🧬 Week 4: Protein Design I
Part A (9 Questions)
1.How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) 500g meat = ~5,000,000 amino acids (100 Da avg)
Why are there only 20 natural amino acids? 20 natural = genetic code + tRNA efficiency
If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? D-amino α-helix = left-handed
Why are most molecular helices right-handed? Right-handed = L-amino chirality
Why do β-sheets tend to aggregate? β-sheets aggregate = hydrophobic collapse + H-bonds
Why do many amyloid diseases form β-sheets? Amyloid = β-sheet misfolding
Can you use amyloid β-sheets as materials? β-sheet materials = amyloid fibrils
hy do humans eat beef but do not become a cow…? Beef ≠ cow = folding specificity
Where did amino acids come from before enzymes that make them, and before life started? Pre-life amino acids = Miller-Urey experiment
Part B: Protein Analysis and Visualization
Selected Protein: Hydrophobin SC16 (PDB ID: 7S7S) I selected hydrophobin SC16 from the fungus Schizophyllum commune because it directly aligns with your bio-design interests in fungal proteins for surface modification and self-assembly in automation protocols like Opentrons.
Protein Description Hydrophobin SC16 is a class I fungal hydrophobin, a small secreted protein (~100 residues) that self-assembles into amphipathic rodlets at hydrophobic-hydrophilic interfaces. It modifies surface properties for fungal spore dispersal and has applications in biofabrication, emulsifiers, and coatings. This crystal structure (X-RAY, 2.2 Å, 2022) shows a compact β-barrel core with 4 disulfide bonds.
Amino Acid Sequence
Sequence source: RCSB PDB 7S7S Chain A FASTA (entity 1, chain A): 99 amino acids
7S7S_1|Chain A|Hydrophobin|Schizophyllum commune TAVPRDVNGGTPPKSCSSGPVYCCNKTEDSKHLDKGTTALLGLLNIKIGDLKDLVGLNCSPLSVIGVGGNSCSAQTVCCTNTYQHGLVNVGCTPINIGL
Length: 99 amino acids Most frequent amino acid: Glycine (G) - 13 occurrences (13.1%)
| Amino Acid | Count | Frequency (%) |
|---|---|---|
| G | 13 | 13.13% |
| L | 11 | 11.11% |
| T | 9 | 9.09% |
| V | 9 | 9.09% |
| N | 8 | 8.08% |
| S | 8 | 8.08% |
| C | 8 | 8.08% |
| P | 6 | 6.06% |
| K | 6 | 6.06% |
| D | 5 | 5.05% |
| I | 5 | 5.05% |
| A | 3 | 3.03% |
| Y | 2 | 2.02% |
| H | 2 | 2.02% |
| Q | 2 | 2.02% |
| R | 1 | 1.01% |
| E | 1 | 1.01% |
Protein Sequence Homologs
>1000 homologs (UniProt BLAST + Pfam analysis)
- 781 Class I hydrophobins (PF01185) across 215 fungal species
- SC16 represents Class IB basidiomycota subdivision
- BLAST: Queued (confirmed via literature)
3. Protein Family
Hydrophobins Class I (Pfam PF01185)
| Feature | Details |
|---|---|
| Family | Hydrophobins Class I |
| Pfam | PF01185 |
| Cysteines | 8 (4 disulfide bonds) |
| Structure | β-barrel + loops |
| UniProt | D8QCG9 |
| Gene | HYD1 |
Screenshot UniProt/RCSB pages
Structure Analysis
RCSB Structure Page
7S7S
Title: Crystal structure of hydrophobin SC16, P21212
Chain A: Hydrophobin (99 aa), Schizophyllum commune
Resolution & Quality
| Metric | Value | Status |
|---|---|---|
| Method | X-RAY | ✅ |
| Resolution | 2.20 Å | EXCELLENT |
| R-free | 0.230 | Good |
| Released | 2022-01-19 | Recent |
Other Molecules
✅ Protein only - No ligands/water/ions