Sandbox122: Difference between revisions

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[[Image:1G28.pdb b.jpg | thumb]]

~~====~~STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3~~====~~{{STRUCTURE_1g28| PDB=1g28 | SCENE= }}

'''STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3'''{{STRUCTURE_1g28| PDB=1g28 | SCENE= }}

'''Phototropin''' is a blue light receptor involved in the phototropism (it is a phenomenon which is growth directed by light).This is a transmembrane protein present on the top of coleoptile.

This protein is a dimer (phot1 and phot2) and each subunit contains three domains : LOV1, '''LOV2''' (light,oxygen or voltage) domains and a kinase domain.

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==Structure of LOV2==

The structure of a flaving domain, LOV2, from the chimeric phototropin photoreceptor PHY3, has been determined thanks to X-Ray diffraction. This domain is composed by four chains which are identical and called A, B, C and D. It's a L-polypeptide which weight 50552,99 Da. Each chains has 104 aminoacids and possess four <scene name='Sandbox122/Helix_of_the_lov2_domain/1'>helix</scene> (28 residues which represents 26%) and six B <scene name='Sandbox122/Beta_sheets_of_lov2/1'>sheets</scene> (37 residues which represent 35%).

The structure of a flaving domain, LOV2, from the chimeric phototropin photoreceptor PHY3, has been determined thanks to X-Ray diffraction. This domain is composed by four chains which are identical and called A, B, C and D. It's a L-polypeptide which weight is 50552,99 Da. Each chains has 104 aminoacids and possess four <scene name='Sandbox122/Helix_of_the_lov2_domain/1'>helix</scene> (28 residues which represents 26%) and six B <scene name='Sandbox122/Beta_sheets_of_lov2/1'>sheets</scene> (37 residues which represent 35%).

==Interaction between FMN et LOV2 domain==

The <scene name='Sandbox122/Fmn_ligand/1'>FMN</scene> (Flavin MonoNucleotide) is the ligand which is responsible for the light absorption. A single molecule of FMN is bound non convalently in the interior of LOV2 domain. FMN is stabilized thanks to hydrogen bonds, Van der Waals and electrostatic interactions. For example, atoms <scene name='Sandbox122/Arg_983/1'>R983</scene> and <scene name='Sandbox122/Arg_963/1'>R967</scene>(alpha C helix) create ionic bond with phosphate group of FMN. <scene name='Sandbox122/Q970/1'>Q970</scene>, <scene name='Sandbox122/N965/1'>N965</scene> , <scene name='Sandbox122/N998/1'>N988</scene>, <scene name='Sandbox122/N1008/1'>N1008</scene> (alpha A helix and beta-strand C, D and E) aminoacid make some electrostatic interaction which stabilize FMN. Some results indicate that the majority of the FMN in the LOV2 domain exist in the protonated form. Researcher propose a reaction mechanism that involves excited-state proton transfer, on the nanosecond time scale , from the sulfhydryl group of the conserved cysteine to the N5 atom of FMN.

Blue light arrives on the only LOV2 <scene name='Sandbox122/Cystein_residue/1'>cystein residue</scene>(situate 4.2A from atom C(4a)) and induces formation of covalent cysteinyl-C(4a)adduct. (To explain that, refer to the scheme). Somes studies showed that temperature have an influence on that adduct. In fact, at low temperature, the microenvironment determine the reactivity of the S-H group of Cys966. A base-catalyzed mechanism for dark state recovery. Imidazole snatch proton from N5 atom of FMN and give it to the cysteine again (explain on the scheme).

Blue light arrives on the only LOV2 <scene name='Sandbox122/Cystein_residue/1'>cystein residue</scene>(situate 4.2A from atom C(4a)) and induces formation of covalent cysteinyl-C(4a)adduct. (To explain that, refer to the scheme). Somes studies showed that temperature have an influence on that adduct. In fact, at low temperature, the microenvironment determine the reactivity of the S-H group of <scene name='Sandbox122/Cys966/2'>Cys966</scene>. A base-catalyzed mechanism for dark state recovery. Imidazole snatch proton from N5 atom of FMN and give it to the cysteine again (explain on the scheme).

[[Image:Noname05.gif | thumb]]

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@@ Line 1: / Line 1: @@
 [[Image:1G28.pdb b.jpg | thumb]]
-====STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3===={{STRUCTURE_1g28|  PDB=1g28  |  SCENE=  }}
+'''STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3'''{{STRUCTURE_1g28|  PDB=1g28  |  SCENE=  }}
 '''Phototropin''' is a blue light receptor involved in the phototropism (it is a phenomenon which is  growth directed by light).This is a transmembrane protein present on the top of coleoptile.
 This protein is a dimer (phot1 and phot2) and each subunit contains three domains : LOV1, '''LOV2''' (light,oxygen or voltage) domains and a kinase domain.
@@ Line 6: / Line 6: @@
 ==Structure of LOV2==
-The structure of a flaving domain, LOV2, from the chimeric phototropin photoreceptor PHY3, has been determined thanks to X-Ray diffraction. This domain is composed by four chains which are identical and called A, B, C and D. It's a L-polypeptide which weight 50552,99 Da. Each chains has 104 aminoacids and possess four <scene name='Sandbox122/Helix_of_the_lov2_domain/1'>helix</scene> (28 residues which represents 26%) and six B <scene name='Sandbox122/Beta_sheets_of_lov2/1'>sheets</scene> (37 residues which represent 35%).
+The structure of a flaving domain, LOV2, from the chimeric phototropin photoreceptor PHY3, has been determined thanks to X-Ray diffraction. This domain is composed by four chains which are identical and called A, B, C and D. It's a L-polypeptide which weight is 50552,99 Da. Each chains has 104 aminoacids and possess four <scene name='Sandbox122/Helix_of_the_lov2_domain/1'>helix</scene> (28 residues which represents 26%) and six B <scene name='Sandbox122/Beta_sheets_of_lov2/1'>sheets</scene> (37 residues which represent 35%).
 ==Interaction between FMN et LOV2 domain==
 The <scene name='Sandbox122/Fmn_ligand/1'>FMN</scene> (Flavin MonoNucleotide) is the ligand which is responsible for the light absorption. A single molecule of FMN is bound non convalently in the interior of LOV2 domain. FMN is stabilized thanks to hydrogen bonds, Van der Waals and electrostatic interactions. For example, atoms <scene name='Sandbox122/Arg_983/1'>R983</scene> and <scene name='Sandbox122/Arg_963/1'>R967</scene>(alpha C helix) create ionic bond with phosphate group of FMN. <scene name='Sandbox122/Q970/1'>Q970</scene>, <scene name='Sandbox122/N965/1'>N965</scene> , <scene name='Sandbox122/N998/1'>N988</scene>, <scene name='Sandbox122/N1008/1'>N1008</scene> (alpha A helix and beta-strand C, D and E) aminoacid make some electrostatic interaction which stabilize FMN. Some results indicate that the majority of the FMN  in the LOV2 domain exist in the protonated form. Researcher propose a reaction mechanism that involves excited-state proton transfer, on the nanosecond time scale , from the sulfhydryl group of the conserved cysteine to the N5 atom of FMN.
-Blue light arrives on the only LOV2 <scene name='Sandbox122/Cystein_residue/1'>cystein residue</scene>(situate 4.2A from atom C(4a)) and induces formation of covalent cysteinyl-C(4a)adduct. (To explain that, refer to the scheme). Somes studies showed that temperature have an influence on that adduct. In fact, at low temperature, the microenvironment determine the reactivity of the S-H group of Cys966. A base-catalyzed mechanism for dark state recovery. Imidazole snatch proton from N5 atom of FMN and give it to the cysteine again (explain on the scheme).
+Blue light arrives on the only LOV2 <scene name='Sandbox122/Cystein_residue/1'>cystein residue</scene>(situate 4.2A from atom C(4a)) and induces formation of covalent cysteinyl-C(4a)adduct. (To explain that, refer to the scheme). Somes studies showed that temperature have an influence on that adduct. In fact, at low temperature, the microenvironment determine the reactivity of the S-H group of <scene name='Sandbox122/Cys966/2'>Cys966</scene>. A base-catalyzed mechanism for dark state recovery. Imidazole snatch proton from N5 atom of FMN and give it to the cysteine again (explain on the scheme).
 [[Image:Noname05.gif | thumb]]