Capsid

Schematic of a Cytomegalovirus

3D model of Helical capsid structure

For the leaf bug, see Miridae.

A capsid is the protein shell of a virus. It consists of several oligomeric 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 capsid encloses the genetic material of the virus.

Capsids are broadly classified according to their structure. The majority of viruses have capsids with either helical or icosahedral ^[1][2] structure. Some viruses, such as bacteriophages, have developed more complicated structures due to constraints of elasticity and electrostatics.^[3] The icosahedral shape, which has 20 equilateral triangular faces, approximates a sphere, while the helical shape is cylindrical.^[4] 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.^[5]

Icosahedral capsid of an Adenovirus

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; some examples would include the inner nuclear membrane, the golgi membrane, and the cell's outer membrane.^[6]

Once the virus has infected the cell, it will start replicating itself, using the mechanisms of the infected host cell. During this process, new capsid subunits are synthesized according to the genetic material of the virus, using the protein biosynthesis mechanism of the cell. During the assembly process, a portal subunit is assembled at one vertex of the capsid. Through this portal, viral DNA or RNA is transported into the capsid.^[7] The structure and assembly of the herpes virus capsid portal protein has been imaged via cryo-electron microscopy.^[8]

It is this capsid or protein shell that makes protective vaccines a possibility. Structural analyses of major capsid protein (MCP) architectures have been used to categorise viruses into families. For example, the bacteriophage PRD1, Paramecium bursaria Chlorella algal virus, and mammalian adenovirus have been placed in the same family.^[9]

T-number

Virus capsid T-numbers

Icosahedral virus capsids are typically assigned a T-number to describe the relation between the number of pentagons and hexagons i.e. their quasi-symmetry in the capsid shell. The T-number idea was originally developed to explain the quasi-symmetry by Caspar and Klug in 1962.^[10]

For example, a purely icosahedral virus has a T-number of 1 (usually written, T=1) and a truncated icosahedron is assigned T=3. The T-number is calculated by (1) applying a grid to the surface of the virus with coordinates h and k, (2) counting the number of steps between successive pentagons on the virus surface, (3) applying the formula:

$T = h^2 + h \cdot k + k^2$

where $h \ge k$ and h and k are the distances between the successive pentagons on the virus surface for each axis (see figure on right). The larger the T-number the more hexagons are present relative to the pentagons.^[11][12]

Representation of Viral Capsid T-numbers

capsid parameters			hexagon/pentagon system				triangle system
h	k	T	# hex	Conway notation	image	geometric name	# tri	Conway notation	image	geometric name
1	0	1	0	D		Dodecahedron	20	I		Icosahedron
1	1	3	20	tI dkD		Truncated icosahedron	60	kD		Pentakis dodecahedron
2	0	4	30	cD=t5daD		Truncated rhombic triacontahedron	80	k5aD		Pentakis icosidodecahedron
2	1	7	60	dk5sD			140	k5sD		Pentakis snub dodecahedron
3	0	9	80	dktI			180	ktI		Hexapentakis truncated icosahedron
2	2	12	110	dkt5daD			240	kt5daD		Hexapentakis truncated rhombic triacontahedron
3	1	13	120				260
4	0	16	150	ccD			320	dccD
3	2	19	180				380
4	1	21	200	dk5k6stI tk5sD			420	k5k6stI kdk5sD		Hexapentakis snub truncated icosahedron
5	0	25	240				500
3	3	27	260	tktI			540	kdktI
6	0	36	350	tkt5daD			720	kdkt5daD
4	4	48	470	dadkt5daD			960	k5k6akdk5aD
...

T-numbers can be represented in different ways, for example T=1 can only be represented as a 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. ^[13]

References

1. ^ Lidmar J, Mirny L, Nelson, DR (2003). "Virus shapes and buckling transitions in spherical shells". Phys. Rev. E 68 (5): 051910. doi:10.1103/PhysRevE.68.051910. 
2. ^ Vernizzi G, Olvera de la Cruz M (2007). "Faceting ionic shells into icosahedra via electrostatics". Proc. Natl. Acad. Sci. USA 104 (47): 18382–18386. doi:10.1073/pnas.0703431104. 
3. ^ Vernizzi G, Sknepnek R, Olvera de la Cruz M (2011). "Platonic and Archimedean geometries in multicomponent elastic membranes". Proc. Natl. Acad. Sci. USA 108 (11): 4292–4296. doi:10.1073/pnas.1012872108. PMC 3060260. PMID 21368184. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3060260. 
4. ^ Branden, Carl and Tooze, John (1991). Introduction to Protein Structure. New York: Garland. pp. 161–162. ISBN 0-8153-0270-3. 
5. ^ "Virus Structure (web-books.com)". http://www.web-books.com/MoBio/Free/Ch1E1.htm. 
6. ^ Alberts, Bruce; Bray, Dennis; Lewis, Julian; Raff, Martin; Roberts, Keith; Watson, James D. (1994). Molecular Biology of the Cell (4 ed.). pp. 280. 
7. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1182615. 
8. ^ Cardone G, Winkler DC, Trus BL, Cheng N, Heuser JE, Newcomb WW, Brown JC, Steven AC (2007-05-10). "Visualization of the Herpes Simplex Virus Portal in situ by Cryo-electron Tomography". Virology 361 (2): 426–34. doi:10.1016/j.virol.2006.10.047. PMC 1930166. PMID 17188319. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1930166. 
9. ^ Khayat et al. classified Sulfolobus turreted icosahedral virus (STIV) and Laurinmäki et al. classified bacteriophage Bam35 – Proc. Natl. Acad. Sci. U.S.A. 103, 3669 (2006); 102, 18944 (2005); Structure 13, 1819 (2005)
10. ^ Caspar, D. L. D. and Klug, A. (1962). "Physical Principles in the Construction of Regular Viruses". Cold Spring Harbor Symp. Quant. Biol. 27: 1–24. PMID 14019094. 
11. ^ Mannige RV, Brooks CL III (2010). "Periodic Table of Virus Capsids: Implications for Natural Selection and Design". PLoS ONE 5 (3): e9423. doi:10.1371/journal.pone.0009423. 
12. ^ "T-number index". VIPERdb. La Jolla, CA: The Scripps Research Institute. doi:10.1093/nar/gkn840. http://viperdb.scripps.edu/virus.php. Retrieved March 17, 2011. 
13. ^ K. V. Damodaran, Vijay S. Reddy, John E. Johnson and Charles L. Brooks III (2002). "A General Method to Quantify Quasi-equivalence in Icosahedral Viruses". J. Mol. Biol. 324 (4): 723–737. doi:10.1016/S0022-2836(02)01138-5. PMID 12460573.