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Protein Engineering, Vol. 14, No. 5, 315-319, May 2001
© 2001 Oxford University Press

Organization of regions with amphiphilic {alpha}-helical potential within the three-dimensional structure of ß-sheet proteins

William Parker1,, Annu Sood and Alice Song

Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA

The observation that strong amphiphilic {alpha}-helical potential exists in all proteins, including ß-sheet proteins, has given rise to the idea that {alpha}-helical intermediates may be critical to the folding paths of all proteins. Here we report that regions with amphiphilic {alpha}-helical potential in ß-sheet proteins are regularly spaced within the native structure of the proteins at an average interval of about 13 Å. This regular spacing did not occur when the location of amphiphilic regions was randomly assigned (p = 0.0056), suggesting some degree of organization with respect to the native fold. However, in the native structure of various non-homologous proteins that contain the same fold, the location of the regions with amphiphilic {alpha}-helical potential was not conserved. Further, there was no apparent association of amphiphilic {alpha}-helical potential with any particular type of secondary structure, confirming that this potential is not involved in maintenance of native structure and suggesting that it may be associated with a highly adaptable process.


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