Study the interaction between proteins and DNA in more than 100 protein-DNA complexes. Arginine: A-7 T-5 G-26 C-1 Glutamate: A-? T-? G-1 C-11 Tryptophan A-? T-? G-? C-? Explain why you could not find any single bonds between tryptophan and one of the DNA bases. Explain why you found single hydrogen bonds between glutamate and some of the DNA bases. Is there a preference of arginine for one of the amino acids?
Answer :)
Tryptophan does not contain any sulfhydryl group, H-bond donor or acceptor group. Therefore, tryptophan-base interactions do not found frequently.
Glutamate binds with cytosine because the amino acid has an H-bond acceptor group but glutamate has a short side chain. Therefore, it can attach to the cytosine with a single H-bond.
Arginine shows interaction with guanine because of partial charge interactions amid amino acid side chains and guanine functional groups. Arginine has an H-bond donor group; therefore, guanine interacts with it.

Study the interaction between proteins and DNA in more than 100 protein-DNA complexes. Arginine: A-7 T-5...
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The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanisms: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix. By comprehensively analyzing the three-dimensional structures of protein-DNA complexes, we show that the binding of arginines to narrow minor grooves is a widely used mode for protein-DNA recognition. This readout mechanism exploits the phenomenon that narrow minor grooves...
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Using Protein A as a bait protein in a CO-IP study, protein B
and protein C were identified as the binding partners of Protein A
in the cell. However, the architectural arrangement of the
association of Protein A with protein B and C can be different. As
shown in the following diagram, in complex I, both protein B and
protein C form direct interactions with Protein A. In complex II,
only protein B directly interacts with Protein A, whereas protein...