title: Topological accessibility shows a distinct asymmetry in the folds of betaalpha proteins.
abstract: A novel measure, called "topological accessibility" quantifies how easy it is to reconstruct a protein structure using only local contacts when starting at any point on the chain. Plotting this measure for all points in the chain gives a picture of how accessible the fold is. Simple folds are accessible from all positions, others are accessible only from limited positions while the most complex folds are not accessible from any position. The distribution of topological accessibility along the chain was found to be completely symmetric for the all-alpha and all-beta protein classes. However, for the betaalpha class, a distinct asymmetry was found (with probability 10(-30) of being due to chance). Examination of the proteins contributing to this signal indicated many that have an ancient origin. This suggests that the folds of these proteins may have become fixed under the influence of amino-terminal folding before the advent of chaperone assisted folding.
authors.affiliation: Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. wtaylor@nimr.mrc.ac.uk
authors.forename: William R
authors.initials: WR
authors.lastname: Taylor
mesh_terms: D007700:Kinetics; D008958:Models, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins