User:Dssalven/sandbox

Matrigel Article

 * Fix spelling of "polymerise" - should be "polymerize"
 * All relevant, updated facts
 * Additional information could be added; proper techniques
 * Tone is neutral
 * Citations function properly
 * No talk page

CDK-2 Article

 * Article detail could be improved
 * It would be interesting to expand on and confirm the following information presented in the article:
 * "The role of this protein in G1-S transition has been recently questioned as cells lacking Cdk2 are reported to have no problem during this transition."

Cyclin E

 * This article is more detailed than the CDK-2 article
 * Contradicts above statement regarding G1-S transition

Interleukin 28B

 * Article describes protein in relation to hepatitis C treatment, but contains no further detail

Prospective Bibliography (CDK2) - Week 4

 * Regulation of the initiation of DNA replication in human cells
 * Low-Molecular-Weight Cyclin E in Human Cancer: Cellular Consequences and Opportunities for Targeted Therapies
 * An integrated view of cyclin E function and regulation
 * Mammalian cell-cycle regulation: several Cdks, numerous cyclins and diverse compensatory mechanisms
 * Cyclin-dependent kinase
 * Recent developments in cyclin-dependent kinase biochemical and structural studies

small Edit
Previous author:

The role of this protein in the G1-S transition has been recently questioned as cells lacking Cdk2 are reported to have no problem during this transition.

New addition:

Previous in vitro experiments demonstrated cell cycle arrest at the G1-S transition resulting from the deletion of Cdk2. When this experiment was replicated in vivo, the mice remained viable despite reduced body size. However, meiotic function of both male and female mice was inhibited. This suggests that Cdk2 is non-essential for the cell cycle, but essential for meiosis and reproduction. Cdk1 is believed to compensate for many aspects of Cdk2 deletion, except for meiotic function.

Cdk2 Dispensability
Previous in-vitro experiments demonstrated cell cycle arrest at the G1-S transition resulting from the deletion of Cdk2. When this experiment was later replicated in vivo, the mice remained viable despite reduced body size. However, meiotic function of both male and female mice was inhibited. This suggests that Cdk2 is non-essential for the cell cycle, but essential for meiosis and reproduction. Cdk1 is believed to compensate for many aspects of Cdk2 deletion, except for meiotic function.

Mechanism of Cdk2 Activation
Like all protein kinases, cyclin-dependent kinase 2 is structured in two lobes. The lobe beginning at the N-terminal contains many beta sheets, while the C-lobe is rich in alpha helices. Cdk2 is capable of binding to many different cyclins, including cyclins A, B, E, and possibly C.

Cdk2 becomes active when a cyclin protein binds at the active site located between the N and C lobes of the kinase. It is unique in the way that it interacts with the respective cyclins over both lobes of the protein. Cdk2 contains an important alpha helix located in the C lobe of the kinase, called the C-helix. Hydrophobic interactions cause the C-helix to associate with another helix in the activating cyclin. Activation induces a conformational change where the helix rotates and moves closer to the N-lobe. This allows the glutamic acid located on the C-helix to form an ion pair with a nearby lysine side chain. This conformational change also relocates the activation loop to the C-lobe, revealing the ATP binding site now available for new interactions.

Finally, a threonine residue is exposed and phosphorylated as the C-lobe activation segment is displaced from the catalytic site. The phosphorylated threonine residue creates stability in the final enzyme conformation. It is important to note that throughout this activation process, cyclins binding to Cdk2 do not undergo any conformational change.

Cdk2-Cyclin E Complex and DNA Replication
The success of the cell division process is dependent on the precise regulation of processes at both cellular and tissue levels. Complex interactions between proteins and DNA within the cell, as well as the cell with the surrounding tissue and extracellular matrix, allow cells to pass genomic DNA to daughter cells and incorporate new cells into a tissue. At the cellular level, the process is controlled by different levels of cyclin-dependent kinases and their partner cyclins throughout the cycle.

Cells utilize various checkpoints as a means of delaying cell cycle progression until it can repair defects. Cyclin E is a major binding partner of Cdk2, and it acts as a G1-S checkpoint control. The S phase is also known as the synthesis phase, when DNA is replicated prior to division. The Cdk2/Cyclin E complex reaches peak activity levels in late G1 phase. The ubiquitin proteasome degrades cyclin E as the cell nears the end of S phase. Therefore, cdk2 and cyclin E have a significant role in the initiation of S phase and, consequently, the DNA replication process. NPAT, a known substrate of the Cdk2-Cyclin E complex, functions to activate histone gene transcription when phosphorylated. This increases the synthesis of histone proteins, the major protein component of chromatin. This subsequently supports the DNA replication stage of the cell cycle.

Relationship Between Cdk2 Defects and Cancer
Although Cdk2 has been proven "dispensable" in the cell cycle, it is critical in the growth and proliferation of cancer cells. Cdk2 has been proven to associate with E2F transcription factors and other tumor suppressor proteins. For example, the retinoblastoma protein (often abbreviated Rb or pRb) is a tumor suppressor protein that prevents S-phase entry and cell growth. It suppresses gene transcription necessary for G1-S phase progression when bound to the E2F transactivation domain and gene promoters.

Notes from Greg:


 * There are a lot of sentences with information that needs to be cited, e.g. the entire CDK2 activation section.
 * You probably want to capitalize the whole acronym CDK to keep the style of the main article.
 * Wikilinks are not present, and they would be particularly useful when mentioning terms unknown to most people -- such as beta sheets/alpha helices -- and when mentioning things most people won't be able to recall -- such as the life cycle of the cell.
 * In CDK2 dispensability, it will probably be worth mentioning when in the life cylce of the mice the in vitro experiment began and how it was performed. i.e. Were the genes knocked out when they were still zygotes, were the proteins inhibited when the mouse was a juvenile, etc.
 * In the DNA replication section, the second sentence is a bit difficult to follow, IMO. First, I think it will be worth breaking it into two separate sentences for clarity. Perhaps state what happens in one sentence, then explain why/how it happens that way in the following sentence. Second, when you say they "incorporate new cells into a tissue," I'm assuming you mean that these daughter cells continue to exist within the same tissue, but maybe clarify it. You could say, for example, that the "daughter cells are incorporated into the parent cell's tissue."
 * In the last sentence of that same paragraph, maybe swap out "controlled" for "regulated," as I think that's a slightly more precise phrasing.
 * In your second paragraph in the DNA replication section, you mention the ubiquitin proteasome out of the blue. Is it present the whole time? Does it get activated at the end of the S phase? It seems like you're trying to go through this process chronologically -- which is good -- but I am struggling to see how this sentence ties in other than simply the fact that the S phase gets stopped.
 * You could think about splitting this same paragraph into two paragraphs. One paragraph could be about the G1-S regulation, and the other could be about histone gene transcription, etc. These feel like independent topics to me.
 * In the last sentence of your cancer section, is "it" CDK2 or Rb? It's probably best to swap the word "it" for whichever protein is doing the suppression.
 * In the cancer section, is CDK2 stopping cancer or aiding its growth? Your first sentence makes it sound like cancer cells require CDK2 to grow and proliferate, but then it seems as though you're talking about CDK2 preventing cancer's growth in subsequent sentences.
 * If you want to add an image, you could probably try to find a picture of meioses happening and label where the CDK2 would be located.

Heather's peer review is in your talk page.

Did You Know - Article Nomination
Did you know that a protein called cyclin-dependent kinase 2 is a possible target for new cancer therapies?

Cyclin-dependent kinase 2, also known as cell division protein kinase 2, is an enzyme that in humans is encoded by the CDK2 gene.

Function
The protein encoded by this gene is a member of the cyclin-dependent kinase family of Ser/Thr protein kinases. This protein kinase is highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, also known as Cdk1 in humans. It is a catalytic subunit of the cyclin-dependent kinase complex, whose activity is restricted to the G1-S phase of the cell cycle. This protein associates with and is regulated by the regulatory subunits of the complex including cyclin E or A. Cyclin E binds G1 phase Cdk2, which is required for the transition from G1 to S phase while binding with Cyclin A is required to progress through the S phase. Its activity is also regulated by phosphorylation. Two alternatively spliced variants and multiple transcription initiation sites of this gene have been reported.

The role of this protein in G1-S transition has been recently questioned as cells lacking Cdk2 are reported to have no problem during this transition. Previous in vitro experiments demonstrated cell cycle arrest at the G1-S transition resulting from the deletion of Cdk2. When this experiment was later replicated in vivo, the mice remained viable despite reduced body size. However, meiotic function of both male and female mice was inhibited. This suggests that Cdk2 is non-essential for the cell cycle, but essential for meiosis and reproduction. Cdk1 is believed to compensate for many aspects of Cdk2 deletion, except for meiotic function.

Inhibitors
Known CDK inhibitors are p21Cip1 (CDKN1A) and p27Kip1 (CDKN1B).

Drugs that inhibit Cdk2 and arrest the cell cycle, such as GW8510 and the experimental cancer drug seliciclib, may reduce the sensitivity of the epithelium to many cell cycle-active antitumor agents and, therefore, represent a strategy for prevention of chemotherapy-induced alopecia.

Rosmarinic acid methyl ester is a plant-derived Cdk2 inhibitor, which was shown to suppress proliferation of vascular smooth muscle cells and to reduce neointima formation in mouse restenosis model.

See also the PDB gallery below showing interactions with many inhibitors (inc Purvalanol B)

Gene regulation
In melanocytic cell types, expression of the CDK2 gene is regulated by the Microphthalmia-associated transcription factor.

Interactions
Cyclin-dependent kinase 2 has been shown to interact with:


 * BRCA1,
 * CDK2AP1,
 * CDKN1B
 * CDKN3,
 * CEBPA,
 * Cyclin A1,
 * Cyclin E1,
 * Flap structure-specific endonuclease 1,
 * ORC1L,
 * P21,
 * PPM1B,
 * PPP2CA,
 * Retinoblastoma-like protein 1,
 * Retinoblastoma-like protein 2,  and
 * SKP2.