Gliding edge dislocations and flipping in the conformational change of helical proteins.

Abstract

The general problem of transconformation of one helical form of protein to another is considered from a topological point of view. A notation is presented which reflects the topology of the bonding. Any helix belongs to one of two geometrical classes, the positive and negative classes. The fundamental mechanism of transconformation between helices of the same class is the edge dislocation. It has two limiting modes of propagation: glide and climb. The first appears as a caterpillar-like wave of slip that travels along the peptide chain. If the second occurs then it would be the vehicle of change in number of peptide chains. The fundamental mechanism of transconformation between molecules of opposite classes is a process we call flipping, which also probably travels as a wave. Examples of transconformation including alpha DL leads to pi 4 DL in poly-gamma-benzyl-glutamate and alpha leads to beta in keratin, are discussed.