CHD4 Sandbox: Difference between revisions
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The state of the minor groove directionality is referred to as SHL (Super Helical Location) [2]. With the DNA wrapping 1.65 turns around the nucleosome, the status of the minor groove conformation with respect to the orientation of the nucleosome with SHL 0 (the Dyad axis) [2]. It is to be noted that SHL positions can be both + and – but the position remains similar, as they reflect over the dyad axis at SHL 0[2]. The sign of the SHL is referring to which pole of the nucleosome the protein domain binds to on the DNA[2]. The directionality of the DNA bound to the nucleosome changes with the ± sign of the SHL as there is an enter and exit direction of the DNA on the nucleosome[2]. | The state of the minor groove directionality is referred to as SHL (Super Helical Location) [2]. With the DNA wrapping 1.65 turns around the nucleosome, the status of the minor groove conformation with respect to the orientation of the nucleosome with SHL 0 (the Dyad axis) [2]. It is to be noted that SHL positions can be both + and – but the position remains similar, as they reflect over the dyad axis at SHL 0[2]. The sign of the SHL is referring to which pole of the nucleosome the protein domain binds to on the DNA[2]. The directionality of the DNA bound to the nucleosome changes with the ± sign of the SHL as there is an enter and exit direction of the DNA on the nucleosome[2]. | ||
==Scaffolding of Histones for DNA== | ==Scaffolding of Histones for DNA== | ||
The alpha1, aplha2, and alpha3 helices fold and form loops within the histone proteins thus connecting each helix within a histone[2]. The interaction of an alpha1 and alpha2 (L1) and an alpha2 and alpha3 (L2) loops is referred to as an <scene name='88/880268/L1l2/ | The alpha1, aplha2, and alpha3 helices fold and form loops within the histone proteins thus connecting each helix within a histone[2]. The interaction of an alpha1 and alpha2 (L1) and an alpha2 and alpha3 (L2) loops is referred to as an <scene name='88/880268/L1l2/2'>L1L2</scene> motif. While the interaction of the N-terminal ends of an alpha1 helix of the histone is referred to as an alpha1alpha1 motif [2]. These interactions of loops form points of interaction between the minor groove of the DNA and the histone octamer. Histone heterodimer H3-H4 has an L1L2 interaction at SHL ± 0.5, alpha1alpha1 interaction at SHL ± 1.5, and L1L2 interaction at SHL ± 2.5[2]. Histone heterodimer H2A-H2B has an L1L2 interaction at SHL ± 3.5, alpha1alpha1 interaction at SHL ± 4.5, and L1L2 interaction at SHL ± 5.5[2]. The H3 histone protein has an alphaN interaction with DNA at SHL ± 0.5/6.5 [2]. | ||
=CHD4 Functions= | =CHD4 Functions= | ||
==Double Chromodomain/PHD Zinc Finger== | ==Double Chromodomain/PHD Zinc Finger== | ||
