Interactions between an α-helix and a β-sheet: Energetics of [formula omitted] packing in proteins

Abstract

Conformational energy computations have been carried out to determine the favorable ways of packing a right-handed α-helix on a right-twisted antiparallel or parallel β-sheet. Co-ordinate transformations have been developed to relate the position and orientation of the α-helix to the β-sheet. The packing was investigated for a CH 3CO-( L-Ala) 16-NHCH 3 α-helix interacting with five-stranded β-sheets composed of CH 3CO-( L-Val) 6-NHCH 3 chains. All internal and external variables for both the α-helix and the β-sheet were allowed to change during energy minimization. Four distinct classes of low-energy packing arrangements were found for the α-helix interacting with both the parallel and the antiparallel β-sheet. The classes differ in the orientation of the axis of the α-helix relative to the direction of the strands of the right-twisted β-sheet. In the class with the most favorable arrangement, the α-helix is oriented along the strands of the β-sheet, as a result of attractive non-bonded side-chain-side-chain interactions along the entire length of the α-helix. A class with nearly perpendicular orientation of the helix axis to the strands is also of low energy, because it allows similarly extensive attractive interactions. In the other two classes, the helix is oriented diagonally relative to the strands of the β-sheet. In one of them, it interacts with the convex surface near the middle of the saddle-shaped twisted β-sheet. In the other, it is oriented along the concave diagonal of the β-sheet and, therefore, it interacts only with the corner regions of the sheet, so that this packing is energetically less favorable. The packing arrangements involving an antiparallel and a parallel β-sheet are generally similar, although the antiparallel β-sheet has been found to be more flexible. The major features of 163 observed α β packing arrangements in 37 proteins are accounted for in terms of the computed structural preferences. The energetically most favored packing arrangement is similar to the right-handed βαβ crossover structure that is observed in proteins; thus, the preference for this connectivity arises in large measure from this energetically favorable interaction.