Principles and Patterns of Protein Conformation

The raw materials of protein structure are the detailed geometry and chemistry of the polypeptide and side chains plus the solvent environment. The end result is a complex tapestry of details organized into a biologically meaningful whole: a variation on one of a few harmonious themes of three-dimensional structure. For the purposes of prediction we are not concerned primarily with either of the endpoints of this process but with the logical connection between the two. Therefore, we summarize what is known of that logical connection into a set of guiding principles: hydrophobicity, hydrogen bonding, handedness, history, and the tension between hierarchy and interrelatedness. In addition, we consider particularly relevant features of the starting and ending states. However, one should bear in mind, as cartooned in Fig. 1, that our abilities to follow the protein through this remarkable transition are still rather limited in both the experimental and the theoritical realms.

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