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Description
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.
Publication Date
1-23-2013
Keywords
biochemistry, protein, teaching
Disciplines
Biochemistry | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Life Sciences | Molecular Biology
Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.
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Recommended Citation
Hall, David J., "Death Domain" (2013). Protein Domains. 5.
https://lux.lawrence.edu/chem_proteindomain/5
Instructions
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 protein structure ever determined are freely available at PDB.org. Below is an explanation of how to take a PDB file and convert it to an STL file.
Convert pdb to stl file
Select structure from pdb.org
open VMD 1.9.1 (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!