Fig. 1: H-bonding in polyproline II helical bundle domains.
From: Hydrogen bonding patterns and cooperativity in polyproline II helical bundles
A Experimentally determined structures from the Protein Data Bank (PDB) for HhAFP short isoform (PDB ID: 3BOG), GrAFP (PDB ID: 7JJV) and ALK Gly-rich domain (PDB ID: 7LS0/7LRZ), and predicted structure from AF2 for HhAFP long isoform (AF2 ID: D7PBP2). Roman numerals denote the distinct helices in each protein. The dashed red circle indicates the PPII helix cloned for the computational model. B Gly-rich PPII helical bundle computational model: red spheres represent oxygen; blue, nitrogen; gray, carbon, and white, hydrogen. Shown with a green dashed line are the potential hydrogen bonds that may exist based on the proximity between the hydrogen donor (i.e., N or C) and hydrogen acceptor (i.e., O) atoms. C Scheme utilized for the calculation of the different parameters between PPII helices in the different interfaces. Blue PPII helices give rise to the ab interface; the red ones, to the bc interface, and the green ones, to the cd interface. The interaction energies are probed at these colored interfaces, i.e., where the n-mers are split for the HBS calculations, both DFT-D and SAPT. The rest of the computational parameters are calculated directly between the colored PPII helices through the NBO and QTAIM analyses. For added clarity, the gray eye symbol indicates the interface under study for each case.
