Sandbox TMV: Difference between revisions
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<StructureSection load="2tmv" size="400" color="" frame="true" spin="on" Scene='Tobacco_Mosaic_Virus/2tmv_lockwasher_ring/1' align="right" caption="TMV coat protein [[2tmv]]" > | <StructureSection load="2tmv" size="400" color="" frame="true" spin="on" Scene='Tobacco_Mosaic_Virus/2tmv_lockwasher_ring/1' align="right" caption="TMV coat protein [[2tmv]]" > | ||
==Tobacco Mosaic Virus== | ==Tobacco Mosaic Virus== | ||
Tobacco Mosaic Virus (TMV)is a positive-sense single stranded RNA virus that infects plants, especially tobacco and other members of the family Solanaceae. The infection causes characteristic patterns, such as "mosaic"-like mottling and discoloration on the leaves (hence the name). TMV was the first virus to ever be discovered. It is composed of 2130 identical coat protein subunits following the | Tobacco Mosaic Virus (TMV) is a positive-sense single stranded RNA virus that infects plants, especially tobacco and other members of the family Solanaceae. The infection causes characteristic patterns, such as "mosaic"-like mottling and discoloration on the leaves (hence the name). TMV was the first virus to ever be discovered. It is composed of 2130 identical coat protein subunits following the | ||
right-handed helix of an accompanying RNA strand to produce a 300 nm hollow cylinder with an | right-handed helix of an accompanying RNA strand to produce a 300 nm hollow cylinder with an | ||
outer diameter of 18 nm and a 4 nm wide central channel. This here is a protein-nucleic acid interactions in the virus. | outer diameter of 18 nm and a 4 nm wide central channel. This here is a protein-nucleic acid interactions in the virus. | ||
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==Carboxylates== | ==Carboxylates== | ||
Two clusters of acidic amino acids are thought to be important for the disassembly of the <scene name='2tmv/2tmv_lockwasher_ring/1'>helical structure of TMV</scene>. When the virus enters cells, the higher pH and lower calcium levels increase the repulsion of neighboring carboxylates, destabilizing the capsid. This concept was originally proposed by Caspar and subsequently examined by site-directed mutagenesis <ref>Caspar carboxylates: the structural basis of tobamovirus assembly. Wang H, Planchart A, Stubbs G. Biophys. J. 1998, 74, 633-638.</ref>. Several carboxylates were identified including <scene name='2tmv/2tmv_carbox1/2'>Glu50 and ASP77</scene>, which contact each other in the helical stack by <scene name='56/561621/Hydrogen_bond/1'> hydrogen bond</scene> (look closely at the <scene name='2tmv/2tmv_carbox1_closeup/1'>two subunits that overlap</scene> in this lockwasher complex), and a cluster of four acidic amino acids, <scene name='2tmv/2tmv_carbox2/2'>GLU95, GLU97, GLU106 and GLU109</scene>, near the center of the ring. | Two clusters of acidic amino acids are thought to be important for the disassembly of the <scene name='2tmv/2tmv_lockwasher_ring/1'>helical structure of TMV</scene>. When the virus enters cells, the higher pH and lower calcium levels increase the repulsion of neighboring carboxylates, destabilizing the capsid. This concept was originally proposed by Caspar and subsequently examined by site-directed mutagenesis <ref>Caspar carboxylates: the structural basis of tobamovirus assembly. Wang H, Planchart A, Stubbs G. Biophys. J. 1998, 74, 633-638.</ref>. Several carboxylates were identified including <scene name='2tmv/2tmv_carbox1/2'>Glu50 and ASP77</scene>, which contact each other in the helical stack by <scene name='56/561621/Hydrogen_bond/1'> hydrogen bond</scene> (look closely at the <scene name='2tmv/2tmv_carbox1_closeup/1'>two subunits that overlap</scene> in this lockwasher complex), and a cluster of four acidic amino acids, <scene name='2tmv/2tmv_carbox2/2'>GLU95, GLU97, GLU106 and GLU109</scene>, near the center of the ring. | ||
There are phosphate carboxylates in the structure of the virus, the <scene name='56/561621/Phosphate_carboxylates/1'>phosphate-carboxylates</scene> are presented in the color teal in the molecule. They are calcium-binding sites along with the carboxylates. When phosphate-carboxylates bind to calcium it makes the capsid more stable. When the phosphate- carboxylates or the carboxylates are not present then capsid will be unstable, since there will not be anything to bind to calcium. Here is a display of pbd 2TMV showing the virus with <scene name='56/561621/Calcium/3'>calcium</scene> binding to carboxylates in order to stabilize the capsid. | There are phosphate carboxylates in the structure of the virus, the <scene name='56/561621/Phosphate_carboxylates/1'>phosphate-carboxylates</scene> are presented in the color teal in the molecule. They are calcium-binding sites along with the carboxylates. When phosphate-carboxylates bind to calcium it makes the capsid more stable. When the phosphate- carboxylates or the carboxylates are not present then capsid will be unstable, since there will not be anything to bind to calcium. Here is a display of pbd 2TMV showing the virus with <scene name='56/561621/Calcium/3'>calcium</scene> in pink binding to carboxylates in order to stabilize the capsid. | ||
This section complements the article on [http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb109_1.html Tobacco Mosaic Virus] in the | This section complements the article on [http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb109_1.html Tobacco Mosaic Virus] in the | ||
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==Repeating Subunits== | ==Repeating Subunits== | ||
Th repeating basic unit consists of 49 subunits which cover a section of 69 Å of height in three turns of the helix (= a rise of 23 Å per turn). A single strand of RNA is placed between the protein subunits at a distance of 40 Å from the outer diameter. The figure depicts one basic unit. Protein and RNA are shown in spacefill mode, RNA in white, the protein changing from red to blue along the helix. The | Th repeating basic unit consists of 49 subunits which cover a section of 69 Å of height in three turns of the helix (= a rise of 23 Å per turn). A single strand of RNA is placed between the protein subunits at a distance of 40 Å from the outer diameter. The figure depicts one basic unit. Protein and RNA are shown in spacefill mode, RNA in white, the protein changing from red to blue along the helix. The uppermost subunit is marked light brown. Each protein subunit covers three nucleotides of the RNA. | ||
[[Image:TMV-colored.gif|left|200px|thumb|Repeating Subunits of Helical Tobacco Mosaic Virus ]] | [[Image:TMV-colored.gif|left|200px|thumb|Repeating Subunits of Helical Tobacco Mosaic Virus ]] | ||