Hydropathy index plots

The excitement generated by these hydropathy index plots, which predict that most of the thylakoid proteins indeed span the membrane, may have led to a view that it is unnecessary to experimentally demonstrate that the proteins have segments exposed at the outer and inner surfaces. Nevertheless, biochemical evidence such as antibody labelling, protease studies and chemical modification is needed to prove all predicted structures. Already it has become evident that caution is needed in the interpretation of the Hydropathy index plots. This need is demonstrated by the hydropathy index plots of the D1 (herbicide-binding) and D2 

The Cyt bIf complex is the only electron transport complex for which the transmembrane organization of all its subunits is established. This membrane-spanning complex that functions as an intermediate electron transport complex between PS II and PS I, and translocates protons across the membrane from the stroma to the lumen, contains 4 proteins Cyt / (33 kDa), Cyt 6-563 (23 kDa), the Rieske Fe-S protein (20 kDa) and the unnamed 17 kDa protein. 

The transmembrane arrangement of these subunits of the Cyt b f complex is also evident in the hydropathy index plots determined from the deduced amino acid sequences obtained from the sequencing of the chloroplast-encoded genes of Cyt /, Cyt 6-563, and the 17 kDa protein (cf. Refs. 4 and 16). Cyt/is anchored in the membrane by a single a-helix located close to the C-terminal end (= 20 amino acid residues). Most of the mainly hydrophilic polypeptide chain ( 250 amino acid 

The nuclear-eiicoded Rieske Fe-S protein is not accessible to proteolytic enzymes in thylakoids [20] or right-side-out vesicles [24], but antibody labelling shows this peptide to be exposed at both thylakoid membrane surfaces [24]. Although this thylakoid gene has not yet been sequenced, it is likely to have a structure similar to that of Neurospora Fe-S protein, which has only one membrane-spanning 

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Fig. 2. A putative transmembranc arrangement of the two hemes of Cyt h-563 cross-linking the membrane-spanning a-helices II and V predicted by the gene sequence data and hydropathy index plots according to Cramer et al. (I6. ...

Fig. 3. A putative transmembrane arrangement of the subunits of the Cyt bif complex using (a) data derived from proteases and antibody labelling [24], and (b) from gene sequences and hydropathy index plots [16],...

Figure 1.3. Diagrammatic scheme showing the possible folding of the Dj polypeptide through a thylakoid membrane in five transmembrane segments. Numbers refer to the amino acid residues. Based on predictions from hydropathy index plots by Trebst. See also Marder and Barber. ...

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.

Figure 2-30 Plot of hydropathy index versus sequence number for bovine chymotrypsinogen. The indices for individual residues have been averaged nine at a time. The solid bars at the top of the plot mark interior regions as determined by crystallography. The solid bars below the plot indicate regions that are on the outside of the molecule. From Kyte and Doolittle.280...

Hydropathy plots are used to predict buried and exposed regions of a protein. Use of these plots was first demonstrated by Rose and Rose and Roy. Hydropathy plots are based on Chothia s " observation that hydro-phobic residues (amino acid residues with hydrophobic sidechains) tend to be buried when the protein exists in its native conformation. More than one set of hydropathy values is available. The best known hydropathy indexing methodology is that of Kyte and Doolittle. 

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. 

Hydropathy plot. The hydropathic index is plotted on they axis, with hydrophobic domains at the top and hydrophilic domains at the bottom. The x axis shows the amino-acid residue number from the amino to the carboxy terminus. The protein shown is a 7-transmembrane receptor (the serotonin receptor), analogous to the epinephrine (adrenalin) receptor. The approximate positions of the seven transmembrane segments are indicated by the purple bars. (Original plot graciously provided by... 

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