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Hydropathy Plot / Sliding Window Approach

Hydropathy Plot is also termed as Hydrophobicity (or hydrophilicity) plots. Hydropathy Plot are designed to display the distribution of polar and nonpolar residues along a protein sequence. This analysis has the goal of predicting membrane-spanning segments (transmembrane proteins) which are highly hydrophobic or regions that are likely exposed on the surface of proteins which have hydrophilic domains and therefore potentially antigenic. Several scales of hydrophobicity have been developed, most of which were derived from experimental studies on partitioning of peptides in nonpolar and polar solvents. Two of the most commonly used hydrophobicity index are incorporated into the hydropathy analysis: (i) Kyte-Doolitle (ii) Hopp-Woods scale

(i) Kyte-Doolittle scale: Hydropathic regions achieve a positive value while hydrophilic values achieve negative values.

(ii) Hopp-Woods scale: This scale was developed for predicting potential antigenic sites of globular proteins, which are likely to be rich in charged and polar residues. This scale is essentially a hydrophilic index, with apolar residues assigned negative values. Scientists suggest that using a window size of 6, the region of maximal hydrophilicity is likely to be an antigenic site.

Hydropathy plot

To generate data for constructing hydropathy plot following process are done:-

1) The protein sequence is scanned with a moving window of some size. Setting window size to 5-7 is suggested to be a good value for finding surface-exposed regions, whereas a window size of 19-21 yields a plot in which transmembrane domains stand out sharply, with values of at least 1.6 at their centers.

2) At each position, the mean hydrophobic index of the amino acids within the window is calculated. It means that the hydrophobicity of a chosen number of residues within a window is summed and divided by the number of residues in the window

3) The resulting score is assigned to the residue in the middle of the window.

4) Then, the window is moved on by one residue and the procedure is repeated.

An example of a hydropathy prediction is shown in figure below. In the cases of bacteriorhodopsin, cytochrome oxidase, and bacterial photosynthetic reaction center, this simple analysis correctly identified the approximate positions of all the transmembrane helices, with no false positives.

A Kyte-Doolittle hydropathy analysis of subunits I (a) and II (b) of the bovine cytochrome c oxidase, with the true locations of the transmembrane helices marked beneath the plot. A window length of 11 residues was used. The C-terminal peripheral domain of subunit II is indicated. Helix VII of subunit I is least well predicted. It contains only 17 residues, whereas hydropathy analysis suggested a length of about 26 that partially overlaps the residues seen in the actual helix in the X-ray structure.