Zinc Finger:Protein Nested Model (POC Soft Mold)

Submitted by:

Thomas Card

Sat, 2016-08-20 23:01

Vertical Tabs

General Information

✓ This model was processed by NetFabb

Model ID

3DPX-003620

Category

Proteins, Macromolecules and Viruses

Keyword(s)

Nested, Zn, Zinc, Finger, NUCLEASE, mold, Silicone, POC

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.

Resolution

2.1

Resolution Units

Angstroms (A)

Model Origin

Molecular data (e.g., crystallography)

Model Details

Associated Species

Mus musculus

How to Make

Recommended 3D Printer(s)

Thermoplastic extrusion, single extruder

Thermoplastic extrusion, multiple extruders

Stereolithography/optical

Binder jetting

Laser/Heat Sintering (Metal)

Recommended Support Material

Dissolvable(not required)

Pre- and Postprocessing Instructions

Pre print:

Filaments have different temperature sensitivities and using catalyst in your resins can create an exothermic reaction that can get hot. keep this in mind when choosing both the resin and filament. You can usually decrease the temperature by using less catalyst, but it might take a few days to cure. There are also some room temperature curing silicone resins.

Model Prep:

Print with 3 shells, clean supports(i recommend dissolvable for reduced residue. You can sand down the residue if necessary), perform acetone treatment if desired.

Casting the Mold:

Use foam board and hot glue to construct a box to encase the "negative space protein model" (or 3D print an open box). place model in the box so that the funnel and vents are on the ground. Mix the silicone and catalyst, then pour it into the box. wait for it to cure then remove from the box. Cut along the backside of the mold(closest to the funnel), making fine cuts until you can take the "negative space protein model" out (beware of the pegs). In the event that you have to cut the mold completely in half (you will in order to remove the vents, POC), you can use the foam board box to ensure the top and bottom line up.

Casting the Model:

Insert pegs into the mold. insert the "Backbone" model into the mold and in the pegs. Spray RELEASE AGENT in the mold. Mix transparent resin and catalyst then pour into the mold through the funnel. let it cure. When complete, remove it from the mold. trim flashing and fill peg holes, let them cure. There was a hole that went through the mesh and I had to block it, you can reopen it with a knife if you want. done.

Attribution

PubMed ID

2 028 256

Digital Object Identifier (DOI)

10.1126/science.2028256

Author(s)

Pavletich, N.P., Pabo, C.O.

Citation Title

Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A

Journal

Science

Citation Year

1991

Month

May

Day

Volume

252

Issue

5007

Abstract

The zinc finger DNA-binding motif occurs in many proteins that regulate eukaryotic gene expression. The crystal structure of a complex containing the three zinc fingers from Zif268 (a mouse immediate early protein) and a consensus DNA-binding site has been determined at 2.1 angstroms resolution and refined to a crystallographic R factor of 18.2 percent. In this complex, the zinc fingers bind in the major groove of B-DNA and wrap part way around the double helix. Each finger has a similar relation to the DNA and makes its primary contacts in a three-base pair subsite. Residues from the amino-terminal portion of an alpha helix contact the bases, and most of the contracts are made with the guanine-rich strand of the DNA. This structure provides a framework for understanding how zinc fingers recognize DNA and suggests that this motif may provide a useful basis for the design of novel DNA-binding proteins.