Membrane amino acid composition

With a knowledge of the methodology in hand, let s review the results of amino acid composition and sequence studies on proteins. Table 5.8 lists the relative frequencies of the amino acids in various proteins. It is very unusual for a globular protein to have an amino acid composition that deviates substantially from these values. Apparently, these abundances reflect a distribution of amino acid polarities that is optimal for protein stability in an aqueous milieu. Membrane proteins have relatively more hydrophobic and fewer ionic amino acids, a condition consistent with their location. Fibrous proteins may show compositions that are atypical with respect to these norms, indicating an underlying relationship between the composition and the structure of these proteins. 

The amino acid compositions and sequences of the /3-strands in porin proteins are novel. Polar and nonpolar residues alternate along the /3-strands, with polar residues facing the central pore or cavity of the barrel and nonpolar residues facing out from the barrel where they can interact with the hydrophobic lipid milieu of the membrane. The smallest diameter of the porin channel is about 5 A. Thus, a maltodextrin polymer (composed of two or more glucose units) must pass through the porin in an extended conformation (like a spaghetti strand). 

Tusnady, G. and Simon, I. (1998). Principles governing amino acid composition of integral membrane proteins application to topology prediction. Mol. Biol. 283, 489-506. 

The abnormal deposits found in the brains of CJD victims consist of an abnormal isoform of PrP. Prion protein is normally found in cells. Detailed structural studies show that normal cellular PrP (PrP ) is a soluble protein whose conformation is rich in a-helices with very little P-sheet. The PrP protein extracted from the brains of CJD victims (i.e., PrP ) is identical in primary amino acid sequence to the normal PrP (PrP ). However, PrP has a much greater content of P-sheet conformation with little a-helical structure. Thus PrP is neurotoxic because of its three-dimensional structure. When the prion protein is predominantly in an a-helical conformation it is nontoxic when the prion protein is predominantly in a P-sheet conformation, it kills neurons. The prion protein is thus made neurotoxic not by its amino acid composition but by its conformation. This concept is both fascinating and terrifying. Prion diseases are transmissible thus prions are infectious agents. However, prions are not like bacteria or viruses, or other infectious microbes—they are simply protein molecules. Prions are not microbes with cell membranes and nucleic acids they are not living things. Indeed, prions are not even infectious molecules, they are infectious molecular shapes. 

In nature, mammalian antibodies occur in five distinct classes IgG, IgA, IgM, IgD, and IgE. These differ in structure, size, amino acid composition, charge, and carbohydrate components. The basic structure of each of the classes of immunoglobulins consists of two identical polypeptide chains linked by disulfide bonds to two identical heavy chains. Differences between classes and subclasses are determined by the makeup of the respective heavy chains. IgG is the major serum immunoglobulin and occurs as a single molecule IgA also occurs as a single molecule but also polymerizes, primarily as a dimer and also associates with a separate protein when secreted. IgM occurs in the serum as a pentamer, with monomers linked by disulfide bonds and the inclusion of an additional polypeptide component, the J-chain. IgD and IgE occur primarily as membrane-bound monomers on -cells, or basophils and mast cells, respectively. 

The amino acid composition of milk lipid globule membranes, as determined by several groups, has been summarized elsewhere (Patton and Keenan 1975). Some differences are evident in the data from differ-... 

Brunner, J. R., Duncan, C. W. and Trout, G. M. 1953. The fat-globule membrane of nonhomogenized and homogenized milk. I. The isolation and amino acid composition of the fat-membrane proteins. Food Res. 18, 454-462. 

Sensitivity of fluorescent stains is very dependent on protein amino acid composition. Minimum amount detected based on amount of protein loaded onto gel. The actual amount on the blot will be slightly lower because of losses during electrotransfer. Values are based on use of a full-sized gel (I I cmx I6cmx 1.5 mm). Sensitivity will be -2 to 5 times higher when minigels (8 cm x 10 cm x 1.0 mm) are used because the protein bands are concentrated on a smaller area of membrane. 

One approach to this problem would be to isolate the intact lectin-receptor molecules from the cell membranes and characterize them. Work in this direction has been initiated in our laboratory, and a method for the isolation of the peanut agglutinin receptor from membranes of neuraminidase-treated human erythrocytes on a column of peanut agglutinin-polyacryl-hydrazido-Sepharose has been developed (21). The amino acid composition, D-glucosamine ancHg-galac-tosamine content, and the electrophoretic mobility on polyacrylamide gel electrophoresis in sodium... 

As pointed out earlier in this article, T differs from other G proteins in that it is a peripheral membrane protein. After activation by Rho it seems to undergo subunit dissociation in which both its a subunit and its /3y complex dissociate from the Rho-containing membranes. Purification of brain G-proteins has shown that free a subunits of G0 and Gj are also water soluble, remaining in solution in the absence of detergents [74], The hydrophobicity of the whole ajSy G and Gj complexes was shown to be due to their j8y complexes 189]. Indeed, purified a subunits associate with phospholipid vesicles only if j8y complexes have been incorporated during vesicle formation [189]. Since the amino acid composition of T-/3 is equal to that of other G-j8s, but their ys differ, it follows that the principal role of y subunits should be to anchor non-T G proteins to the plasma membranes. This conclusion assumed, of course, that j8 subunits are not post-translationally modified in a tissue specific manner such that that they become water soluble in retinal photoreceptor cells and... 

The N-terminal amino acid sequence of both of these polypeptides has been determined [11,12]. Polypeptides of 7, 6.5, 5.5 and 5 kDa have been shown to be associated with a spinach PS II preparation [13]. The three larger polypeptides are hydrophobic, as shown by partitioning in Triton X-114, and are presumed to be intrinsic membrane proteins. The 5 kDa polypeptide is hydrophilic and therefore presumably peripheral to the core complex. This polypeptide has been purified and its amino acid composition determined [13]. 

Amino Acid Composition. Values vary substantially with differences of species, body location, and technique of isolation, purification, or analysis. However, distinctive patterns are associated with some membrane and fibrous protein isolates (Table 1). High proportions of proline and cystine are consistent with observed chemical and mechanical resistance of membranes (32, 68, 71). Similarly, increased methionine and... 

The morphological location of the fibrous protein principally responsible for the deformation and viscoelastic behavior is uncertain. Both the cell membrane and intracellular regions are composed of fibrous proteins which differ considerably in amino acid composition. Since the alpha-keratin within the cells shows few orientation properties until high elongations, it has been suggested that the membrane proteins determine the viscoelastic behavior at low deformations (84). 

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