By R F Bruinsma
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Sample text
The first panel shows the pattern of chemical bonds. There is a C2 rotation symmetry. This symmetry is a characteristic of many prokaryote repressor proteins. The DNA operator sequence has a corresponding (approximate) rotation symmetry. Simple repressor proteins like cro address the DNA with “reading heads”. A reading head is an α-helix that can be inserted into the major or minor groove of the DNA double helix (usually the major groove). The second panel is a cartoon of the cro repressor/DNA complex showing the α-helices of the protein.
The only solution of Laplace’s Law with spherical symmetry is the monopole field. 19) The diffusion current density J = −D3 ∇c is along the radial inward direction, so the diffusion current I equals J(r) times the surface area 4πr2 : I = −4πD3 bc(∞). F. 13) for the case kd = 0. 13) is the number of complexes forming per second. That must equal (minus) the incoming current I. On the righthand side we can identify c(∞) with the repressor concentration [R] far from the operator. 21) known as the Debye–Smoluchowski (DS) rate.
That indicates that nucleosome particles are rather close to the unbinding transition under physiological conditions. 6 kB T /A per bp. It is actually a very reasonable design strategy for nucleosomes to be close to the unwrapping transition. , by reducing the positive charge of the histones through acetylation). Polach and Widom developed a clever way of measuring λ in an independent way [35]. Recall that digestion enzymes can cut DNA strands that are not protected by proteins. If the nucleosome “operating point” indeed is close to the Marky–Manning transition, we might expect significant thermal fluctuations in the wrapping length L.
Physics of protein-DNA interaction by R F Bruinsma
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