WordNet

the outer covering of protein surrounding the nucleic acid of a virus

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/08/25 03:38:53」(JST)

wiki en

Schematic of a Cytomegalovirus

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]

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.^[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]

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.^[8]

Specific shapes

Icosahedral

Icosahedral capsid of an Adenovirus

Although the icosahedral structure is extremely common among viruses, size differences and slight variations exist between virions. Given an asymmetric subunit on a triangular face of a regular icosahedron, with three subunits per face 60 such subunits can be placed in an equivalent manner. Most virions, because of their size, have more than 60 subunits. These variations have been classified on the basis of the quasi-equivalence principle proposed by Donald Caspar and Aaron Klug.^[9]

An icosahedral structure can be regarded as being constructed from 12 pentamers. The number of pentamers is fixed but the number of hexamers can vary.^[10] These shells can be constructed from pentamers and hexamers by minimizing the number T (triangulation number) of nonequivalent locations that subunits occupy, with the T-number adopting the particular integer values 1, 3, 4, 7, 12, 13,...(T = h² + k² + hk, with h, k equal to nonnegative integers). These shells always contain 12 pentamers plus 10 (T-1) hexamers. Although this classification can be applied to the majority of known viruses exceptions are known including the retroviruses where point mutations disrupt the symmetry.^[10]

Prolate

This is an icosahedron elongated along the fivefold axis and is a common arrangement of the heads of bacteriophages. Such a structure is composed of a cylinder with a cap at either end. The cylinder is composed of 10 triangles. The Q number, 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 number.^[11]

Helical

3D model of a helical capsid structure of a virus

Many rod-shaped and filamentous plant viruses have capsids with helical symmetry.^[12] The helical structure can be described as a set of n 1-D molecular helices related by an n-fold axial symmetry.^[13] The helical transformation are classified into two categories: one-dimensional and two-dimensional helical systems.^[13] Creating an entire helical structure relies on a set of translational and rotational matrices which are coded in the protein data bank.^[13] 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.^[14] The most understood helical virus is the tobacco mosaic virus.^[12] 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,^[12] while the influenza A virus has a 28 amino acid tail loop.^{[citation needed]}

Triangulation number

Virus capsid T-numbers

Icosahedral virus capsids are typically assigned a triangulation number (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.^[15]

For example, a purely dodecahedral 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:

=

where 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.^[16]^[17]

For the hexagonal system, the polyhedra have 20T vertices, 30T edges, 10T+2 faces (12 pentagons and 10(T-1) hexagons). For the dual triangular, the vertex and face counts are flipped.

Representation of Viral Capsid T-numbers up to (6,6)
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		Truncated pentagonal hexecontahedron	140	k5sD		Pentakis snub dodecahedron
(3,0)	9	80	dktI		Hexapentatruncated pentakis dodecahedron	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
(4,2)	28
(5,1)	31
(6,0)	36	350	tkt5daD			720	kdkt5daD
(4,3)	37
(5,2)	39
(6,1)	43
(4,4)	48	470	dadkt5daD			960	k5k6akdk5aD
(6,2)	48
(5,3)	49
(5,4)	61
(6,3)	64
(5,5)	75
(6,4)	76
(6,5)	91
(6,6)	108
...

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]

Functions

The functions of the virion are to protect the genome, deliver the genome and interact with the host. The virion 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. Delivery of the genome is also important by specific binding to external receptors of the host cell, transmission of specific signals that induce uncoating of the genome, and induction of fusion with host cell membranes.^[14]

Chemical properties

The viral particle must be metastable so that interactions can be reversed readily when entering and uncoating a new host cell. If it attains the minimum free energy state conformation will be irreversible associated with attachment and entry. Each subunit of the capsid has identical bonding contacts with its neighbors, and the two binding contacts are usually noncovalent. The non-covalent bonding holds the structural unit together. The reversible formation of non-covalent bonds between properly folded subunits leads to error-free assembly and minimizes free energy.^[14]

References

^ Lidmar J, Mirny L, Nelson, DR; Mirny; Nelson (2003). "Virus shapes and buckling transitions in spherical shells". Phys. Rev. E 68 (5): 051910. Bibcode:2003PhRvE..68e1910L. doi:10.1103/PhysRevE.68.051910.
^ Vernizzi G, Olvera de la Cruz M; Olvera de la Cruz (2007). "Faceting ionic shells into icosahedra via electrostatics". Proc. Natl. Acad. Sci. USA 104 (47): 18382–18386. Bibcode:2007PNAS..10418382V. doi:10.1073/pnas.0703431104.
^ Vernizzi G, Sknepnek R, Olvera de la Cruz M; Sknepnek; Olvera de la Cruz M (2011). "Platonic and Archimedean geometries in multicomponent elastic membranes". Proc. Natl. Acad. Sci. USA 108 (11): 4292–4296. Bibcode:2011PNAS..108.4292V. doi:10.1073/pnas.1012872108. PMC 3060260. PMID 21368184.
^ Branden, Carl and Tooze, John (1991). Introduction to Protein Structure. New York: Garland. pp. 161–162. ISBN 0-8153-0270-3.
^ "Virus Structure (web-books.com)".
^ Alberts, Bruce; Bray, Dennis; Lewis, Julian; Raff, Martin; Roberts, Keith; Watson, James D. (1994). Molecular Biology of the Cell (4 ed.). p. 280.
^ Newcomb WW, Homa FL, Brown JC; Homa; Brown (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.
^ 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)
^ Caspar DLD, Klug A (1962) Q. Biol. 27, 1–24.
^ ^a ^b Johnson, J. E. and Speir, J.A. (2009). Desk Encyclopedia of General Virology. Boston: Academic Press. pp. 115–123. ISBN 0-12-375146-2.
^ Casens, S. (2009). Desk Encyclopedia of General Virology. Boston: Academic Press. pp. 167–174. ISBN 0-12-375146-2.
^ ^a ^b ^c Yamada S, Matsuzawa T, Yamada K, Yoshioka S, Ono S, Hishinuma T; Matsuzawa; Yamada; Yoshioka; Ono; Hishinuma (December 1986). "Modified inversion recovery method for nuclear magnetic resonance imaging". Sci Rep Res Inst Tohoku Univ Med 33 (1–4): 9–15. PMID 3629216.
^ ^a ^b ^c Aldrich RA (February 1987). "Children in cities--Seattle's KidsPlace program". Acta Paediatr Jpn 29 (1): 84–90. doi:10.1111/j.1442-200x.1987.tb00013.x. PMID 3144854.
^ ^a ^b ^c Racaniello, Vincent R.; Enquist, L. W. (2008). Principles of Virology, Vol. 1: Molecular Biology. Washington, D.C: ASM Press. ISBN 1-55581-479-4.
^ 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. doi:10.1101/sqb.1962.027.001.005. PMID 14019094.
^ Mannige RV, Brooks CL III; Brooks Cl (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.
^ "T-number index". VIPERdb. La Jolla, CA: The Scripps Research Institute. doi:10.1093/nar/gkn840. Retrieved March 17, 2011.
^ 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.

UpToDate Contents

全文を閲覧するには購読必要です。 To read the full text you will need to subscribe.

1. 成人および思春期の伝染性単核球症 infectious mononucleosis in adults and adolescents
2. 鼻咽頭癌の疫学、病因、および診断 epidemiology etiology and diagnosis of nasopharyngeal carcinoma
3. 急性外陰潰瘍（リプシュッツ潰瘍） acute genital ulceration lipschutz ulcer
4. エプスタインバーウイルス（EBウイルス）感染の臨床的特徴および治療 clinical manifestations and treatment of epstein barr virus infection
5. ヒトパピローマウイルスのライフサイクル、自然史、および免疫学 the life cycle natural history and immunology of human papillomaviruses

English Journal

Oncolytic viral therapy with a combination of HF10, a herpes simplex virus type 1 variant and granulocyte-macrophage colony-stimulating factor for murine ovarian cancer.

Goshima F1, Esaki S, Luo C, Kamakura M, Kimura H, Nishiyama Y.Author information 1Department of Virology, Graduate School of Medicine, Nagoya University, Nagoya, Japan.AbstractOvarian cancer is the most frequent cause of gynecological cancer-related mortality as a majority of patients are diagnosed at an advanced stage with intraperitoneal dissemination because of the absence of initial symptoms. Granulocyte-macrophage colony-stimulating factor (GM-CSF) plays an important role in the maturation of specialized antigen-presenting cells. In this study, we utilized a herpes simplex virus (HSV) amplicon expressing murine GM-CSF combined with HF10 (mGM-CSF amplicon), a highly attenuated HSV type 1 strain functioning as a helper virus to strengthen anti-tumor immune response, for the treatment of ovarian cancer with intraperitoneal dissemination. A mouse ovarian cancer cell line, OV2944-HM-1 (HM-1), was intraperitoneally injected, following which HF10 only or the mGM-CSF amplicon was injected intraperitoneally three times. HF10 injection prolonged survival and decreased intraperitoneal dissemination, but to a lesser extent than the mGM-CSF amplicon. Although HF10 replication was not observed in HM-1 cells, expression of VP5, a late gene coding the major capsid protein of HSV, was detected. Moreover, mGM-CSF production was detected in transfected HM-1 cells. Immunohistochemical staining revealed the infiltration of CD4- and CD8-positive cells into the peritoneal tumor(s). A significantly increased CD4(+) T cell concentration was observed in the spleen. Murine splenic cells after each treatment were stimulated with HM-1 cells, and the strongest immune response was observed in the mice that received mGM-CSF amplicon injections. These results suggested that the mGM-CSF amplicon is a promising agent for the treatment of advanced ovarian cancer with intraperitoneal dissemination.
International journal of cancer. Journal international du cancer.Int J Cancer.2014 Jun 15;134(12):2865-77. doi: 10.1002/ijc.28631. Epub 2013 Dec 2.
Ovarian cancer is the most frequent cause of gynecological cancer-related mortality as a majority of patients are diagnosed at an advanced stage with intraperitoneal dissemination because of the absence of initial symptoms. Granulocyte-macrophage colony-stimulating factor (GM-CSF) plays an important
PMID 24265099

Modification of FP-HIV activity by peptide sequences of GB virus C: A biophysical approach.

Domènech O1, Ortiz A2, Pujol M2, Haro I3, Muñoz M2, Alsina MA2, Prat J2, Busquets MA2, Girona V4.Author information 1Physical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Institute of Nanoscience and Nanotechnology (IN2UB), Avda Joan XXIII, s/n. 08028 Barcelona, Catalonia, Spain.2Physical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Institute of Nanoscience and Nanotechnology (IN2UB), Avda Joan XXIII, s/n. 08028 Barcelona, Catalonia, Spain; Associated Unit to the CSIC Peptides and proteins: Physicochemical properties, Spain.3Unit of Synthesis and Biomedical Applications of Peptides, Department of Biomedical Chemistry (IQAB-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.4Physical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Institute of Nanoscience and Nanotechnology (IN2UB), Avda Joan XXIII, s/n. 08028 Barcelona, Catalonia, Spain; Associated Unit to the CSIC Peptides and proteins: Physicochemical properties, Spain. Electronic address: vgirona@ub.edu.AbstractThree synthetic peptide sequences of 18 amino acid each, corresponding to different fragments of the E2 capsid protein of GB virus C (GBV-C): SDRDTVVELSEWGVPCAT (P45), GSVRFPFHRCGAGPKLTK (P58) and RFPFHRCGAGPKLTKDLE (P59) have been characterized in order to find a relationship between their physicochemical properties and the results obtained in cellular models. Experiments were performed in presence and absence of the HIV fusion peptide (FP-HIV) due to the evidences that GBV-C inhibits AIDS progression. P45 peptide showed lower surface activity and less extent of penetration into 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) (3:2, mol/mol) lipid monolayers than P58 and P59. However, P45 peptide presented higher capacity to inhibit FP-HIV induced cell-cell fusion than the other two sequences. These results were supported by fluorescence anisotropy measurements which indicated that P45 had a significant effect on the inhibition of FP-HIV perturbation of liposomes of the same lipid composition. Finally, atomic force microscopy (AFM) studies have evidenced the modification of the changes induced by the FP-HIV in the morphology of lipid bilayers when P45 was present in the medium.
Biochimica et biophysica acta.Biochim Biophys Acta.2014 May;1838(5):1274-80. doi: 10.1016/j.bbamem.2014.02.001. Epub 2014 Feb 11.
Three synthetic peptide sequences of 18 amino acid each, corresponding to different fragments of the E2 capsid protein of GB virus C (GBV-C): SDRDTVVELSEWGVPCAT (P45), GSVRFPFHRCGAGPKLTK (P58) and RFPFHRCGAGPKLTKDLE (P59) have been characterized in order to find a relationship between their physicoc
PMID 24530897

The impact of hepatitis B virus precore/core gene carboxyl terminal mutations on viral biosynthesis and the host immune response.

Wu JF1, Ni YH, Chen HL, Hsu HY, Chang MH.Author information 1Department of Pediatrics.AbstractBackground. We aimed to elucidate the impact of hepatitis B virus (HBV) precore/core gene mutations on spontaneous hepatitis B e antigen (HBeAg) seroconversion, HBV biosynthesis, and the human immune responses in chronic HBV-infected patients. Methods. We analyzed the HBV precore/core gene sequences by cloning method in 33 chronic HBV-infected patients during the inflammatory phase before spontaneous HBeAg seroconversion. The impact of the most prevalent mutant on HBeAg biosynthesis was assessed by Western blotting and native agarose gel analysis in Huh7 cells, and the human immune responses were assessed by in vitro stimulation of CD3(+)CD8(+) T lymphocytes of chronic HBV-infected subjects. Results. The P135Q and G1896A were the most prevalent mutants before HBeAg seroconversion, acting as markers of HBeAg seroconversion (hazard ratios = 2.75 and 4.50; P = .01 and <.001, respectively). The P135Q mutants displayed decreased HBeAg secretion and HBV capsid molecular weight, while showing increased 22 kD HBeAg proprotein accumulation in Huh7 cells. The P135Q mutant peptide induced less interferon-γ expression in CD3(+)CD8(+) T lymphocytes in HBeAg-negative subjects compared to the wild-type peptide (P = .03). Conclusions. The HBV P135Q mutant emergence during the inflammatory phase was associated with HBeAg seroconversion. It was associated with altered HBV capsid assembly, HBeAg biosynthesis, and reduced human immune responses following HBeAg seroconversion.
The Journal of infectious diseases.J Infect Dis.2014 May;209(9):1374-81. doi: 10.1093/infdis/jit638. Epub 2013 Nov 22.
Background. We aimed to elucidate the impact of hepatitis B virus (HBV) precore/core gene mutations on spontaneous hepatitis B e antigen (HBeAg) seroconversion, HBV biosynthesis, and the human immune responses in chronic HBV-infected patients. Methods. We analyzed the HBV precore/core gene seque
PMID 24273041

Japanese Journal

ブタのサーコウイルス2型カプシド・タンパク質の独特の構造的形状に対する認識が感染転帰を決定する

中根崇
All about swine (44), 16-28, 2014-02
NAID 40020010834

Cysteine Residues in the Major Capsid Protein, Vp1, of the JC Virus Are Important for Protein Stability and Oligomer Formation

Kobayashi Shintaro,Suzuki Tadaki,Igarashi Manabu,Orba Yasuko,Ohtake Noriko,Nagakawa Keita,Niikura Kenichi,Kimura Takashi,Kasamatsu Harumi,Sawa Hirofumi
PLoS One 8(10), e76668, 2013-10-09
… The capsid of the human polyomavirus JC virus (JCV) consists of 72 pentameric capsomeres of a major structural protein, Vp1. … The cysteine residues of the related Vp1 of SV40 are known to contribute to Vp1 folding, pentamer formation, pentamer-pentamer contacts, and capsid stabilization. … These findings suggest that C80 of JCV Vp1 is required for Vp1 stability and pentamer formation, and C247 is involved in capsid assembly in the nucleus. …
NAID 120005350093