Protein structure analysis
We use several example to learn the general steps for protein modeling.
Structure display
- Display the structure of pig insulin
4INS
find out the hydrophobic residues between the surface of dimer interaction.
- Display the structure of sperm whale myoglbin
1MBN
and compare the difference of the alpha helices.
- Display the structire of mouse immunoglobulin
1IGT
and find out the disulphide bridges between the two heavy chains, the heavy
and light chain, and within each domian.
- Display the structire of Xenopus nucleosome
1AOI
and find the DNA helix and 8 protein subunits. Show the histone tail and the
lysine resdues.
- Display the structire of green fluorescent proteins
1GFL,
1KYS,
1EMA
Find the Ser65-Tyr66-Gly67 residues and the CRO66 residue which is the source
of the light.
Structure analysis
- Compare the differences of the heme group of human hemoglobin alpha
subunit in deoxy
2HHB
and oxy
1HHO
form.
- Compare the N-terminal domain of human cacinoembryonic antigen
2QSQ
and the variable domain of human immunoglobulin light chain
7FAB
make superimposition with three residue pairs (C22-V21, W37-W33, C83-L88)
- Compare the structure of pokeweed antifungal peptide
1DKC
and spider toxin
1QK6
and measure the Ca-Ca distance and dihedral angles of three
disulfide bonds for each molecule, make superimposition based on three
disulfide bonds
- Make analysis of rat metallothionein structure
4MT2
and human metallothonein alpha
1MHU
and beta
2MHU
domain, measure the distances of the metal-Cys clusters of both domains