PAGAL - Properties and corresponding graphics of alpha helical structures in proteins.

Abstract

Alpha helices (AH) are peptide fragments characterized by regular patterns of hydrogen bondingbetween the carbonyl oxygen and amino nitrogen of residues regularly spaced in sequence, resulting inspiral conformations. Their preponderance in protein structures underlines their importance. Interestingly, AHs are present in most anti-microbial peptides, although they might remain in random-coil conformations depending on the solvent dielectric. For example, the cecropin componentof the chimeric anti-microbial protein designed previously by our group comprises of two AHs linked bya short stretch of random coil. These anti-microbial peptides are often amphipathic (quantified by ahydrophobic moment), aligning hydrophobic residues on one surface and charged residues on the others. In the current work, we reproduce previously described computational methods to compute thehydrophobic moment of AHs - and provide open access to the source code (PAGAL). We simultaneously generated input files for TikZ (a package for creating high resolution graphics programmatically)to obtain the Edmundson wheel and showing the direction and magnitude of the hydrophobic moment,and Pymol scripts to generate color coded protein surfaces. Additionally, we have observed an empiricalstructural property of AHs: the distance between the Cα atoms of the ith and (i+4)th residue is equalto the distance between the carbonyl oxygens of the ith and (i+4)th residue. We validated this using100 non-homologous high resolution structures from the PISCES database. The source code and manual is available at http://github.com/sanchak/pagal and on http://dx.doi.org/10.5281/zenodo.11136.