title: Alpha-alpha linking motifs and interhelical orientations.
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.
authors.affiliation: Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Donald E
authors.initials: DE
authors.lastname: Engel
authors.forename: William F
authors.initials: WF
authors.lastname: DeGrado
mesh_terms: D020816:Amino Acid Motifs; D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry
chemical_list: D000596:Amino Acids; D011506:Proteins