Characterization of alpha helices interacting with nucleic acids

Protein–nucleic acid interactions play a vital role in most genetic processes. An enhanced insight into such interactions can be obtained from the structure database of these complexes. Here, we report an overall survey on the geometry of alpha helices which interact with nucleic acids through hydrogen bonds and/or non-bonded interactions. Using the program RADIL based on an algorithm developed from this laboratory, 161 alpha helices in 70 non-redundant nucleic acid binding protein chains solved using X-ray crystallography are analysed. The helical geometry has been characterized as bent, canonical, terminally or completely distorted. The analysis reveals that ∼70% of the alpha helices possess distortions of any one kind, viz., bend, terminal distortion or complete distortion. Nearly one-third of the total helices possess bends, with a majority of the bending occurring in 5–15° range. In addition, a majority of the bent helices approach the nucleic acid helix in a perpendicular direction. The program RADIL has been useful in characterizing the nucleic acid-induced structural variations in alpha helices, however small they may be.