Helix-helix packing angle preferences for finite helix axes

Abstract

Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger.

An Amino Acid Packing Code for α-Helical Structure and Protein Design

“…Like previous analyses of helix crossing angles, 62;92;93 the 4 major peaks can be seen at −150°, −45°, 25°, and 130°. Closer inspection of the curve indicates a shoulder due to a 5 th peak at 175° for the anti-parallel undecatad (11mer) repeat coiled-coil.…”

Group theory and biomolecular conformation: I. Mathematical and computational models

“…This verifies the result of Walther et al [150]. However, this is not the end of the story, because the line-on-line case is not the only way that helices can interact.…”

Characterization of the backbone geometry of protein native state structures

“…The early ideas of steric models such as knobs‐into‐holes by Crick5 and ridges‐into‐groves by Chothia7 help in understanding the role of side‐chains in helix–helix interaction. The ideas were quantified by the parameters such as the dihedral angle between the interacting helices, “Ω,” obtained using the two helical axes 7–13. The distribution of this Ω angle and its dependence on other factors were evaluated from protein crystal structures so as to understand packing of helices in proteins 7–13.…”

“…The ideas were quantified by the parameters such as the dihedral angle between the interacting helices, “Ω,” obtained using the two helical axes 7–13. The distribution of this Ω angle and its dependence on other factors were evaluated from protein crystal structures so as to understand packing of helices in proteins 7–13. Furthermore, there are exciting articles that describe the shortcomings of the methods of statistical analysis9–11 and rigorous attempts have been made recently to obtain bias‐free distribution of the Ω angle 12, 13.…”

“…These include the “knobs into holes” model proposed by Crick5 and later elaborated by Richmond and Richards6 and the “ridges into groove” model proposed by Chothia and coworkers 7. Furthermore, the packing angles of helices have been studied in great detail by Efimov,8 Bowie,9 Walther and coworkers,10, 11 Trovato and Seno,12 and Lee and Chirikjian 13. In the present study, we observe preferences in the packing of amino acid side‐chains in helical bundles based on the geometrical constraints posed by the helical backbone.…”