User:AnthonyOpped/sandbox

Overview of Current article

 * Included the gene name of the protein
 * Included several other factors of which the CBX5 protein interacts with

What I plan on Doing with the Article
I plan on further discussing the function of this protein and its role in gene silencing via methylated lysines on histones. This protein plays a huge part in epigenetic regulation and I would like to explore more into that. Another thing I plan on adding is a mechanism of action paragraph, potentially going deeper in as to how the protein does its job. Another possible header is "structure", where I would discuss the physical properties of my protein. Lastly, there appears to be much conservation spanning vast kingdoms which draws my attention to its evolutionary history.

Possible Headers

 * Structure
 * Mechanism of function
 * Evolutionary conservation
 * Further expand on function

Structure

 * 191 amino acids in length containing 6 exons
 * N-terminal chromodomain which can bind to histone proteins via methylated lysine residues
 * C-terminal chromoshadow domain is responsible for the homodimerization and interaction with many chromatin associated non-histone proteins.

Chromodomain

 * Folds into globular conformation consisting of β-sheets packed against an α helix in the carboxy terminal segment
 * Binds to the DNA as a protein-interaction motif rather than as a DNA-binding motif due to negatively charged residues on β-sheets.

Chromoshadow Domain

 * Similar to that of the chromodomain
 * Has a globular globular conformation and 3 β-strands to complete an anti-parallel sheet
 * Readily dimerizes
 * As a result of dimerization, a groove is formed which can accommodate HP1 associated proteins containing specific consensus sequences
 * PXVXL, where X is any amino acid

Mechanism of Action

 * Gene silencing function of HP1 depends on an interaction between the chromodomain and the methylated lysine-9 (K9) on histone 3 (H3)
 * The hydrophobic pocket of the chromodomain provides the appropriate environment for the methylated residue

Sentences for final article
Chromobox protein homolog 5 is a protein that in humans is encoded by the CBX5 gene.[1][2] It is a highly conserved, non-histone protein part of the heterochromatin family. The protein itself is more commonly called (in humans) HP1α[3] and acts on methylated lysines residues leading to epigenetic repression.[4] Heterochromatin protein-1 (HP1) possesses an N-terminal chromodomain which binds to histone proteins via methylated lysine residues leading to epigenetic repression. The C-terminal of this protein has a chromo shadow-domain (CDS) that is responsible for homodimerizing, as well as interacting with a variety of chromatin-associated, non-histone proteins.

Structure
HP1α is 191 amino acids in length containing 6 exons. As mentioned above, this protein contains two domains: an N-terminal chromodomain (CD) and a C- terminal chromoshadow domain (CSD). The CD binds with histone 3 through a methylated lysine residue at position 9 (H3K9) while the C-terminal CSD homodimerizes and interacts with a variety of other chromatin-associated, non-histone related proteins. Connecting these two domains is the hinge region.

Chromodomain
Once translated, the chromodomain will take on a globular conformation consisting of three β-sheets and one α-helix. The β-sheets are packed up against the helix at the carboxy terminal segment. The charges on the β sheets are negative thus making it difficult for it to bind to the DNA as a DNA-binding motif. Instead, HP1α binds to the histones as a protein interaction motif. Specific binding of CD to the methylated H3K9 is mediated by three hydrophobic side chains called the "hydrophobic box". Other sites on HP1 will interact with the H3 tails from neighbouring histones that will give structure to the flexible N-terminal tails of the histones. Neighbouring H3 histones can affect HP1 binding by post-translationally modifying the tails.

Chromoshadow Domain
The CSD much resembles that of the CD. Similarly, it has a globular conformation containing three β-sheets, however it possesses two α-helices as opposed to just the one in the CD. The CSD readily homodimerizes in vitro and as a result forms a groove that can accommodate HP1 associated proteins that have a specific consensus sequence: PxVxL, where P is Proline, V is Valine, L is Leucine and x is any amino acid.

Mechanism of Function
HP1α primarily functions as a gene silencer, which is dependent on the interactions between the CD and the methyl H3K9 mark. The hydrophobic box on the CD provides the appropriate environment for the methylated lysine residue. While the exact mechanism of how gene silencing is done is unknown, experimental data concluded the rapid exchange of biological macromolecules in and out of the heterochromatin region. Molecules and proteins competing and interacting within the closed chromosome give the heterochromatin its genetically silenced structure. Due to the fact HP1 concentrations are higher and more static in areas of the chromosome where methylated H3K9 residues reside, it is able to out compete other open-complex associated proteins that would otherwise activate gene expression in these areas. It has also been shown that the more methylated the H3 lysine is, the higher the affinity HP1 has for it. That is, trimethylated lysine residues bind tighter to HP1 than dimethylated residues, which bind better than monomethylated residues.

The localisation driving factor is currently unknown.

Evolutionary Conservation
HP1α is a highly evolutionary conserved protein, existing ina vast range of species such a Schizosaccharomyces pombe, a type of yeast, to humans. The N-terminal chromodomain and C-terminal chromoshadow domain appear to be much more conserved (approximately 50-70% amino acid similarity) than the hinge region (approximately 25-30% similarity with the Drosophila HP1 homolog).

Interactions
CBX5 (gene) has been shown to interact with:
 * CBX1,[8]
 * CBX3,[8]
 * CHAF1A,[9][10]
 * DNMT3B,[11]
 * HDAC4,[12]
 * HDAC9,[12]
 * Histone deacetylase 5,[12]
 * Ku70,[13]
 * Lamin B receptor,[14]
 * MBD1,[9][15]
 * MIS12,[16]
 * SMARCA4,[17]
 * SUV39H1,[12][15][18]
 * TAF4,[19] and
 * TRIM28.[8][10][17][20]
 * STAT5A,[21]