Homework 3 (due on 11/12>

Viewing Protein/PDB
題目1. Find the structure of prion from PDB. (A) List the following information : (1) ID number, (2) Authors, (3) The number of residues in one monomer, (4) The number of disulfide bonds. (B) Put the structure of prion on your homepages. Show different color for different secondary structure in cartoon form with sidechains on (helix in blue, sheets in red). Show the script that makes the final picture.

Ans:(A)
(1)ID number=1AG2
(2)Author:M.BILLETER,R.RIEK,G.WIDER,K.WUTHRICH,S.HORNEMANN, R.GLOCKSHUBER
(3)There are 103 residues (from GLY124 to TYR226) in one monomer.
(4)the number of disulfide bonds: 1 .
(B)the structure of prion:(兩圖為不同角度看)
script script

題目: 2. Transcription of the ant gene during lytic growth of bacteriophage P22 is regulated by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Please find the co-crystal structure of this Arc tetramer-operator complex from PDB. (a) Make an animation (by Gifbuilder) of whole complex. (b) Show the DNA sequences of the Arc operator. (c) The picture below is the hydrogen bonds between beta-sheet side chains and DNA bases. Show three side chains (gln9, asn11, arg13) from one monomer and corresponding DNA bases of them on your home page. Color three side chain with different color. Measure the distance between possible hydrogen bonds.
Ans:
(a)the Arc repressor with DNA ----please press the picture ----you will see the animation.

(b)the DNA sequence of the Arc operator:
E chain: TATAGTAGAGTGCTTCTATCAT
F chain: ~ TATCATCTCACGAAGATAGTAA
(c)three side chains (gln9, asn11, arg13) from one monomer and corresponding DNA bases:
( the dash lines mean the possible position of hydrogen bonds and I show their probable distance)