Workshops

1. Write SMILES strings for fumaric acid, D-gluconic acid, cholesterol, histidine, and AMP.

2. Use ISIS/Draw to sketch the above biochemical compounds.

3. Use ISIS/Draw to sketch maltotriose (malt3) and an octapeptide, GRAPHICS.

4. Convert the 2D sketch of matl3 and GRAPHICS into 3D and save them as pdb files. Compare these files with the pdb file you retrieve from the Protein Data Bank at RCSB.

5. Retrieve protein topology cartoons (TOPS) for alcohol dehydrogenase (3BTO), concanavalin (2CNA), lysozyme (1LZ1), papain (1PPN), phosphofruc-tokinase (1PFK), and rhodopsin (1BRD) or their representative TOPS. Compare their domain structures.

6. Retrieve a nucleic acid pdb file and visualize its 3D structure with RasMol. Save the structure as a graphic file in GIF format for printing.

7. Retrieve a protein pdb file and visualize its 3D structure with RasMol in different representations (Display menu). Identify the structural features or characteristics for which each display is best illustrative.

8. Retrieve a pdb file of an enzyme - substrate complex and visualize its 3D structure with KineMage. Save the structure as a graphic file in GIF format for printing.

9. Retrieve a structure file of a protein-DNA complex from Molecular Modeling Database at NCBI and visualize its 3D structure with Cn3D. Identify the interaction between the protein and DNA molecules.

10. Retrieve atomic coordinate files of two metalloenzymes, alcohol dehyd-rogenase (ADH) and Fe-superoxide dismutase (SOD), from PDB or MMDB. The subunit structure of ADH displays two metal ions, one catalytic and the other structural. The catalytic metal atom is chelated to Cys46, His67, Cys174, and a water molecule. Identify the catalytic metal atom and measure the approximate geometry of its chelation. The dimeric Fe-SOD similarly contains two Fe atoms per monomer. Search the literature to supplement the 3D structure view and present your findings regarding the function and geometry of the Fe atoms of Fe-SOD.

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