Amino acid hydropathy scale

Table 15.1 Hydropathy index (or hydropathy scale) of different amino acids. This scale determines how more hydrophobic a particular amino acid is compared to others. The more positive is the number, the more hydrophobic it is and vice versa. (Table 15.1 has been adapted with permission from J. Mol. Biol,. 157 (1982), 105-132. Copyright (1982) Elsevier.)...

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.

HINT), is a hydrophobic field calculated by -> Leo-Hansch hydrophobic fragmental constants scaled by surface area and a distance-dependent function [Kellogg et al., 1991 Kellogg and Abraham, 1992a Abraham and Kellogg, 1993]. Hydropathy is a term used in structural molecular biology to represent the hydrophobicity of amino acid side chains. 

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. 

Figure 4 shows the hydropathy plots for the L-, M- and H-polypeptides of Rb. sphaeroides R-26, using a moving window of 19 amino-acid residues for each scan. The plots for the L- and M-polypeptides [Fig. 4 (A) and (B)] are very similar, showing that both polypeptides have five hydrophobic segments. Each of these hydrophobic segments contains enough amino acids to form a membrane-spanning a-helix. Note that the residue-number scale strictly applies only to the L- and H-polypeptides that for the M-polypep-tide has been shifted in order to maximize the coincidence of its hydrophobic regions with those of the L-polypeptide. The hydropathy plot for the H-polypeptide [Fig. 4 (C) ] shows that it has only one hydro-phobic region, indicating the presence of just one a-helix. Thus the presence of eleven transmembrane helices in the L-, M- and H-subunits as predicted by hydropathy plots is in accord with conclusions drawn from previous studies by circular dichroism and polarized infrared spectroscopy and later confirmed by X-ray diffraction studies.

Our algorithm can give partial answer to the question what attributes are optimal predictors for specific folding motifs. Kyte-Doolittle type hydropathy values and Chou-Fasman type conformational preferences are two obvious answers to the question what amino acid attributes are good predictors for majority of transmembrane helices. Indeed, three such scales MODKD, KYTDO and CPREF (Table 4), are on the very top of the list of the best amino acid scales (Table 5). Performance parameters that punish overprediction (A-j y and Qp) give advantage to hydropathy values. Modifications to the Kyte-Doolittle values in the MODKD... 

Orientation-dependent PMF gives valuable insight into the nature of the orientation-dependent interaction between any two amino acid residues. The orientation-dependent PMF also reveals many unexpected pair interactions which defy the trend given by the hydropathy scale. An example is provided by the Arg-Arg pair interaction, which is found to be surprisingly attractive at short separahon, even though it is one of the most hydrophilic residues. 

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