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PubMed · 16104016

Alpha-alpha linking motifs and interhelical orientations.

Donald E Engel·William F DeGrado
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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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Amino Acid MotifsAmino AcidsComputational BiologyHydrogen BondingModels, MolecularMolecular StructureProtein Structure, SecondaryProteinsJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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Donald E Engel, William F DeGrado. 2005-11-01. Alpha-alpha linking motifs and interhelical orientations.. https://doi.org/10.1002/prot.20522

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