Orientation of structural segments in globular proteins

Abstract

Twelve globular proteins have been examined to test whether structural segments are oriented at random. Structural segments are defined as the primary sequence of linear chain neighbors bounded by consecutive peptide chain turns. It is shown that, with this definition, a structural segment can be well approximated by a straight-line segment. Each protein in the test set was exhaustively partitioned into its constituent structural segments, and a method is presented for comparing pairwise intersegment orientations. Within a protein, it is found that three-dimensionally close-segments exhibit a pronounced tendency toward parallel orientation while distant segments are randomly oriented. Finally, some conclusions are presented relating to the general problem of segment packing in globular proteins.