Protein domains

by educator, published

Protein domains by educator Jan 23, 2013


Proteins are polymers of amino acids. The primary sequence of amino acids conveys to the protein the ability to fold into particular structures in three-dimensional space. Thus a protein is a series of 3D domains strung together to give a protein a particular set of functions. For example, if death and EF hand domains are part of the same protein, the protein may trigger cell death with a rise in cellular calcium levels. New proteins are selected by evolutionary pressure when different domains are mixed and matched. I have uploaded a second version of CFP that is easier to remove the support material

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Thanks so much when I used the browse button instead of just typing the file name it worked fine. We are having a high school open house coming up so I am trying to print a model of GFP (PDB: 1GFL) Sadly I am terrible with programming things so I have difficulty troubleshooting in with anything DOS. I really like how on the SH2 domain you have secondary structures what drawing method did you used for that? I was able to use polyhedral to get really great looking beta sheets in the beta can fold but I am afraid the connecting loops might be too thin and there isn't a radius option with that one. Do you have a suggestion for the method I should use? I would like the students to be able to see how GFP structure is a beta can which is a bit difficult to tell with the tube method.

I really appreciate your help. Everyone in the lab is fascinated with the printer. We are still having some problems with the PLC it was working great for a while after being in the dessicator at the end of each day. However now it seems to be acting up again not melting evenly or something. I am hoping our new filament will arrive soon and I can try a fresh spool.

It sounds like everything is working. What PDB are your trying to render? BTW I posted a version of CFP that is a bit easier to remove the scaffolding from.The file is being saved to where ever you have VML pointed to to save. Solutions: 1)search for the name you save the file as on your computer (in this case "gfp.stl" as shown in the Filename: box) and find out where the file is being saved (it is being made I believe) 2) in VML on the same line as filename: there is a button for browse. Click on this and select where you want the file to be saved. Let me know how this works out!

The error isn't in replicator I am sorry for the confusion. The error is when I am trying to convert a PDB file to stl using the instructions you gave. I get stuck at the following step...

File→ render → “enter file name” → STL → render

I am still not entirely sure what to do.

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Students learn in many different ways. One important way to learn is tactile. Some people learn best by actually touching three-dimensional models. In biochemistry classes, students usually visualize protein structures using programs such as pymol, rasmol etc. For teaching protein structure and function, I have paired 3D printed models with pymol visualization in an iPad.

There are over 40 different protein domains. The three dimensional structure of proteins and their domains is determined by x-ray crystallography or nuclear magnetic resonance (NMR). The 3D coordinates of each atom in a domain is determined and provided in a protein database (PDB) format. The PDB files for every proteins structure ever determined are freely available at PDB.org. Below is a brief description of ten different domains, followed by an explanation of how to take a PDB file and convert it to an STL file. A shout-out to PMOEWS whose work (thing:12283) inspired me and offered direction.

SH2 domain #1BFJ
Src-homology 2 (SH2) domains are modules of ~100 amino acids that bind to specific phospho tyrosine (pY) containing peptide motifs. Conventional SH2 domains have a conserved pocket that recognizes pY, and a more variable pocket that binds 3-6 residues C-terminal to the pY and confers specificity.

SH3 domain #1NEB
Src-homology 3 (SH3) domains bind to Pro-rich peptides that form a left-handed poly-Pro type II helix, with the minimal consensus Pro-X-X-Pro. Each Pro is usually preceeded by an aliphatic residue. Each in the aliphatic-Pro pair binds to a hydrophobic pocket on the SH3 domain.

CARD domain #1CY5
Caspase Recruitment Domains (CARDs) are modules of 90–100 amino acids involved in cell death (apoptosis) signaling pathways. CARDs mediate the association of adaptor proteins and procaspases (death proteins) through heterodimerization of their respective CARDs, recruiting procaspases to upstream signaling complexes and allowing autoactivation.

Death Domain #1DDF
Death domains (DD) are 80–100 residues long motifs involved in cell death (apoptotic) signal transduction. Death domains serve as recruiting modules through their ability to heterodimerize with the death domains of distinct proteins, including adaptor proteins such as FADD.

EF hand domain #2PMY
The EF-hand motif contains approximately 40 amino acids (residues) and is involved in binding intracellular calcium. Binding of calcium to regulatory EF-hand domain—containing proteins induces a conformational change, which is transmitted to their target proteins, often catalyzing enzymatic reactions.

Beta barrel (cyan fluorescent protein) #4AR7
This fluorescent protein is a variation of green fluorescent protein from a jellyfish and is the only domain that is a complete protein. The protein is routinely used to visualize a variety of biological processes. The beta barrel domain is a beta sheet wrapped around the fluorescent active site to provide structure.

Ring domain #1CHC
The RING finger is a specialized type of Zn finger consisting of 40–60 residues that binds two atoms of zinc, and is involved in mediating protein—protein interactions. Many zinc fingers bind nucleic acids. The presence of a RING finger domain is a characteristic of RING-class E3 ubiquitin protein ligases capable of transferring ubiquitin from an E2 enzyme to a substrate protein.

WW domain #1EOM
WW domains are small 38 to 40 amino acid residue modules that have been implicated in binding to Pro-rich sequences.

Helix turn helix domain #3V1A
The helix-turn helix is a DNA-binding domain. The two alpha helices are the reading or recognition helices, which bind in a groove in the DNA and recognize specific gene regulatory sequences in the DNA. This pairs well with thing:17343 by emmett!

Ig domain #2CKN
This particular domain is named for the first protein in which it was found, the immunoglobulin. An immunoglobulin is a antibody. Antibodies are generated by our immune system to recognize the specific size, shape and charge of pathogens. This domain is also found on the extracellular portion of many receptors including the interleukin-1 family of receptors.

Convert pdb to stl file

Select structure from pdb.org

open VMD 1.9.1 (http://ks.uiuc.edu/Research/vmd/)
Load pdb file →file “new molecule”

“graphics” → representations → drawing method “tube”

Radius 1.5

Resolution 10

Display →axes → off

File→ render → “enter file name” → STL → render

Open in replicator G

Scale to appropriate size (many times very small and unseeable!)

Upload to cloud.nettfabb.com to fix stl

Slice and print!


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Manda on Mar 4, 2013 said:

I was finally able to get everything to work. I switched to ReplicatorG which made much better supports than makerware as a far as ability to remove and determined that the problems with the print sticking were due to humidity effects on the plastic overcome by storing the spool in a dessicator. But I am now moving on to trying to print my own PDB model. I am trying to do GFP and I get through all the steps except the rendering. Nothing happens I am not sure the file is being made. The script says

Info>Rendering current scene to 'GFP.stl'...

Info>Executing post-render cmd 'true'...

'true' is not recognized as an internal or external command

Info>Rendering complete.

Do you know what is wrong? I think I need to change the render command from the default of true but I am not sure what I should change it too. Incidentally false does not work either. Thanks

educator on Mar 5, 2013 said:

I have not see the error in replicator before. What version of replicator are you using? What do you mean by rendering? Do you mean generating a tool path?

Manda on Feb 20, 2013 said:

Hello. These are very neat models and I am new at the 3D printing with a Makerbot Replicator2 I am having trouble printing these though. Did you use supports or rafts? I tried supports but removing them was impossible I ended up breaking the model. I am working at a University and the goal is to print some PDB proteins but right now I am having trouble just printing the chain model provided on the SD (it keeps slipping even with the tape.) Any suggestions would be appreciated.

educator on Feb 20, 2013 said:

Ah, so I have not tried printing in PLA. However, here are some suggestions that will help. 1) I use raft and full support for printing 2) if the model breaks when trying to remove the support material print the model at 20-30% infill (you select this when you are generating gcode in replicatorG) to strengthen the model 3) give the model to a patient undergrad and provide some tweezers. they do a great job of removing support material. (you will find some of them become obsessive about removing plastic). 4) if the model does break while removing the support material , do not despair, glue it back together :)

destroyer2012 on Jan 23, 2013 said:

Very cool! What printer did you make these with, and what material did you use? I use UCSF Chimera and when exported as STL, the scale becomes 1 angstrom = 1mm. Then I scale down by 50% which yields a reasonable sized object most of the time, and means all my structures are on the same scale. You should try slicing with KISSlicer as I have found the support structures KISSlicer makes to be very effective. Keep up the good work :D

educator on Jan 24, 2013 said:

I used a replicator 1 with ABS. Thanks for the scaling and slicing tips! On scaling, I was experimenting to find a size that is quickly printable with reasonable detail. My goal is to have 20 of each model for my 40 student biochemistry class! I am a great admirer or your work as well!