Protein-DNA interactions

Non-Structure, non-Sequence Specific

1. Z-DNA binding proteins 2. Non-sequence specific interactions by sequence specific DNA binding proteins

Sequence Specific

The Importance of non-specific DNA binding

Specific binding is a competition between the target site and all other accessible DNA. Non-specific binding reduces the dimensionality of the search from a 3D volume to a 1D line. Speeds up finding target by as much as 1,000x. Sequence specific binding usually accompanied by conformational change.
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Z DNA Binding proteins

Almost all contacts to DNA backbone.

Schwartz et al., NSB, 2001, 8, 9, p.761

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Pox Viruses Contain a Z DNA binding protein required for infectivity

Yaba monkey tumor virus (YMTV) induces tumors in monkeys and humans. The viral protein E3L is oncogenic and antiapoptotic. It has 2 domains, one binds Z DNA and one binds dsRNA.

Common Features of Z DNA Binding Proteins

The lac repressor-DNA complex

Protein dimer interacts with (approximately) palindromic DNA to repress transcription Binding of the inducer (lactose) relieves repression by reducing specificity for DNA

The lac repressor

Hinge DBD

Overview of the specific lac repressor DNA complex

DBD generally poorly stable w/o DNA. The hinge is unfolded in the absence of DNA. Hinge inserts into minor groove causing an opening and bending of 8 DNA. Binding of inducer disrupts hinge-DNA interaction.

How does sequence specific binding occur?

Hinge helix Asn50 C-term helix

The dissociation of the lac repressor from DNA, which presumably, is the inverse of the association. First, the hinge helix unfolds, followed by a H-bond between Asn50 and the DNA. The loss of this H-bond destabilizes the C-terminal helix which in turn destabilizes the surrounding helices. Only the recognition helix remains stable and this forms part of a hydrophobic core of the protein. Val15 and a few other hydrophobic residues stabilize this core. If this core is disrupted, all interaction with the DNA is lost and the protein dissociates. This order was determined by measuring the exchange rate of the backbone amide 1H.

DNA recognition by the HelixTurn-Helix motif

This clearly means that there is a profound reduction in the number of conformational states from which exchange can occur. Kalodimos et al, NSB, 10 2002, 9, p.193. Thus DNA binding in an entropically unfavored process.

Sequence-specific protein DNA interactions.

Major groove

Minor groove
Hinge helix interaction.

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Specific contacts (cont.)

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The non-specific complex of lac repressor and DNA

Kalodimos et al, Science, 2004, 305, p. 386

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Specific Non Specific

Comparison of Protein-DNA Contacts

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The DNA binding coordinate of the lac repressor

This coordinate follows perfectly the presumed association pathway shown earlier.
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Take-Home Lessons
Sequence specific DNA binding is always in competition with nonsequence specific binding. The ratio is defined by the Boltzmann distribution and therefore is dependent on the energy difference between the 2 states. Non-sequence specific binding to DNA usually occurs via the backbone and involves week coulombic interactions. These type of interactions generally display a high level of dynamic behaviour and are therefore enthalpy driven. Sequence specific protein-DNA complexes are characterized by direct interaction between the bases and protein. These interactions may well be hydrophobic and coulombic. They are more rigid and usually involve conformational changes from the free state and since DS goes down, the enthalpic changes must be much larger than for non-specific interactions.

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