Summary

Build a super accurate, scaled 3D-model of a polypeptide chain that can be folded into all the basic protein structures, like α-helices, β-sheets, and β-turns. The model, called a Peppytide, is made by linking together many 3D-printed molecular subunits with a series of precisely placed magnets and screws. Once built, the Peppytide chain faithfully reproduces the size, shape and flexibility of proteins. When it is carefully folded into the protein helix and sheet structures, the model becomes locked in by all the magnets and becomes quite rigid.

Introduction

Proteins make up over half the dry weight of our cells. They are all built by the same amino acid units, linked together into long linear chains (called polypeptides). What makes each protein unique is the way these chains fold into precise 3D shapes. This folding process is quite complex and usually studied with the aid of computer graphics. But wouldn’t it be cool if you could hold these chains in hand, and actually fold them into real protein structures?
Here we demonstrate how to assemble a polypeptide chain model which you can hold and play with, and explore the protein structural motifs. The model is made from custom 3D-printed parts and some readily available parts. For the interested ones who want to explore the model in a greater detail, we have published a deeper scientific analysis of the model in a recent research article (Promita Chakraborty, Ronald N. Zuckermann. A coarse-grained, foldable, physical model of the polypeptide chain. Proc. Natl. Acad. Sci. U.S.A., vol. 110 (33) 13368-13373 (2013).).

Overview:

A Peppytide chain with eleven repeating units (an “11-mer”) is sufficiently long to explore the folding of various protein secondary structures. To build an 11-mer chain, you will need to 3D-print each of the three molecular subunits (M1-M3) as specified in Table 1, followed by machining and assembly. Here’s what the final product will look like.

Peppytides

Drilling and assembly blueprint

Drilling and assembly blueprint

You can get these printed by an online 3D printing service, or print them yourself if you have access to a 3D printer. A shortcut would be to print all the parts using the same color in a single run. However, if you want to make the model more interesting and informative, it is more preferable to use 3 different colors for the three different types of parts. We have chosen black for the amide unit M1, white (ivory) for the alpha-carbon unit M2, and red/blue for the methyl-group unit M3. For ease of drilling and tapping of the alpha-carbon unit, you can also 3D-print one part holder M4. Similarly, for drilling the amide unit nitrogen atom and carbon atom magnet holes, you can 3D-print the respective holders M5 and M6. Lastly, you will need to 3D-print one helix template that also doubles as a stand M7. It helps to initiate the folding of an α-helix. Here is a link to download all the .STL files necessary.

Materials

Table 1: 3D-printed parts

Part Description Quantity

M1

Amide unit 3D-printed part(M1_amideUnit.stl) 12

M2

Alpha-carbon unit 3D-printed part(M2_alphacarbonUnit.stl) 11

M3

Methyl-group unit 3D-printed part(M3_methylGroupUnit.stl) 11

M4

Alpha-carbon unit-holder 3D-printed partTo hold the alpha carbon part in place during drilling and tapping(M4_alphacarbon_holder.stl) 1

M5

Amide-unit-holder nitrogen-atom 3D-printed partTo hold the amide part in place during drilling of the nitrogen atom magnet holes(M5_amideUnit_drillNitrogenAtom_holder.stl) 1

M6

Amide-unit-holder carbon-atom 3D-printed partTo hold the amide part in place during drilling of the carbon atom magnet holes(M6_amideUnit_drillCarbonAtom_holder.stl) 1

M7

Helix stand and template 3D-printed partTo help fold an α-helix(M7_helixTemplate.stl) 1

Table 2: Readily obtainable parts

Part Description Quantity

M8

Neodymium rod magnets,3/16″D x 1/8″H For hydrogen bonding 27 (2 for each amide, 3 for helix template M10)

M9

Neodymium rod magnets1/8″D x 1/8″H For bond faces (4 for each alpha-carbon unit, and 5 for each amide unit)

M10

Screw(Pan-head machine screw 5/8″H, 4-40 thread) For bonds 33

M11

Nut(3/32″H, 0.25″D, 4-40 thread) For bonds 33

M12

Spacer(Nylon spacer; 0.25″D x 3/8″H) For bonds 33 (3 for each alpha-carbon unit)

M13

Epoxy (JB-weld) For gluing H-bond magnets to amide units; bought from local hardware store 1

Table 3: Our suppliers for the readily obtainable parts

Part

Supplier Part Number
Screw (M10) McMaster-Carr(mcmaster.com) 91735A109
Nut (M11) 91841A005
Spacer (M12) 94639A202
Magnet (for bond faces, 1/8″D x 1/8″H) (M9) Magcraft.com NSN0658
Magnet (for H-bond, 3/16″D x 1/8″H) (M8) K&J Magnetics, Inc.(kjmagnetics.com) D32-N52

The Peppytide model is an exact scale model where 1 Angstrom (10-10 meters) equals 0.368”. Thus, the model subunits are held at a precise distance from each other. It is therefore extremely important that the spacers, screws, nuts used are of the exact size described in Table 2. Any variation would result in deviation from the effective bond lengths, and you may not be able to ultimately fold the chain into a perfect helix after all the hard work of assembly.

Tools Needed:
• 3D printer (we used uPrint Plus)
• Drill press and a set of numbered drill bits
• Tapping tools (4-40 thread)