Hydropathy

When the hydropathy indices are plotted against residue numbers, the resulting curves, called hydropathy plots, identify possible transmemhrane helices as broad peaks with high positive values. Such hydropathy plots are shown in Figure 12.23 for the L and M chains of the reaction center. 

Figure 12.23 Hydropathy plots for the polypeptide chains L and M of the reaction center of Rhodobacter sphaeroides. A window of 19 amino acids was used with the hydrophohicity scales of Kyte and Doolittle. The hydropathy index is plotted against the tenth amino acid of the window. The positions of the transmembrane helices as found by subsequent x-ray analysis by the group of G. Feher, La Jolla, California, ate indicated by the green regions.

Reaction center hydropathy plots agree with crystal structural data... 

The hydropathy plots in Figure 12.23 were calculated and published several years before the x-ray structure of the reaction center was known. It is therefore of considerable interest to compare the predicted positions of the transmembrane-spanning helices with those actually observed in the x-ray structure. These observed positions are indicated in green in Figure 12.23. 

FIGURE 10.5 A model for the arrangement of the glucose transport protein in the erythrocyte membrane. Hydropathy analysis is consistent with 12 transmembrane helical segments. 

M FIGURE 10.14 The arrangement of Ca -ATPase in the sarcoplasmic reticulum membrane. Ten transmembrane segments are postulated on the basis of hydropathy analysis. 

Figure 3. Hydropathy Profile and mature protein primary sequence of the deduced p-Subunit Precursor Protein.

Upper panel The hydropathy profile of the entire 69 kD precursor protein is shown. The abscissa is amino acid residues and the ordinate, positive values indicate hydrophilic. The black and hatched rectangles at the bottom of the figure denote the calculated signal sequence and amino-terminal propeptide domains, respectively. The mature and carboxyl-terminal domains are labeled. N-linked core glycosylation consensus sites are depicted by branched structures. 

Information about the putative folding of the H,K-ATPase catalytic subunit through the membrane has been obtained by the combined use of hydropathy analysis according to the criteria of Kyte and Doolittle [51], identification of sites sensitive to chemical modification [46,48,50,52-55], and localization of epitopes of monoclonal antibodies [56]. The model of the H,K-ATPase catalytic subunit (Fig. 1) which has emerged from these studies shows ten transmembrane segments and contains cytosolic N- and C-termini [53]. This secondary structure of the catalytic subunit is probably a common feature of the catalytic subunits of P-type ATPases, since evidence supporting a ten a-helical model with cytosolic N- and C-termini has also been published recently for both Ca-ATPase of the sarcoplasmic reticulum and Na,K-ATPase [57-59]. 

Hydropathy analysis predicted that there are four major transmembrane domains (M1-M4) prior to the phosphorylation site at Asp . The existence of these four transmembrane segments in the N-terminal half of the catalytic subunit is generally accepted for all P-type ATPases. The four transmembrane sequences are followed by a large cytosolic loop that contains the phosphorylation site Asp, the pyridoxal... 

Hydropathy plots [133] of the slow and fast Ca -ATPase isoenzymes are nearly identical and provide unambiguous prediction of four of the proposed transmembrane segments (Mi, M2, M3 and M4) [8,11]. Similar hydropathy plots were also obtained for other closely related cation transporting ATPases [31,46,47,134]. 

Although the sequence identity averaged over the whole length of the molecule is generally low among different P-type ion transport ATPases, the conserved sequences around the phosphate acceptor aspartyl group and in the ATP binding domain are well preserved [30,32,46]. Structure predictions based on the hydropathy plots... 

With this information in hand, we may now consider how the -ATPase polypeptide chain might fold into its functional three-dimensional structure. First, regarding the actual number of membrane-spanning stretches, the available experimental data indicate only that each of the three membrane-embedded peptides must have an even number of and a minimum of two such stretches. However, hydropathy analysis by the method of Mohana Rao and Argos [48] suggests that the second mem-... 

Fig. 2. Conditional probability plot for Sweet and Eisenberg s (1983) hydropathy scale. The black line is the probability ( axis) that a residue is ordered given the hydropathy score indicated on the x-axis. The dashed line is the probability of disorder. Negative values for hydropathy indicate hydrophilicity, positive values indicate hydrophobicity. The area between the two curves is divided by the total area of the graph to obtain the area ratio.

Uversky and co-workers recently used a pair of sequence attributes, specifically the Kyte-Doolittle hydropathy scale and net charge, to... 

Fig. 20.2. Percentage of amino acids with H-bond donor side chains in the 12 putative transmembrane sequences of P-glycoprotein (P-gp). The transmembrane sequences were determined by means of a hydropathy plot according to Kyte and Doolitttle [100] and chosen to be 22 amino acids long. The first amino acid of each transmembrane sequence...

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