Alpha-alpha linking motifs and interhelical orientations |
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Authors: | Engel Donald E DeGrado William F |
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Affiliation: | Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. |
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Abstract: | While the geometry and sequence preferences of turns that link two beta-strands have been exhaustively explored, the corresponding preferences for sequences that link helical structures have been less well studied. Here we examine the interhelical geometry of two connected helices as a function of their link's length. The interhelical geometry of a helical pair appears to be significantly influenced by the number of linking residues. Furthermore, for relatively short link lengths, a very limited number of predominant conformations are observed, which can be categorized by their phi/psi angles. No more than two predominant linking backbone conformations are observed for a given link length, and some linking backbone conformations correlate strongly with distinctive interhelical geometric parameters. In this study, sequence and hydrogen-bonding patterns were defined for predominant interhelical link motifs. These results should assist in both protein structure prediction and de novo protein design. |
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Keywords: | de novo design helical hairpin turns motifs |
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