Proof of concept(POC) model, not intended for printing but might work. This method requires the creation of a silicone mold and casting transparent resins within it.  

This is the protein part of a two-part zinc finger mold, where the DNA model binds into the Zn Model. This is a nested model design was inspired by, "A Soft and Transparent Handleable Protein Model" but uses an alternate, easier method (their method here). This model is comprised of the negative space of the surface mold and an inner stiff cardinal backbone model that will be encased in transparent silicone (though acrylic and other clear resins may work). It comes with a built-in funnel, two vents, and three built in pegs (with clearance) to align the inner model with the mold (pegs 1&2 are interchangeable). Depending on the resin, you should be able to use any material for the inner model, including flexible filaments (see How To Print). For the mold, I recommend ABS. Performing an acetone treatment on the ABS mold will clear support residue and provide a smoother finish on silicone surface for improved visibility. Additionally, the ABS may ease any clearance issues between the mold segments. (I realize I should have me the funnel and vents removable pegs, but this was just a POC, If you want me to fix it leave a comment and I will add a new version).

Materials: 3D printer, Filament, Silicone resin for mold, Transparent silicone resin, foam board, hot glue gun, spray silicone release agent, sharp knife

Cast Volume≈ 290mL

DC: 8/20/16 

For more Information on modeling and printing proteins, visit here. It is still a work in progress, some if the finishing steps can be found here. Feed back is very much appreciated, feel free to leave a comment.