User:Emma Wozniak/sandbox1: Difference between revisions

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This protein has a molecular mass of 114 kDa and is a one chain structure that consists of 1049 amino acids, and organizes itself as a homotrimer in shape similar to that of a jellyfish. Each protomer in this protein is composed of a 50 A thick transmembrane region, as well as a protruding headpiece that is 70 A in size. It is believed by some that this headpiece section opens up at the top like a funnel, which the TolC protein can directly dock itself onto. Direct disulfide cross-linking experiments have also shown the interactions between the AcrB and TolC trimers, suggesting that the headpiece-TolC belief might be true.

AcrB is shaped like a funnel with its ends found in both the cytoplasm and periplasm of the bacterial cell. The C terminus of AcrB is located in the cell’s cytoplasm, while the N terminus links with AcrA in the periplasm. The N- and C- terminal halves of AcrB are connected to each other with an alpha-helix that runs parallel to the cytoplasmic membrane of the bacteria. Subunits within the protein have three possible conformational states, which include the access (L), binding (T), and extrusion (O) states. However, binding of substrates and inhibitors will affect the conformational states of the protein. For example, binding of the MBX3132 inhibitor creates a TTT conformation state for the protein as a whole, which makes the inhibitor bind tightly to the protein and negatively affects substrate binding/protein function.

AcrB is shaped like a funnel with its ends found in both the cytoplasm and periplasm of the bacterial cell. The C terminus of AcrB is located in the cell’s cytoplasm, while the N terminus links with AcrA in the periplasm. The N- and C- terminal halves of AcrB are connected to each other with an alpha-helix that runs parallel to the cytoplasmic membrane of the bacteria. Subunits within the protein have three possible conformational states, which include the access (L), binding (T), and extrusion (O) states. However, binding of substrates and inhibitors will affect the conformational states of the protein. For example, binding of the MBX3132 inhibitor creates a TTT conformation state for the protein as a whole, which makes the inhibitor bind tightly to the protein and negatively affects substrate binding/protein function.<ref name="inhibition">DOI: 10.7554</ref>

It has first been found that a Asp-Lys-Asp triad was found to be essential in AcrB. Later, three individual subunits in the transmembrane region have been identified to play key roles in AcrB function. The <scene name='91/911201/Residue_1_tm4_subunit/1'>Asp407-Asp408 residue</scene> has been found to be essential in the TM4 subunit in ''E. coli'', and this residue works in conjunction with the <scene name='91/911201/Residue_2_tm11_subunit/1'>Thr978 residue in the TM11</scene> and <scene name='91/911201/Residue_3_tm10_subunit/1'>Lys940 residue of the TM10</scene> subunits to allow the protein to function. <ref name="transmembrane">doi: 10.1128</ref>

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 This protein has a molecular mass of 114 kDa and is a one chain structure that consists of 1049 amino acids, and organizes itself as a homotrimer in shape similar to that of a jellyfish. Each protomer in this protein is composed of a 50 A thick transmembrane region, as well as a protruding headpiece that is 70 A in size. It is believed by some that this headpiece section opens up at the top like a funnel, which the TolC protein can directly dock itself onto. Direct disulfide cross-linking experiments have also shown the interactions between the AcrB and TolC trimers, suggesting that the headpiece-TolC belief might be true.
-AcrB is shaped like a funnel with its ends found in both the cytoplasm and periplasm of the bacterial cell. The C terminus of AcrB is located in the cell’s cytoplasm, while the N terminus links with AcrA in the periplasm. The N- and C- terminal halves of AcrB are connected to each other with an alpha-helix that runs parallel to the cytoplasmic membrane of the bacteria. Subunits within the protein have three possible conformational states, which include the access (L), binding (T), and extrusion (O) states. However, binding of substrates and inhibitors will affect the conformational states of the protein. For example, binding of the MBX3132 inhibitor creates a TTT conformation state for the protein as a whole, which makes the inhibitor bind tightly to the protein and negatively affects substrate binding/protein function.
+AcrB is shaped like a funnel with its ends found in both the cytoplasm and periplasm of the bacterial cell. The C terminus of AcrB is located in the cell’s cytoplasm, while the N terminus links with AcrA in the periplasm. The N- and C- terminal halves of AcrB are connected to each other with an alpha-helix that runs parallel to the cytoplasmic membrane of the bacteria. Subunits within the protein have three possible conformational states, which include the access (L), binding (T), and extrusion (O) states. However, binding of substrates and inhibitors will affect the conformational states of the protein. For example, binding of the MBX3132 inhibitor creates a TTT conformation state for the protein as a whole, which makes the inhibitor bind tightly to the protein and negatively affects substrate binding/protein function.<ref name="inhibition">DOI: 10.7554</ref>
 It has first been found that a Asp-Lys-Asp triad was found to be essential in AcrB. Later, three individual subunits in the transmembrane region have been identified to play key roles in AcrB function.  The <scene name='91/911201/Residue_1_tm4_subunit/1'>Asp407-Asp408 residue</scene> has been found to be essential in the TM4 subunit in ''E. coli'', and this residue works in conjunction with the <scene name='91/911201/Residue_2_tm11_subunit/1'>Thr978 residue in the TM11</scene> and <scene name='91/911201/Residue_3_tm10_subunit/1'>Lys940 residue of the TM10</scene> subunits to allow the protein to function. <ref name="transmembrane">doi: 10.1128</ref>