DNA unwinding protein

FIGURE 1.15 Electron density from a monoclinic unit cell of the Gene 5 DNA Unwinding Protein crystal, lying between y = 0.125 and y = 0.250, is projected onto a single plane. Superimposed upon this electron density is a portion of the atomic model of the Gene 5 Protein. Electron density planes, like those shown here, are the images obtained directly by X-ray diffraction from computed Fourier... 

It has a molecular weight of 60,000 to 90,000 daltons and requires NH4, Mg2, and native DNA for activity. It interacts with the DNA unwinding protein and this reaction accelerates the rate of DNA synthesis. The synthesis proceeds from the 5 toward the 3 direction. RNA polymerase generates the primer. 

A number of enzymes which bind polyanions such as DNA may be separated broadly into those which recognize special sequences with higher affinity than "bulk DNA" and those which bind nonspecifically. The first group includes RNA polymerases, repressors, cAMP receptor protein (CRP), the rho factor, restriction endonucleases, and methy-lases the second group includes histones and DNA-unwinding proteins. 

Figure 36-17. The generation of "replication bubbles" during the process of DNA synthesis. The bidirectional replication and the proposed positions of unwinding proteins at the replication forks are depicted.

Two proteins are initially involved in the nonho-mologous rejoining of a ds break. Ku, a heterodimer of 70 kDa and 86 kDa subunits, binds to free DNA ends and has latent ATP-dependent helicase activity. The DNA-bound Ku heterodimer recruits a unique protein kinase, DNA-dependent protein kinase (DNA-PK). DNA-PK has a binding site for DNA free ends and another for dsDNA just inside these ends. It therefore allows for the approximation of the two separated ends. The free end DNA-Ku-DNA-PK complex activates the kinase activity in the latter. DNA-PK reciprocally phos-phorylates Ku and the other DNA-PK molecule, on the opposing strand, in trans. DNA-PK then dissociates from the DNA and Ku, resulting in activation of the Ku helicase. This results in unwinding of the two ends. The unwound, approximated DNA forms base pairs the extra nucleotide tails are removed by an exonucle-... 

Figure 36-25. Double-strand break repair of DNA. The proteins Ku and DNA-dependent protein kinase combine to approximate the two strands and unwind them. The aligned fragments form base pairs the extra ends are removed, probably by a DNA-PK-associated endo- or exonuclease, and the gaps are filled in and continuity is restored by ligation.

Figure 20.14 Preparation for DNA replication. At Least three proteins are involved DNA helicases disrupt hydrogen bonds between bases to allow the two strands to unwind single-strand DNA-binding proteins stabilise the unbound strands in preparation for base pairings DNA topoisomerase relaxes strain in the strands to facilitate polymerisation.

For self-associating protein systems, third-order polynomial functions provided a good fit over the accessible range The data on AG° must show the direction of the chemical change, toward the minimum in the Gibbs function. If this proves true, the equation can be applied in the standard or nonstandard state. For protein unfolding or DNA unwinding, nonlinear models are needed Consistent with Occam s razor, the simplest description is used to describe the system, and complexity is increased only if warranted by the experimental results. 

This formalism may also be valuable in addressing protein unfolding, DNA unwinding, cold denaturation, and effects of site-direct mutagenesis on lysozyme unfolding. ... 

Single-stranded DNA binding proteins (SSBs) bind to this short region of ssDNA, which promotes further unwinding of a nearby A+T-rich region. 

DnaB protein (helicase) 300,000 6 DNA unwinding primosome constituent... 

A group of proteins form the prepriming complex. They recognize the origin of replication (dnaA protein), maintain the separation of the parental strands (single-stranded DNA-binding proteins), and unwind the double helix ahead of the advancing replication fork (helicase). 

Unwinding proteins. Proteins that help to unwind double-stranded DNA during DNA replication. 

They are unwinding proteins. They attach themselves to one strand of the DNA and promote the separation of the two strands of DNA. 

These studies [45] [47] suggest that specific protein-protein interactions between a single-stranded-DNA-binding protein and two replicative DNA-helicases allows substantial unwinding of substrates containing the major cisplatin lesion, but the mechanisms of stimulation of the helicases activities by the ICP8 protein appears to be different for the two enzymes. 

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