Membrane-bound proteins amino acid sequence

Alpha helices that cross membranes are in a hydrophobic environment. Therefore, most of their side chains are hydrophobic. Long regions of hydrophobic residues in the amino acid sequence of a protein that is membrane-bound can therefore be predicted with a high degree of confidence to be transmembrane helices, as will be discussed in Chapter 12. 

The reaction center is built up from four polypeptide chains, three of which are called L, M, and H because they were thought to have light, medium, and heavy molecular masses as deduced from their electrophoretic mobility on SDS-PAGE. Subsequent amino acid sequence determinations showed, however, that the H chain is in fact the smallest with 258 amino acids, followed by the L chain with 273 amino acids. The M chain is the largest polypeptide with 323 amino acids. This discrepancy between apparent relative masses and real molecular weights illustrates the uncertainty in deducing molecular masses of membrane-bound proteins from their mobility in electrophoretic gels. 

A relatively small minority of APP molecules enter the p-secretase pathway in which p-secretase cleaves APP and releases a soluble fragment, sAPPp. The C-terminal membrane-bound C99 peptide is then cleaved by y-secretase within the transmembrane domain, and two major isoforms of 40 and 42 amino acid lengths with different C-termini, Ap40 and Ap42, are generated. Based on the amino acid sequence, p-secretase is predicted to be a type I transmembrane protein with the active site on the lumenal side of... 

Many known drug receptors, and many prospective drug targets, exist as molecular arrays within membrane-bound macromolecules that cannot be readily crystallized neither can they be isolated or purified for the application of NMR methods. Moreover, even if an amino acid sequence were available, rule-based methods for the prediction of secondary structure, being derived as they are from a database of soluble proteins, cannot be applied with any confidence to the membrane-bound state. 

Cytochrome exists in a soluble form in erythrocytes and in a membrane bound form in microsomes. A soluble derivative of hepatic cyt bs with 93 amino acids can be isolated by treatment of microsomes with pancreatic lipase and this form has essentially the same amino acid sequence as the erythrocyte protein. Further treatment of the soluble form with trypsin cleaves two residues from the N-terminal and seven from the carboxylate-terminal and leaves the heme core with only 84 residues. Rat liver cyt b has been prepared by expression in Eschericha coli (E.coli). The structure of... 

A hydrophobic 10 kDa protein is also associated with PS II preparations [14], but its function is obscure. The protein is phosphorylated by a membrane-bound protein kinase [15] and the identity of this phosphoprotein has been the subject of much speculation [16]. It is clearly not the 9 kDa polypeptide of Cyt 6-559 or the 8 kDa proteolipid subunit of ATP synthase as shown by N-terminal amino acid sequence [14]. 

Cytochrome c, is an amphiphilic protein with a molecular weight of 28-31000. Weiss et al. [212] found that it may be isolated only with the help of a detergent. However, by mild proteolysis they could release the haem-binding domain from the rest of the protein. This segment is soluble in aqueous solutions. The amino acid sequence of the bovine protein [181] shows that it has only one continuous hydrophobic segment that is close to the C-terminus. This segment probably acts as an anchor to the membrane. The covalently bound haem is located in the water-soluble part, with its plane perpendicular to the membrane plane [206], The two-domain structure makes the architecture of cytochrome c, very similar to that of microsomal cytochrome [213]. 

Figure 1.25 presents part of the amino acid sequence of a membrane-bound protein. The amino acids embedded within the membrane are those with lipophilic R groups. The amino adds residing in the fluids surrounding the membrane are mostly those with ionic R groups. 

Proteins also can be classified as those that are soluble and remain in the cell, those that are membrane-bound in the cell, and those that are soluble and secreted from the cell. The specific sequence and nature of the amino acids in the polypeptide chain determine the eventual location of the polypeptide in the cell. Insulin, a secretrxl polypeptide, is of great interest to nutritionaJ scientists and the medical profession, Sucrase-isomaltase is a membrane-bound protein of occasional interest in nutrition. 

The plasma membrane of the cell is a lipid bilayer sheet in which membrane-bound proteins are embedded. Steps 4B-6B of Figure 1.21 illustrate some events in the production of a membrane-bound protein. After synthesis of the protein, the ribosome on which it was formed dissociates from the membrane but the protein remains bound to the membrane (Step 4B). This binding is mediated by a short stretch of lipophilic amino acids that may occur near the C terminus, as shown in Figure 1.21, or near the N terminus in the case of other proteins. Subsequently, part of the ER membrane forms a bud that breaks off (Step 5B) to form a secretory vesicle (Step 6B). The continued association of the entire membrane-bound protein during the budding process and during subsequent events is maintained by the special lipophilic sequence. Eventually, the secretory vesicle fuses with the plasma membrane in a process that resembles a reversal of Steps 4B-6B. After completion of the insertion of the membrane-bound protein into the plasma membrane, its N terminus is in contact with the extracellular fluid and its C terminus is in contact with the cytoplasm, at least for the protein depicted in Figure 1.21. 

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