You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Introduction
Chromodomain helicase DNA-binding factor 4 (CHD4) is involved in the chromatin remodeling process and a component of the NuRD (Nucleosome Remodeling Deacetylase) complex. CHD4’s role in the NuRD complex is to slide the DNA with respect to the nucleosome thus changing the relative position of DNA to the nucleosome through the utilization of an ATPase motor domain. CHD4 in the NuRD complex is responsible for gene repression constitutively and gene activation alternatively. It has also been shown that CHD4 in the NuRD complex responds to double stranded DNA breaks[4].
NuRD Complex
The NuRD complex is comprised of histone protein deacetylase 1/2 HDAC1/HDAC2, GATA2A ,GATA2b, MTA1 ,MTA2, MTA3, MBD2, MBD3, RBBP7, RBBP4, and CHD3, CHD4, CHD5[3]. HDAC1/2 is responsible for the deacetylation of lysine residues on the histone tails, Gata2a/2b are zinc fingers that bind DNA and scaffold to Mbd2/3 which is a Methyl CpG domain that interacts methylated DNA[3]. Rbbp4/7 acts as a scaffold for MTA1 and bind to Histone H4, while MTA1 has a GATA and HDAC binding domain connecting the NuRD complex[3].
The Nucleosome
The nucleosome is comprised of 146-147 DNA base pairs wrapped around an octamer of four different proteins called histones.
The Histones
The four histone proteins: H4, H3, H2A, and H2B make up the nucleosome with two sets of two heterodimers[2]. Heterodimers consisting of H3 and H4 as well as H2A and H2B[2]. These heterodimers form an octamer through the presence of hydrophobic interaction between dimers[2].
The Dyad Axis
The formation of the histones via hydrophobic interactions forms the octamer[2]. This octamer has dyad symmetry between the H3 and H3 histones, forming the dyad axis and referred to as super helical location 0 (SHL 0) [2].
Super Helical Position
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
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 L1L2 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
Double Chromodomain/PHD Zinc Finger
CHD4 has a double chromodomain that interacts CHD4 to the backbone of DNA electrostatically at SHL ±1[1]. The double chromodomain also interacts at the H3 histone tail. The PHD zinc finger is located at SHL ± 0.5 at the C-terminus and the H3 histone tail.
ATPase motor domain Binding
CHD4 also has an ATPase motor domain towards the N-terminus which interacts to the nucleosome at SHL ±2[1]. The ATPase has 2 lobes each containing multiple ATPase motifs and binding sites for the minor groove of DNA, specifically Trp1148, Asn1010, and Arg1127 [1]. Trp1148 inserts into the minor groove from motif Va; Asn1010 inserts at SHL ± 2.5 into the minor groove as well as Arg1127 at SHL ± 2[1]. The ATPase domain lobe 2 also interacts at the acidic residues: Asp1080, Glu1083, Asp1084, and Glu1087 forming a pocket for the H4 histone tail Arg17 to insert into [1]. The acetylation of the H4 histone tail Lys16 weakens the acid-base interaction between the ATPase domain and the H4 histone tail[1]. The ATPase domain lobe 2 interacts with H3 histone core residues Gln76 and Arg83 on the alpha helix 1 at ATPase domain lobe 2 residues Asn1004 and Leu1009 [1].
ATPase motor domain Function
The binding of the CHD4 ATPase motor domain to the DNA at SHL ± 2 – SHL ± 2.5 and the subsequent closing of the conformation due the binding of ATP pre-hydrolysis, causes a twist and bulge in the DNA thus causing a forward untwisting motion of 1bp toward the dyad axis resulting in the movement of the DNA with relation to the nucleosome[1]. The hydrolysis of ATP causes a reset in conformation of the ATPase for the process to start once more[1]. While the motion of a ratchet on a ratchet strap is not an accurate metaphor for how CHD4 moves, the functionality of a ratchet strap is accurate for the function of CHD4[1].
Nucleosome-CHD42 Complex
The nucleosome is able to bind twice to CHD4 due to its symmetric duality with each SHL location roughly mirrored over the dyad axis[1]. A second CHD4 interaction with the nucleosome doesn’t change the complex’s stability or the DNA stability at SHL ± 7, the region of entrance and exit[1].
Structure Information
A 3.1 Å resolution model from cryo-EM.
