Orientation of structural segments in globular proteins

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Abstract
Twelve globular proteins [D-glyceraldehyde-3-phosphate-dehydrogenase, carboxypeptidase, flavodoxin, papain, subtilisin, thermolysin, lactate dehydrogenase, lysozyme, myoglobin, myogen, cytochrome b5 and insulin] were 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. 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 3-dimensionally close segments exhibit a pronounced tendency toward parallel orientation, while distant segments are randomly oriented. Some conclusions are presented relating to the general problem of segment packing in globular proteins.

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