269829 a b Krupovic M Koonin EV March 2017 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 doi 10 1073 pnas 1621061114 PMC 5373398 PMID 28265094 a b Krupovic M Dolja VV Koonin EV July 2019 Origin of viruses primordial replicators recruiting capsids from hosts PDF Nature Reviews Microbiology 17 7 449 458 doi 10 1038 s41579 019 0205 6 PMID 31142823 S2CID 169035711 Jalasvuori M Mattila S Hoikkala V 2015 Chasing the Origin of Viruses Capsid Forming Genes as a Life Saving Preadaptation within a Community of Early Replicators PLOS ONE 10 5 e0126094 Bibcode 2015PLoSO 1026094J doi 10 1371 journal pone 0126094 PMC 4425637 PMID 25955384 Further reading EditWilliams R 1 June 1979 The Geometrical Foundation of Natural Structure A Source Book of Design pp 142 144 Figures 4 49 50 51 Custers of 12 spheres 42 spheres 92 spheres ISBN 978 0 486 23729 9 Pugh A 1 September 1976 Polyhedra A Visual Approach Chapter 6 The Geodesic Polyhedra of R Buckminster Fuller and Related Polyhedra ISBN 978 0 520 02926 2 Almansour I Alhagri M Alfares R Alshehri M Bakhashwain R Maarouf A January 2019 IRAM virus capsid database and analysis resource Database The Journal of Biological Databases and Curation 2019 doi 10 1093 database baz079 PMC 6637973 PMID 31318422 External links EditIRAM Virus Capsid Database and Analysis ResourceWikimedia Commons has media related to Capsid Retrieved from https en wikipedia org w index php title Capsid amp oldid 1049367039, wikipedia, wiki, book,

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