Structural Biochemistry/Analysis of Membrane Proteins

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Lipopeptide detergents for membrane protein studies[edit]

  • In a cell there are two main groups of proteins, there are cytoplasmic proteins and membrane bound proteins. The cytoplasmic proteins are floating around in the cell and have a particular structure. This structure is the polar and hydrophilic amino acids all tend to be on the outside of the protein, and the non polar hydrophobic amino acids are buried inside the protein (Fig 1)
    Protein in membrane
    . The reason for this assembly is because the proteins have to be stable in the cytoplasm which is mostly water. Since the structure is not complex in terms of the positions of certain amino acids it is much easier to look at a crystal or an NMR spectroscopy of cytoplasmic proteins. The membrane bound proteins have a unique structure because of the position of the protein. The cell is bounded by a phospholipid bilayer, which is hydrophilic on the outsides and hydrophobic on the inside. This structure of the cell membrane has to be mimicked in the protein or it will not be able to stay stable in the membrane. Due to the more complex nature of the membrane bound proteins it is harder to purify and perform a NMR spectroscopy of these proteins.
  • In order to perform a NMR of a stable membrane protein, it would have to be place in an environment which mimics the phospholipid bilayer. Scientist then saw that detergents had a similar structure and that they formed micelles, with a hydrophobic inside and hydrophilic outside (Fig 2)
    Protein in detergent
    . The only problem with the detergents is that they move around and are hard to get an NMR because it created a lot of noise. Another problem is that the micelles don’t completely replicate the membrane in that they are not attached parallel to the proteins non polar region, instead they are perpendicular and so can cause distortions in the proteins functionally and shape. To solve these problems the scientists created a lipopeptide detergent of LPD for short. The LPD’s is a chain of 25 amino acids that for an alpha helix. On the second and 24th amino acids there is an attachment to two alkyl chains that are about eight to twelve carbons in length (Figure 3)
    Lipopeptide detergent
    .
  • The advantage of using a LPD is that unlike a micelle, the LPD’s are closer in function to a membrane since they attach parallel to the protein (Fig 4)
    LPD and protein
    . Another advantage is that they are rigid and don’t move around and so reducing the noise that is present during a NMR spectroscopy. Since these structures are rigid and span the entire hydrophobic region of the protein, there only has to be a few LPD’s in place to keep the membrane protein stable. The only problem with the use of an LPD is that it is financially expensive and so is used as a last resort when all detergents fail. When LPD’s are used in experiments detergents still have to be present to surround the protein at first. Then the LPD is inserted and since it is more structurally favored it replaces the detergent’s micelle and creates the “membrane” and then the detergent is centrifuged out of the solution. After a few rounds of this process one can assume that the proteins are purely surrounded by LPD’s