Bioinformatics

Homework 3
1. Trp Repressor
  • What is the molecular mechanism by which the binding of tryptophan-the allosteric effector-confers DNA-binding capacity on this molecle?


answer for (c)--
    The structure changes of Trp repressor are induced by binding to the cofactor, L-tryptophan. Where the structure is altered by binding of l-tryptophan, the shaded model is that without the ligand. Helices A - F are from one polypeptide chain of the dimer, a - f are from the other. The ligand binds between helices B, C, and E of each half of the dimeric protein , pushing helices D and E of the helix-turn-helix motif away from the center of the molecule and placing the two equivalent recognition helices E and e to the adjacent major groove of normal double-helical DNA. However, the binding affinity for DNA is increased 1000-fold by the presence of the ligand.

2. Arc Repressor
  • DNA sequences of Arc operator

    5'-A T A G T A G A G T G C T T C T A T C A T-3' (21 mer)

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