Alpha helix expansion for space-filling molecular models

thingiverse

Note: my photos aren't in CPK colors. (I like the BORN color scheme better.) This is an add-on to allow creating alpha helices of proteins in combination with: https://www.thingiverse.com/thing:1720048 https://www.thingiverse.com/thing:1730299 After printing Harfigger's really awesome space-filling molecular models, I wanted to build an alpha helix of a protein that would stay together. So I had the computer measure out the average N-H-O and H-O-C angles of a sample helix, and designed this remix of the hydrogen and oxygen atoms. The hydrogen is too small to fit a second bond inside, so I gave it a little prong instead, that is designed to fit the extra hole in the oxygen atom. You can use either the HydrogenAHB or HydrogenAHBsolid STL. My printer didn't have much luck forming a small hollow shape in TPU, so I did my hydrogens in the solid shape. Note I haven't tested any of these STLs in rigid filament and the hydrogens are likely to not fit unless printed in flex. Each HydrogenAHB fits one OxygenAHB. You will also want the following atoms from the original sets: Carbon6; CarbonDB3 in the carbon color as well as the nitrogen color; Hydrogen1; and whatever atoms for your side chains. In the photo I used all alanines, so each side chain has one Carbon6 and three Hydrogen1 atoms. Multiply these by the number of residues you wish to make. You will probably also want two OxygenDB2s for the C terminus and a Carbon6 in the nitrogen color, with three HydrogenS atoms, for the N terminus. (Real life proteins are zwitterionic.) Most of the atoms will be connected in the usual way for an amino acid. For L-aminos, as occur in nature, if the nitrogen is on your left and the carbonyl is on your right, the alpha hydrogen will be facing away from you and the side chain will be pointing up. For the peptide bond, you want the double bond to be between the C and the next residue's N, since peptide bonds are rigid with double-bond quality. The HydrogenAHB will attach to the nitrogen and will fit into the OxygenAHB of the amino acid *four* places previous. If you assemble the protein strand, keeping all the amino hydrogens pointing in the same direction, and all the carbonyl oxygens pointing in more or less the opposite direction, it will tend to self assemble into an alpha helix.