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Topological accessibility shows a distinct asymmetry in the folds of βα proteins
Author(s) -
Taylor William R.
Publication year - 2006
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2006.08.070
Subject(s) - asymmetry , protein folding , topology (electrical circuits) , chaperone (clinical) , fold (higher order function) , measure (data warehouse) , polypeptide chain , folding (dsp implementation) , physics , evolutionary biology , biology , combinatorics , paleontology , computer science , mathematics , amino acid , genetics , microbiology and biotechnology , data mining , medicine , engineering , pathology , quantum mechanics , electrical engineering , programming language
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‐α and all‐β protein classes. However, for the βα 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.