DNA-Protein Interactions 1. 1.5 pt Some DNA-binding proteins bind in a general,
ID: 188422 • Letter: D
Question
DNA-Protein Interactions
1. 1.5 pt Some DNA-binding proteins bind in a general, non-specific manner (i.e., they bind any DNA sequence). Examples include histone and scaffold proteins that package double-stranded DNA into cells or nuclei, and single-strand binding proteins that coat single strands of DNA during replication and recombination. Describe the properties of the DNA and the proteins that are important for such non-specific binding.
2. Other proteins bind DNA in a sequence-specific manner and make most of their contacts in the major groove.
(a) 1 pt. What are these contacts?
(b) 2 pts. You’ll recall that the wildtype sequence of the EcoRI site is: 5’ . . . .GAATTC. . . .3’. From the perspective of the major groove, draw a mutant version of the EcoRI site in which the 3’ C is replaced by T. Indicate the donors and acceptors
(c) 1.5 pts. How does this change affect the major groove? Do you think it could eliminate and/or decrease recognition by EcoRI? Why or why not?
Explanation / Answer
1.All known site specific DNA-binding proteins bind relatively weakly to non-specific DNA. The binding affinity for specific sites are much higher than that of non-specific DNA sites. But non specific sites are present in very large molar excess over recognition sites. So DNA binding protein must spend most of the time by interacting with non-specific DNA sites.
Protein based H-bonds should be absent in non-specific binding.
protein-phosphate interaction is more favorable.
DNA-distortion will be absent in such binding.
vibrational restriction will be less
coupled protein folding will be absent
2.
a. Sequence specificity via a direct readout mechanism entails noncovalent interactions. These are hydrogen bonding,electrostatic forces,salt bridges,van der Waals contacts between the functional groups of the amino acids or backbone atoms of the protein and the functional groups available on the bases in the major groove of the DNA.
The R-groups of amino acids, with basic residues such as Lysine, Arginine, Histidine, Aspargine and Glutamine can easily interact with adenine of the A: T base pair, and guanine of the G: C base pair, where NH2 and X=O groups of the base pairs can preferably form hydrogen bonds with amino acid residues of Glutamine, Aspargine, Arginine and Lysine.
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