Analysis of Protein Secondary Structure Geometry with Implications for Protein Folding. A database of 65 proteins with crystallographically defined helices, and 47 proteins with crystallographically defined strands was created. A program written by the authors that generates axes and parameters for helices and strands was used to define the 95% confidence limits for helical and strand-like geometry. This data was analyzed. It was found that some areas within the crystallographically defined boundaries of helices and strands did not fit within the confidence limits (9.2% of helix tetrads and 27.6% of strand tetrads). Conversely, some secondary structures (28% of helices and 45% of strands) had tetrads that fit our defintion of helical and strand-like geometry but which extend beyond the crystallographically defined boundaries. The study of these areas to determine the reasons for these observations could yield important insights into the protein folding process.
by
Diana Mallows, Frederic M. Richards and Peter C. Kahn