1azp is a model of sac7d (available at the Protein Data Bank) complexed with an 8-base pair long DNA fragment. Scientist have used sac7d to study DNA protein contacts and how solvent conditions eaffect the DNA conform.

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The interactions at the interface of an “icey dna backbone” provide a general model for incorporating B factors into atomic scale biosubstrates. B factors are a statistical measure of the probability that a particular atom lies at a particular place. The more uncertainty associated in the placement of an atom at some molecular coordinate, is interperted as having greater intrinsic temperature. In the language of thermodynamics this is expressed as,

We will look closer at B factors later.

As mentioned earlier, the exact mechanism by which thermophiles bind "hot spots" of DNA is unknown, but we can make a “decent guess” based on measured thermodynamic properties. Portions of the beta sheets on the side facing the minor groove of the DNA are rich in hydrophobic and acidic residues. Met29, Trp24, Val 26 form core hydrophobic contacts with DNA bases, while multiple lysine residues (Lys) , Arg 42, and Ser 46 form hydrogen bonds along the phosphate backbone of the major groove.

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Thermodynamic data suggests that folding of the Sac7d polypeptide requires both proton and anions binding to Sac7d for favorable free energy conditions to take place. DNA nicely fits this role and may keep the protein in a compactly folded conformation under higher then average thermal energy conditions.

Sac7d exhbits an ubiquitous population within Solfolbus, when this fact is combined with experimental results showing structural stability across a large temperature range, and the observation that the bound protein causes a sharp kink in the DNA, scientist theorize that sac7d plays an important role in DNA packaging.

Unlike eubacteria and eukaryotes there is only a small margin of research investigating how so much DNA+ fits into such a small space. Recall from elementary cell/molecular biology that archae bacteria do not have histones--even those inhabitating Yellowstone. Therefore, extreme thermophilic proteins may provide a clue as to how DNA is able to compactify while retaining sequence integrity and stability in the harshest environments that life has been found.

+ Note: The complete sulfobus genome has been characterized and found to have _number_ nucleotides.