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Hydrophobicity Profiles for Protein Sequence Analysis

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Abstract
Table of Contents
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Literature Cited

Abstract

Hydrophobic interactions are a major force in protein folding and numerous hydropathy scales have been developed to quantify the relative hydrophobicity of the amino acids. Hydropathy profiles can be used to examine the surface features of proteins in order to generate hypotheses that can be confirmed experimentally. This unit describes the application of hydrophobicity plots to typical problems and provides suggested uses for a few selected scales.

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Introduction
Methodology
Applications
Conclusions
Accessibility of Software
Figures
Tables

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Figure 2.2.1 Hydropathy profiles of hen egg white lysozyme. The three profiles were created with the Kyte and Doolittle, the Hopp and Woods, and the Eisenberg scales using a scanning window of 7 amino acids. The Hopp and Woods scale was modified as described in the text to match other hydropathy scales.

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Figure 2.2.2 Schematic depicting the scanning window averaging technique.

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Figure 2.2.3 Effect of altering the scanning window size on the resolution of the hydropathy profile of lysozyme. All profiles were created with the Kyte and Doolittle scale. Window sizes were set to (A ) 1, (B ) 7, (C ) 11, (D ) 15, and (E ) 19 amino acids. Note that the scale in A is reduced to show the profile more clearly.

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Figure 2.2.4 Hopp and Woods profile for sperm whale myoglobin using a scanning window of 7 amino acids. Lines below the profile indicate the locations of five experimentally determined antigenic sites (Atassi, ).

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Figure 2.2.5 Hopp and Woods profile for human hemoglobin β‐subunit using a scanning window size of 7 amino acids. Bars above the profile mark the locations of β‐subunit surfaces in contact with α‐subunits (Yoshioka and Atassi, ). Lines below the profile indicate the locations of antigenic sites.

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Figure 2.2.6 Hydropathy profiles for interleukin 1β using a scanning window size of 7 amino acids. Bars above the profile indicate locations of the β strands, and lines below the profile mark the locations of turns (Finzel et al., ). (A ) Profile generated using the Eisenberg scale. (B ) Profile generated using the Kyte and Doolittle scale.

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Figure 2.2.7 Kytes and Doolittle hydropathy profile for sperm whale myoglobin generated with a scanning window size of 7 amino acids. Bars above the profile mark the locations of the helices in myoglobin.

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Figure 2.2.8 Hydropathy profiles for bacteriorhodopsin. Bars above the profiles mark the locations of the helices. (A ) Kyte and Doolittle profile generated using a scanning window size of 7 amino acids. Brackets indicate the helices predicted on the basis of the profile alone. (B ) GES profile generated using a scanning window size of 19 amino acids.

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Literature Cited

Literature Cited
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Key References
	Engleman et al., 1986. See above.
	Provides applications of hydropathy profiles to transmembrane region prediction.
	Kyte and Doolittle, 1982. See above.
	Describes the fundamental development and application of hydropathy profiles.

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