Hydropathy plot

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. 

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... 

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...

Another, but less well defined, class of molecules, some of whose members mediate adhesion interaction, is the four-transmembrane domain family, which shares similar hydropathy plots and may have similar dispositions with respect to the phospholipid bilayer, for example the myelin proteolipid proteins, the connexins of gap junctions, the ryanodine receptor and others. 

The amino acid sequences of the glutamate transporters show a high degree of similarity with between 40-60% of amino acid residues identical between subtypes. At present, the three-dimensional (3D) structure of the transporters is unknown and indirect methods based on amino acid sequence hydropathy plots and amino acid accessibility methods have been employed to predict the transmembrane topology of the transporters. Two similar models developed by the groups of Amara (12,13) and Kanner... 

In the method by Schirmer and Cowan (1993), a kind of hydropho-bicity plot like the hydropathy plot of Kyte and Doolittle (1982) is used. The amino acid index representing hydrophobicity is modified to emphasize the effect of aromatic residues. Considering the structural feature of /3 strands, the averaged value of 4 positions (i — 2, i, i + 2, and i + 4 for position i) is taken, and the plot is drawn for both even- and odd-numbered positions. The peaks correspond well to the observed positions of the /3 strands. 

The transmembrane domain may be made up of one or many transmembrane elements. Generally, the transmembrane elements include 20-25 mostly hydrophobic amino acids. At the interface with aqueous medium, we often find hydrophilic amino acids in contact with the polar head groups of the phospholipids. In addition, they mediate distinct fixing of the transmembrane section in the phospholipid double layer. A sequence of 20-25 hydrophobic amino acids is seen as characteristic for membrane-spaiming elements. This property is used in analysis of protein sequences, to predict possible transmembrane elements in so-called hydropathy plots". 

On the basis of their amino acid sequences and hydropathy plots, many of the transport proteins described in this chapter are believed to have multiple membrane-spanning helical regions—that is, they are type III or type IV integral proteins (Fig. 11-8). When predictions are consistent with chemical studies of protein localization (such as those described above for glycophorin and bacteriorhodopsin), the assumption that hydrophobic regions correspond to membrane-spanning domains is much better justified. 

Very few integral membrane proteins have been crystallized. The reaction-center proteins purified from membranes of photosynthetic bacteria are a notable exception. These proteins were discussed in chapter 15. Before their crystal structures were elucidated, analysis of hydropathy plots suggested that each of the two main protein subunits is folded into five transmembrane a helices, and one such helix was predicted to occur in another subunit. The crystal structures provided a beautiful confirmation of these predictions (see fig. 15.11a). Successful crystallization of the reaction-center proteins was achieved by including small,... 

Figure 2. Pn-slieled setnnJary strueiure of salamander red rod Tliudupsiii. The iriuiKiueiiihrane helices (boxed) are lie lined bused or Kylc-tJoolillle hydropathy plots hiuI siinikiriiy (o bovine rhodopsin. Lys29tjainlO Ll ]J are indi-...

Answer Construct and analyze a hydropathy plot for the protein. You can assume that any hydrophobic regions of more than 20 consecutive residues are transmembrane segments of an integral protein. To determine whether the external domain is carboxyl- or amino-terminal, treat intact erythrocytes with a membrane-impermeant reagent known to react with primary amines and determine whether the protein reacts. If it does, the amino terminus is on the external surface of the erythrocyte membrane and this is a type I protein (see Fig. 11-8). If it does not, a type II protein is indicated. 

Figure 7. Hydropathy plot of the 34 kOa herbicide binding protein.

Link, T. A., Sch%ogger, H., and Von Jagow, G., 1987, Structural analysis of the bpcomplex from beef heart mitochondria by the sidedness hydropathy plot and by comparison with other be complexes, in Cytochrome Systems Molecular Biology and Bioenergetics, (S. Papa, B. Chance, and L. Emster, eds.) Plenum Press, New York, pp. 289n301. 

The amino acid sequences of the subunits of bovine heart enzyme have been determined primarily by Buse and his colleagues (Buse et al., 1986). Many of the sequences have been determined not only by DNA sequencing but also by peptide analysis. Peptide analysis is an indispensable method for the detection of post translational modifications, and an example of such a modification has been recently shown in this enzyme, and will be described below. Hydropathy plots for these amino acid sequences have provided an astonishingly successful predictions of which regions contain a-helices. This is quite remarkable considering the limited accuracy of this method for structural identification (Hosier et al., 1993 Tsukihara et al., 1996). 

Fig. 4.1. Topology, conservation, andRHPmotif oftheStel4poI5. cerevisiae. (A) Hydropathy plots predict six transmembrane segments (TMs). In this model, the N-and C-termini are disposed toward the cytosol. TM 5 and 6 are proposed to form a helix-turn-helix hehcal hairpin within the membrane [25]. Fifteen unique Icmt protein sequences were ahgned using ClustalW 2.0.1.1 [27]. The blue residues denote amino acid identity and the magenta residues denote amino acid similarity. The C-terminal portion of the enzyme (136-239) contains the majority of the identical amino acids. (B) Sequence of the RHP motif, a C-terminal consensus sequence common to Icmt enzymes, a number of bacterial open reading frames, and two phosphatidyl-ethanolamine methyltransferases. Numbers denote the amino acid position in Stel4p.

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