User:Sakura1997/sandbox

Article Evaluation
Article: Phosphoramidite ligand

- all of the information in the article is factual and relevant, but so specific in some cases that it is difficult to understand.

- in one paragraph, the information is cited from a 1996 article which is over 20 years old so I would consider that out-of-date and check it to make sure its still valid.

- in the opening paragraph, there is no footnote/citation and in some other places the footnotes are in places where sentences follow without citations. In those cases, it is hard to tell if the information came from the last footnote or if it has no citation at all.

- there were a couple grammatical errors throughout the article.

- in the last paragraph, the chemical symbol Ir is used but it is more clear to the reader (if they are someone unfamiliar with chemical symbols) to just type iridium. That is something that can be improved.

- the article is very neutral and factual. However, the word 'superb' is used in the last paragraph which may imply subjectivity, but its hard to tell.

- there seems to be no bias in the article.

- most of the references are peer reviewed articles from good chemistry articles which are neutral, scholarly sources. However, the dates that the articles were published are all from the 90s or early 2000s. Therefore, information from some newer articles should be added if possible.

- On the talk page, there were no direct discussions because this article is part of WikiProject Chemistry which aims to improve chemistry articles on the site. As well, this article is labelled as a Start-Class article meaning that it is in need of maintenance because it is not good enough quality at the moment. However, it is also labelled as low importance.

- The article goes way more in depth about the topic of 'monodentate ligands' than we did in class.

Week 3 Tasks - Info for tert-Butyl(dichloromethyl)dimethylsilane
1.1

Properties of tert-Butyl(dichloromethyl)dimethylsilane

 * Molecular Formula: C7H16Cl2Si
 * Molar Mass: 199.19 g/mol
 * Melting Point: 42-45°C
 * Boiling Point: 70°C (at 20 mmHg)
 * Solubility in Water: N/A

1.2

tert-Butyl(dichloromethyl)dimethylsilane

tert-Butyl(dichloromethyl)dimethylsilane

1.3

Internal Link: silanes

1.4

The Sigma-Aldrich catalog SDS for tert-Butyl(dichloromethyl)dimethylsilane

1.5

Mechanism of Molybdenum Nitrogenase

Structural models for the metal centers in the nitrogenase molybdenum-iron protein

Nitrogenase MoFe-Protein at 1.16 Å Resolution: A Central Ligand in the FeMo-Cofactor

First 250 Words (Revised)
Subtopics:


 * Structure: discussing the structure of carboxypeptidase including details about binding site and specificity.
 * Activation: improving the sentence structure of the subtopic plus including more examples of how/when carboxypeptidase is activated, what molecules activate it, and what other precursors are there.
 * Adding citations to the lead paragraph, Activation, and Function.

Types of Contributions:


 * Adding new content: adding a whole new subtopic - Structure - and adding new content to Activation subtopic.
 * Editing existing material (Activation)
 * Adding citations (lead paragraph, Activation, and Function

Bolded words/sentences are taken directly from original article (ie. not new content, I just added a couple edits and citations to the original article content):

= Carboxypeptidase = A carboxypeptidase (EC number 3.4.16 - 3.4.18) is a protease enzyme that hydrolyzes (cleaves) a peptide bond at the carboxy-terminal (C-terminal) end of a protein or peptide .

Classification

 * In this classification system, carboxypeptidases that have a stronger preference for those amino acids containing aromatic or branched hydrocarbon chains are called carboxypeptidase A (A for aromatic/aliphatic) .

Structure
The structure of carboxypeptidases are characterized by the presence of zinc at the active site. However, different carboxypeptidases have different structural characteristics. For example, carboxypeptidase A (CPA) has an active site with a single zinc ion bonded to a peptide chain of 307 amino acids. Because the active site is non-polar, it mainly binds hydrophobic C-terminal protein side chains as substrates. CPA has the ability to accommodate diverse substrates and produce various conformational changes to these substrates. This was the first structural evidence for Koshland's "induced fit" hypothesis. In contrast to CPA, which is monomeric, carboxypeptidase N (CPN) is a tetramer. CPN has an active site containing zinc but it also has two catalytic subunits and two regulatory subunits.

Activation
Some carboxypeptidases are initially found '''in an inactive form; this precursor form is referred to as a procarboxypeptidase. In the case of (CPA), the inactive zymogen form, ProCPA, is converted to active CPA by the enzyme trypsin .''' This active CPA is referred to as an exopeptidase. This mechanism ensures that the cells wherein pro-carboxypeptidase A is produced are not themselves digested. Some carboxypeptidases are only present as precursors in the body meaning they are not found in an active form unless activation occurs first. Such is the case with carboxypeptidase B2 (CPB2) which is produced in the liver and activated by either a thrombin-thrombomodulin complex or a glycosaminoglycan-bound plasmin. The activation mechanism involves removal of the activation peptide and cleavage by thrombin or plasmin. The reason CPB2 is only found in its precursor form is because it contains a mobile 55 amino acid segment as part of the active site. As a precursor, the activation peptide restricts the movement of these amino acids and keeps the enzyme stable.

Second 250 Words + 400 Additional Words
Subtopics:


 * Structure: going into more detail about the structure of carboxypeptidase, specifically the binding site (what residues and interactions are invovled).
 * Activation: going into more detail about CPB2 and why it is an unstable CP and how this relates to its activation/deactivation. I will also be discussing how it is related to fibrinolysis.
 * Inhibition: adding this new subtopic going into some detail on the inhibition of CPs: what kind of inhibitors are out there and how they interact with the binding site.

Types of Contributions:


 * Adding new content: adding a new subtopic, Inhibition, and adding new content to the Structure and Activation subtopics.

Bolded text is everything from my revised first 250 words that connects to my new additions.

Structure
'''The structure of carboxypeptidases are characterized by the presence of zinc at the active site. However, different carboxypeptidases have different structural characteristics. For example, carboxypeptidase A (CPA) has an active site with a single zinc ion bonded to a peptide chain of 307 amino acids .''' The main amino acid residues relevant to catalysis in and substrate binding in CPA are Glu-270, Arg-71, Arg-127, Asn-144, Arg-145, Tyr-248, Zn2+, and a zinc-bound water molecule. '''Because the active site is non-polar, it mainly binds hydrophobic C-terminal protein side chains as substrates. CPA has the ability to accommodate diverse substrates and produce various conformational changes to these substrates.''' A significant conformational change occurs in Tyr-248 and its peptide side chain when ligands bind to the active site of CPA. This is because the phenolic hydroxyl group of Tyr-248 can then participate in hydrogen bonding with the terminal carboxylate of the bound substrate. Because a conformational change is required in order to effectively bind the substrate, this was the first structural evidence for Koshland's "induced fit" hypothesis . There are various subsites within the CPA binding site. For instance, S1’ subsite is a hydrophobic pocket and Tyr-248 closes or ‘caps’ this pocket once the substrate has bound. The specificity for terminal carboxylates in this subsite is further enhanced by a salt link between the substrate and the positively charged guanidinium moiety of Arg-145, and an additional hydrogen bond provided by the amide group of Asn-144. The S1 subsite dictates whether catalysis will occur or not. Here, the zinc ion is bound to amino acid residues Glu-72, His-69, and His-196. Two residues that are important for catalysis, Glu-270 and Arg-127, are located opposite to each other with the zinc-water group between them. Beside the S1 subsite is a separate hydrophobic cleft that binds the P1 side chains of substrates. Non-polar aromatic P1 side chains are preferred by the hydrophobic cleft. However, x-ray crystallography studies have also indicated the preference for benzyl side chains due to the weak polar interactions with aromatic side chains of enzyme residues such as Tyr-248. These are known as “edge-to-face” interactions because the aromatic rings interact in a perpendicular fashion. Furthermore, subsite 2 contains Arg-71, Tyr-198, Ser-197, Ser-199, and Tyr-248 and it is considered a secondary site for catalysis. Subsites 2 and 3 are still hypothetical and are thought to be specific to a range of different subtrates. '''In contrast to CPA, which is monomeric, carboxypeptidase N (CPN) is a tetramer. CPN has an active site containing zinc but it also has two catalytic subunits and two regulatory subunits .'''

Activation
Some carboxypeptidases are initially f'''ound in an inactive form; this precursor form is referred to as a procarboxypeptidase. In the case of (CPA), the inactive zymogen form, ProCPA, is converted to active CPA by the enzyme trypsin . This active CPA is referred to as an exopeptidase . This mechanism ensures that the cells wherein pro-carboxypeptidase A is produced are not themselves digested. Some carboxypeptidases are only present as precursors in the body meaning they are not found in an active form unless activation occurs first. Such is the case with carboxypeptidase B2 (CPB2) which is produced in the liver and activated by either a thrombin-thrombomodulin complex or a glycosaminoglycan-bound plasmin .''' CPB2 is also called the thrombin-activatable fibrinolysis inhibitor (TAFI) or carboxypeptidase U (CPU) because it is commonly found unstable. The role of the CPB2 enzyme is that it maintains the balance between coagulation and fibrinolytic systems which add and remove fibrin, respectively. This balance is essential for haemostasis because fibrin is the main component of blood clots and maintains the fluidity of blood. '''The activation mechanism involves removal of the activation peptide and cleavage by thrombin or plasmin. The reason CPB2 is only found in its precursor form is because it contains a mobile 55 amino acid segment as part of the active site. As a precursor, the activation peptide restricts the movement of these amino acids and keeps the enzyme stable .''' Furthermore, when a conformational change occurs due to the amino acid mobility, usually in the presence of high temperatures, CPB2 becomes inactive and is further cleaved into two fragments. This is means fibrinolysis is no longer inhibited and the coagulation cascade (the cycle of platelet adhesion, activation, and aggregation) is not regulated. Although this is problematic, it is a part of the natural CPB2/TAFI deactivation mechanism.

Inhibition
There are very few natural inhibitors of carboxypeptidases. For instance, there is a 39-residue CP inhibitor found in potatoes and other solanacea (nightshade plants), and a 65-residue inhibitor found in the intestinal worm, Ascaris lumbricoides. The potato CP inhibitor has been explored in depth and its 3D structure has been determined by NMR. Evidently, it has a globular structure with N-terminal and C-terminal extensions. The five reverse turns and the 310 helix within its folding pattern are stabilized by three disulfide bridges. It was highly suspected that the role of the C-terminal extension is to interact with the CP binding site and that the N-terminal interacts with and binds to the main globular region. Later, kinetic studies and chemical modifications confirmed the role of the C-terminal and it was found to prefer CPA (Ki = 5nM) over CPB (Ki = 50nM).

As suggested by the crystal structure of CP-inhibitor and CPA bound together, the inhibitor acts similar to a peptide product (ie. after cleavage) that is tightly bound to the active site. The C-terminal Gly is cleaved by the enzyme and the rest of the inhibitor stays in place due to the interaction of other residues with the active site. The new C-terminal Val-38 carboxylate coordinates to the Zn ion at the active site and hydrogen bonds with the phenolic hydroxyl of the Tyr-284 residue.