Sandbox Reserved 960: Difference between revisions
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=== Cavity === | === Cavity === | ||
The dynamic structure of the protein is responsible of the ligand’s binding by adjustment of position. The successful delivery of the effector to the receptor relies on this property. The ligand binding pocket consists in a cavity formed by the helices H2, H4 and H5 (scene), arranged in a globular shape which leads to a clear separation of the ligand from the | The dynamic structure of the protein is responsible of the ligand’s binding by adjustment of position. The successful delivery of the effector to the receptor relies on this property. The ligand binding pocket consists in a cavity formed by the helices H2, H4 and H5 (scene), arranged in a globular shape which leads to a clear separation of the ligand from the {{Template:ColorKey_Polar}} environment. | ||
The top of the cavity is not closed and can establish contacts with the solvent. The cavity is prone to accept ligand such as 9-ODA because of its specific composition. Indeed, cavity's components are mainly <scene name='60/604479/ | The top of the cavity is not closed and can establish contacts with the solvent. The cavity is prone to accept ligand such as 9-ODA because of its specific composition. Indeed, cavity's components are mainly <scene name='60/604479/hydrophobic_residues/2'>hydrophobic and aromatic</scene>.They consequently interact with the ligand's {{Template:ColorKey_Hydrophobic}} carbon chain and are localized on the internal face of the helix.Thus, it implies that these residues respect a regular distance pattern in the primary structure of the AmelASP1. | ||
=== pH influence === | === pH influence === | ||
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In order to determine this protein’s structure, several ligands has been used at pH 5.5 because this low pH fits with the natural medium of this protein in the bee antenna. | In order to determine this protein’s structure, several ligands has been used at pH 5.5 because this low pH fits with the natural medium of this protein in the bee antenna. | ||
The three ligands used to characterize and purify AmelASP1 are : | The three ligands used to characterize and purify AmelASP1 are : | ||
*<scene name='60/604479/Cmj/3'>CMJ</scene> also known as (20s)-20-Methyldotetracontane, is a serendipitous ligand. This term signify that the purification of this molecule was completely fortuitous. It is a big unsaturated mono-methyl branched carbone chain with formula C43H88. This ligand fits in the | *<scene name='60/604479/Cmj/3'>CMJ</scene> also known as (20s)-20-Methyldotetracontane, is a serendipitous ligand. This term signify that the purification of this molecule was completely fortuitous. It is a big unsaturated mono-methyl branched carbone chain with formula C43H88. This ligand fits in the {{Template:ColorKey_Hydrophobic}} cavity of AmelASP1 thanks to several interactions with <scene name='60/604479/Cmj_binding_residues/2'>specific residues.</scene> | ||
