Characterization of fold diversity among proteins with the same number of amino acid residues.
Chain entanglements provide a simple and global measure of folding in a macromolecule. The complexity of these entanglements can be expressed by the pattern of projected bond-bond crossings, or "overcrossings", associated with the molecular backbone. In this work, we use this approach to characterize quantitatively the range of tertiary folds observed in proteins with a given chain length. To discriminate among folding features, we use two shape descriptors derived from the probability distribution of overcrossings: the mean overcrossing number, N, and the most probable overcrossing number, N*. The values of N and N* relate to the content of secondary structure in a protein as well as its global three-dimensional organization. We propose a measure of folding diversity based on the properties of these descriptors. In addition, we discuss the application of our method to study how tertiary folds evolve during protein dynamics.
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Département de chimie et biochimie, Laurentian University, Sudbury, Ontario, Canada.
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D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D013058:Mass Spectrometry; D008970:Molecular Weight; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins