1. (a) What is the molecular mechanism by which the binding of tryptophan-the allosteric effector-confers DNA-binding capacity on this molecule? The structures of the trp repressor with and without bound tryptophan provide a simple and satisfying answer. Find the structure of trp repressor itself and complexed with its operator from PDB. List the following information : (1)ID number, (2) Authors, (3) Resolutions, (4) How many residues in one monomer, (5) How many cofactors in whole complex.

(b) (i) Show the structure of trp repressor itself on your home page. Show different color for different chain in cartoon form. Indicate the residue 77 in spacefill form and yellow color.(ii) Show the complex molecule on your homepages. Show different color for different chain in cartoon form. Indicate all the cofactors in spacefill form and blue color. Indicate the residue 77 in spacefill form and yellow color.

(c) Could you answer the question stated in (a) by looking the picture you made? [reference: Introduction to Protein Structure. Branden & Tooze. p105.]

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) Show the DNA sequences of the Arc operator.

(b) 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 (at least three).