L8 types of membrane proteins (MP2)

• Phospholipid synthesis occurs in the cytosolic side of the ER membrane, involving the recognition of fatty acids, insertion into the membrane, removal of the hydroxyl group, and addition of the glycerol group and the lipid head
• Proteins called scrambalses in the ER flip phospholipids to balance the membrane, ensuring the same amount of lipids on each leaflet
• Transport of lipids involves proteins recognizing and protecting lipids, transporting them across the cytosol, and using intracellular organelles for transport, often in vesicles
• Integral membrane proteins can be transmembrane proteins that pass from one region to another, with different types based on their structure like alpha helices or beta strands
• Transmembrane helices are a common type of integral membrane protein, characterized by hydrophobic amino acids and hydrophilic amino acids that interact with the aqueous environment
• Transmembrane barrels are another type of integral membrane protein, with the number of strands determining the size of the substrate transported across the cell
• Membrane proteins are asymmetrical and cannot flip from one layer to another, with different amino acids undergoing post-translational modifications in the cytosol versus the ER lumen
• Transmembrane proteins are classified into channels that regulate the flow of ions and transporters that move molecules against the gradient, with different mechanisms and regulation
• Glycosyl-phosphatidyl-inositol (GPI) anchors are complex molecules found in the membrane, providing flexibility for proteins attached to them
• Phospholipid synthesis:

  • Created in the cytosolic side of the ER membrane
  • Steps:

  1. Protein recognizes fatty acid (hydroxyl group faces aqueous environment) and protects the fatty acid tail

  2. Brings it to the cytosolic side of the ER membrane

  3. Inserts it into the ER membrane

  4. Hydroxyl group is removed and acetyl CoA is inserted (intermediate)

  5. Facilitates insertion of glycerol group (links tails to polar head) after removing the phosphate of glycerol

  6. The head of the lipid gets added
• Fatty acid tails are brought by a carrier into the membrane, and steps are taken to add the head part of the phospholipid
• The membrane becomes unbalanced due to all phospholipids being on the leaflet facing the cytosol, so proteins called scrambalses in the ER flip the phospholipids to balance the distribution
• Example of lipid synthesis in the plasma membrane:

  • If certain types of phospholipids are facing out and then facing in, a vesicle can disrupt this asymmetry
  • Flippase proteins, specific and requiring ATP, in the plasma membrane, restore the asymmetry of the plasma membrane
• Transport of lipids:

  • Lipids can be recognized by a protein that protects the hydrophobic area of the lipid and transports it across the cytosol
  • Lipids are often transported in vesicles, formed in the ER, transported in vesicles, fused in the membrane, and then released
• amino acid sequence determines structure of a protein. it will also determine PTMs, and it determines where the protein is going to be located in the cell.
• proteins inserted into the membrane need to have hydrophobic interactions with the lipids. those proteins in the cytosol or the lumen are soluble.
• integral membrane proteins: proteins that are inserted completely into the lipid bilayer. they serve as cell surface receptors and transporters.
• transmembrane proteins are a type of integral membrane protein. they pass from one region of the cell to another region. type 1: has more than one alpha helix. type 2: depends on formation of beta strands that create cylinders or beta barrels. type 3: amphipathic alpha helix which has one side that is hydrophobic (inserted into membrane) and another that is hydrophilic
• lipid anchored proteins are transversing the membrane. they covalently bind to the lipid in the membrane via PTMs. these function on one side of the cell, playing a role in intracellular signaling. a type of these proteins are peripheral membrane proteins that are attached to the membrane via non-covalent interactions
• integral membrane proteins are anchored into the membrane via (1) transmembrane helices (2) transmembrane barrels
• to anchor integral membrane proteins via transmembrane helices, the side chains that face the outside of the helix are hydrophobic. they are usually characterized by hydrophobic amino acids and serine, tyrosine, and histidine. we need these hydrophilic amino acids because they be needed for aqueous environment, or because they serve as the pore for an ion to pass through or a transmembrane transporter.
• to anchor integral membrane proteins via transmembrane barrels, the beta strands have the same structure as the cytosilic proteins. the higher the amount of strands will determine how big the substrate is that will be transported from one part of the cell to another part of the cell.
• proteins in the membrane have directionality because the environment in cytosol and ER lumen are different, and different amino acids undergo different PTMs in cytosol vs ER lumen.

  • PTMs in cytosol are: phosphorylation, acetylation, methylation, ubiquitinylation
  • ER: proteins bound to sugars
• transmembrane proteins can be a channel or a transporter.
• transmembrane protein channels regulate the flow of ions from one side to another. in water these ions are engaged in non-covalent interactions, and the interior of the channels are polar. the specificity of the channels come from the size of the channel. example is a potassium ion channel that engages in non-covalent polar interactions with the peptide backbone of the channel (4 with potassium and only 2 for sodium).
• transmembrane protein transporters cause movement of molecules against the gradient, they will make the ions move from areas of low concentration to areas of high concentration (against diffusion). ATP dependent and regulated by ATPase activity. it moves an example is the sodium potassium pump or a multidrug resistance transporter that recognizes toxins, binds to ATP releasing the toxin into the exterior of the cell.
• lipid anchored proteins have post translational modifications, linking the protein to a lipid (considered a PTM). proteins anchored in the membrane need to be acetylated or prenylated.
• for the lipid anchored protein to be linked to the lipid through acetylation:

  • (1) remove methionine and it has to be a glycine or a cystine. once these are the second amino acid, they will create an amide linkage with the lipid.
  • (2) those with a cystiene anywhere will create a thioester linkage with the lipid
  • fatty acid!! second amino acid has to be glycine or cysteine. this is not reversible! the protein will be attached.
  • the cysteine anywhere in the protein creating a thioester bond however is reversible. so this can be changed.
• for the lipid anchored protein to be linked to a lipid via prenylation:

  • prenyl group is needed. will depend on cysteine where the order of the last four amino acids is Cys-a-a-x-COO- (carboxyl terminus)
  • we need a prenyl group with a cysteine that is the 4th last amino acid. this modification is not reversible, it will be attached and stays there.
  • prenylation motif is CaaxCOO-, where a is having an alkyl side chain
• a lipid anchored protein can be attached to the membrane via a glycosyl-phosphatidyl-inositol (GPI) anchor.it has a glycosylated (has sugar added to it) phosphatidylinositol anchor. the reason the lipid anchored protein binds to the GPI and not its own alpha helix is that this binding provides flexibility. a larger molecule will be able to move more in the ER lumen, maybe it needs more movement and therefore the transmembrane protein will be attached to the GPI protein.