Hydrophobic Moments as Tools for Analyzing Protein Sequences and Structures
This chapter deals with the two main themes of this book—prediction of protein structure from sequence and principles of protein conformation—but from a narrow point of view. The point of view is that the interaction with water of the amino acid side chains is a major determinant of protein structure. Charged and polar side chains seek contact with water, and apolar side chains avoid water, preferring to cluster together beneath the surface of the protein. This avoidance of water is the hydrophobic interaction, first described in detail by Kauzmann (1959). In this point of view, it is the simultaneous attraction of some amino acid side chains to water and the avoidance of water by others that is a major factor in dictating the conformation taken by the polypeptide backbone.
KeywordsAmino Acid Side Chain Triose Phosphate Isomerase Amino Acid Analogue Hydrophobicity Scale Polar Side Chain
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