Recall classification of nuclear receptors and provide examples of ligands
Nuclear receptors can be classified into four categories, imaginatively named Class I, Class II, Class III and Class IV. I'm going to present them in a table, because y'know, madddd HTML skillz:
| Ligands | Location | Structure | Response Elements (RE)* | |
| Class I | Hormones | Cytoplasm- translocates to nucleus | Homodimers | Inverted repeats |
| Class II | Lipids | Nucleus | Heterodimer (one of the monomers is always RXR, the retinoid receptor) | Direct repeats |
| Class III | ** | ** | Homodimers | No inverted repeats |
| Class IV | ** | ** | Monomers or dimers | Only to one RE half-site |
*REs are recognition sites that the nuclear receptors recognise and bind to.
**Not in the lecture or the textbook, so I assume it's not important.
Describe the general structure of nuclear receptors
Nuclear receptors have four main domains, which I'm going to illustrate using my maddddd HTML skillz (since the excitement of finding out that I still remember how to use HTML still hasn't worn off...)
| N- | N-terminal domain | DNA Binding Domain | Hinge region | Ligand-binding domain | -C |
The N-terminal domain is the least conserved (i.e. most prone to variation in length and sequence). It contains Activation Function 1 (AF1), which binds to co-regulators independent of ligand binding (i.e. it doesn't care whether ligands are bound or not, it'll bind to co-regulators no matter what).
The DNA-binding domain is highly conserved. As the name suggests, it is where the nuclear receptor binds to DNA by recognising response elements (REs, or if you want to be more technical, HREs- hormone response elements). It has two zinc fingers formed by cysteine-rich loops. (For more information about zinc fingers, please see my earlier post on transcription factors.)
The hinge region is quite flexible, and may be responsible for dimerisation and conformation changes of the receptor.
The ligand-binding domain, as the name suggests, is where ligands bind. It is highly conserved and has 12 α-helices which form a hydrophobic "pocket." It also contains Activation Function 2 (AF2), which is kinda like AF1, but unlike AF1, AF2 actually cares if ligands are bound or not (i.e. it binds co-regulators in a ligand-dependent manner).
Describe the mechanism of activation of glucocorticoid receptor and peroxisome proliferator-activated receptor, and the effects on gene transcription
Glucocorticoid Receptor
Glucocorticoid receptors are class I receptors that is synthesised from the splicing together of 9 exons (the ninth of which has an α and β isoform, but I don't know how important it is for us to remember that). From the table above, you should have already figured out that the glucorticoid receptor's Class I categorisation means that it is activated by hormones (glucocorticoids in this case, hence the name), hangs around in the cytoplasm but translocates to the nucleus when bound, forms homodimers and recognises inverted repeat recognition sequences. Now I'm going to expand on that a bit more!
In the cytoplasm, the glucocorticoid receptor usually associates with heat-shock proteins. When bound, the glucocorticoid receptor can dissociate, which allows it to dimerise and translocate to the nucleus. Once in the nucleus, the glucocorticoid receptor dimers can have effects in three ways. Firstly, the homodimers can bind to GRE (glucocorticoid response element), which activates the transcription of its genes. Secondly, the homodimers can bind to nGRE (negative glucocorticoid receptor), which, as the name suggests, has the opposite effect of GRE: it suppresses gene transcription. The third pathway is a little bit different. In this pathway, a monomer of the glucocorticoid receptor binds to a transcription factor called NFκB (that little K is the Greek letter "kappa" btw), which in turn is bound to NRE (which I presume is NFκB response element). This can increase or decrease transcription.
Peroxisome proliferator-activated receptor (PPAR)
PPAR is a class II nuclear receptor that comes in four isoforms: α, β, γ and δ. α, β and δ are all involved in fatty acid oxidation whereas γ is involved in adipogenesis, lipid metabolism and glucose homeostasis. Over a long time, PPARγ can also lead to insulin sensitisation. Their locations are also somewhat different: while β and δ are expressed ubiquitously, α is expressed predominantly in the liver, heart and brown adipose tissue, whereas γ is found in white and brown adipose tissue. The isoform that we're going to focus on is PPARγ.
So, back to the nitty-gritty how it works stuff. As you can guess from PPARγ being a class II receptor, it exists in the nucleus, forms heterodimers with the retinoid receptor (RXR) and binds to response elements with direct repeats. Like the insulin receptor, PPARγ doesn't dimerise after binding as it already exists in a dimerised state. PPARγ is also usually already bound to its response elements before ligand binding, but it's prevented from having an effect by a corepressor. When the ligand comes in, it kicks out the corepressor and brings in a coactivator. In this way, the ligand activates PPARγ and allows it to have its effects.
Now for some other random facts about PPARγ that I don't know where to put! Firstly, Ser112 (that's the 112th residue of the amino acid chain making up PPARγ that happens to be a serine) can be phosphorylated by different enzymes, including the cyclin-dependent kinases Cdk9 and Cdk7 and good ol' MAP Kinase of the Ras -> Raf -> Mek -> MAP Kinase pathway fame. The trick here is that when Ser112 is phosphorylated by Cdk9 and Cdk7, PPARγ's activity increases; when phosphorylated by MAP Kinase, its activity decreases. Why? Well, I have no idea, but it was kinda interesting.
Summarise the similarities and differences between four receptor superfamilies in terms of their location, activation and signal transduction
I've done this before, but I thought I'll put it in a nice neat table now that I know how to make them on Blogspot. (Hopefully Blogspot doesn't have the bright idea of putting in heaps of line breaks before the table after I hit "update." And yup, I'm updating because our ever-vigilant unit coordinator pointed out that I didn't actually address this point last time :) )
| Receptor superfamily | Location | Activation (Ligands, time scale) | Signal transduction |
| Ion-channel coupled receptor | Cell membrane: N-extracellular, C-intracellular | Fast neurotransmitters, very fast (milliseconds) | Channel opens, allowing ion flow |
| G-protein coupled receptors | Cell membrane: N-extracellular, C-intracellular | Hormones or slow neurotransmitters, fast (seconds) | Activate G-proteins, which go on to activate other pathways |
| Enzyme-linked receptors | Cell membrane: N-extracellular, C-intracellular | Hormones, slow (minutes) | Act as enzymes or recruit enzymes such as JAK (Janus Kinase) |
| Nuclear receptors | Intracellular: cytoplasm and/or nucleus | Steroid hormones etc., very slow (hours) | Bind to response elements, induce transcription of genes |
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