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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.
biochemistry, protein, teaching
Biochemistry | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Life Sciences | Molecular Biology
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Hall, David J., "CARD Domain" (2013). Protein Domains. 2.
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”
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!