Hydropathy index

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...

Gibbs energies of, table 294 of proteins 116-118 Hydropathy index 78, 79 Hydrophobic effect 50 Hydrophobic interaction chromatography 103... 

Thr, Ala, Gin, Lys. Explain your reasoning. (Hint See the hydropathy index in Table 3-1.)... 

Hydropathy Index (of Central AA) ANLAIDV 1 Value varied... 

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 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... 

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],...

Hydrophilic and hydrophobic are terms used to denote the relative water-attracting and water-repelling property, respectively, of the side-chain when the amino add is condensed into a polypeptide (see Chapter 5). The term hydropathy index may be used to place the amino acids in order of their hydrophilicity (Kyte and Doolittle, 1985), and their relative positions are shown here on an arbitrary scale. 

Amino acid Abbreviation/ symbol Mr pKi (-C00H) pKi (-NHn pKr (R group) pi Hydropathy index Occurrence in proteins (%) ... 

Amino Acid Pka, (Carboxyl) PK,2 (Amino) PK R (R Group) Hydropathy Index ... 

The hydropathy index is a measure of the hydrophobicity of the amino aoid (the higher the number, the more hydrophobic). Values based on Kyte J, Doolittle RF. J Mol Biol 1982 157 105B132. 

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