NalP: Difference between revisions
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===Beta Barrel=== | ===Beta Barrel=== | ||
The unique structure that makes this pore is able to allow for transportation in and out of the gram-negative cell is what is called a beta barrel. This beta barrel is created with 12 anti-parallel beta-pleated sheets that have wrapped around creating anti-parellel interaction between sheet one and sheet 12. This creates a tube structure that transcends through the membrane of a cell creating a new environment that allows for polar molecules to move through the cell membrane and cell wall when they would have otherwise been stopped by the hydrophobic center of peptidoglycan. The start and end of the beta barrel is on the periplasmic side of the membrane and a short tight turn, T0, connects the alpha-helix to the N-terminal beta strand. The alpha helix has its N-terminus side facing outward toward extracellular material. <ref name=" | The unique structure that makes this pore is able to allow for transportation in and out of the gram-negative cell is what is called a beta barrel. This beta barrel is created with 12 anti-parallel beta-pleated sheets that have wrapped around creating anti-parellel interaction between sheet one and sheet 12. This creates a tube structure that transcends through the membrane of a cell creating a new environment that allows for polar molecules to move through the cell membrane and cell wall when they would have otherwise been stopped by the hydrophobic center of peptidoglycan. The start and end of the beta barrel is on the periplasmic side of the membrane and a short tight turn, T0, connects the alpha-helix to the N-terminal beta strand. The alpha helix has its N-terminus side facing outward toward extracellular material. <ref name="PMID: 8254661> PMID: 8254661 </ref> | ||
=== Alpha Helix === | === Alpha Helix === | ||
The Alpha Helix within the Beta Barrel is a major obstruction, which allows for regulated channel. The Alpha Helix corresponds to the .15nS opening that is observed and without this obstruction a 1.3nS open pore is created which allows for a much more free flowing pore. This is found to be infrequent occurrence which could be caused by a detergent and high salt concentration. Due to this being the more infrequent type of pore it is able to be deduced that the internal alpha helix is what is found in vivo. The alpha helix is found internally on the N-terminus side of the protein and extends from n-terminus facing the extracellular space leading inward toward the cytoplasm which turns then into a beta pleated sheet that creates the barrel shape. This structure is consistent with the final stage of translocation which allows for proteins to be released in to the extracellular space. The alpha helix is charged almost solely on one side. This charged side is able to interact with an axial line of charged side chains that point inward from the beta barrel. Through seven salt bridges as well as through 16 hydrogen bonds and several van der Waals contacts, the alpha helix is able to interact with one side of the beta barrel.<ref name=" | The Alpha Helix within the Beta Barrel is a major obstruction, which allows for regulated channel. The Alpha Helix corresponds to the .15nS opening that is observed and without this obstruction a 1.3nS open pore is created which allows for a much more free flowing pore. This is found to be infrequent occurrence which could be caused by a detergent and high salt concentration. Due to this being the more infrequent type of pore it is able to be deduced that the internal alpha helix is what is found in vivo. The alpha helix is found internally on the N-terminus side of the protein and extends from n-terminus facing the extracellular space leading inward toward the cytoplasm which turns then into a beta pleated sheet that creates the barrel shape. This structure is consistent with the final stage of translocation which allows for proteins to be released in to the extracellular space. The alpha helix is charged almost solely on one side. This charged side is able to interact with an axial line of charged side chains that point inward from the beta barrel. Through seven salt bridges as well as through 16 hydrogen bonds and several van der Waals contacts, the alpha helix is able to interact with one side of the beta barrel.<ref name="PMID: 8254661" /> | ||