Week 4 HW — Protein Design Part1
Week 4 — Protein Design I
Selected Protein
For this assignment, I selected Calmodulin (CaM), a calcium-binding signaling protein found in many organisms, including humans.
Calmodulin plays an essential role in cellular signaling by detecting calcium ion (Ca²⁺) concentration changes and transmitting this information to other proteins.
Protein sequence source (UniProt):
https://www.uniprot.org/uniprotkb/P62158
3D structure (Protein Data Bank):
https://www.rcsb.org/structure/1CLL
Part A — Conceptual Questions
1. How many molecules of amino acids are in 500 g of meat?
Amino acids have an average molecular weight of approximately 100 Daltons (100 g/mol).
500 g / 100 g per mole ≈ 5 moles
Using Avogadro’s number:
5 × 6.022 × 10²³ ≈ 3 × 10²⁴ amino acid molecules
2. Why do humans eat beef but do not become a cow?
During digestion, proteins are broken down into individual amino acids.
These amino acids are reused to build human proteins, according to our DNA instructions.
3. Why are there only 20 natural amino acids?
The 20 canonical amino acids provide enough chemical diversity to create complex protein structures while maintaining a stable genetic code.
4. Can we design non-natural amino acids?
Yes. Scientists can design synthetic amino acids containing fluorescent groups, reactive groups, or photo-responsive elements.
5. Where did amino acids come from before life began?
Prebiotic chemistry experiments such as the Miller–Urey experiment showed that amino acids can form from simple molecules under early Earth conditions.
6. If an α-helix were made from D-amino acids, what handedness would it have?
Natural proteins use L-amino acids and form right-handed helices.
D-amino acids would produce left-handed helices.
7. Why are most molecular helices right-handed?
Because proteins are built from L-amino acids, which energetically favor right-handed helical conformations.
8. Why do β-sheets tend to aggregate?
β-sheets form strong hydrogen-bond networks that allow strands to stack together and form stable aggregates.
9. Can amyloid β-sheets be used as materials?
Yes. Despite their association with disease, amyloid structures have strong self-assembly and mechanical stability, making them promising biomaterials.
Selected Protein
For this analysis I selected Calmodulin (CaM).
Calmodulin is a calcium-binding protein that functions as a molecular sensor, detecting changes in calcium concentration and transmitting signals to other proteins.
Amino Acid Sequence
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
Sequence length: 149 amino acids