User:MursalSadat/sandbox

Revisions of first 250 words:

Metallochaperones: Metallochaperones bind to specific metals and guide them towards their specific binding site in the appropriate protein. Free forms of certain metals can be toxic to the cell so metallochaperones are used to transport these metals to their appropriate protein, safely. Metallochaperones are present at different locations inside the cell including the cytoplasm, Golgi apparatus, and the mitochondria. An example of an intermembrane space chaperone is COX17. This Cu chaperone is used to transport copper to its appropriate protein.

ATX1 or ATOX1: Atox1 is a metal chaperone that is able to coordinate to copper in the cytosol and deliver it to its appropriate protein, ATP7B. This protein is a membrane transporter that distributes copper to biosynthetic pathways as well as regulate copper levels in the liver, brain and other tissues. Copper binding to ATP7B is crucial in the P-type ATPase catalytic cycle because it allows the formation of the phosphorylated enzyme intermediate. The absence of Atox1 would result in a excess of copper in the body and the inability to activate ATP7B which leads to a fatal hepatoneurologic disorder, Wilson's disease.

LYS7: Lys7 is a copper metallochaperone that is used to bind copper in the cytoplasm of the cell and deliver it to the apoprotein Cu/Zn superoxide dismutase.

Fe Metallochaperones: The toxicity of Iron to cells is like that of copper, hence, homeostatic control mechanisms can be put in place to ensure very low levels of toxic free Iron in the cell. Therefore, Iron metallochaperones exist to prevent any damage to the cell by binding to and directing Iron to its corresponding protein.

Other Revisions:

CCS: These copper chaperones are used to transport Cu into the CU and Zn requiring SOD1. the SOD1 is used to guard the cell against oxidation damage by collecting toxic superoxide anion radicals.

PBT2: The metallochaperone PBT2 has been shown to improve cognition in a clinical trial with recipient with Alzheimer disease. PBT2 is used to transport Zinc and Copper from outside the cell, where it can be toxic, into the cell and transport it to specific proteins/enzymes where they are beneficial. PBT2 has been shown to promote AB degradation, inhibit GSK3, tau phosphorylation and calcineurin which all contribute to improved cognition with AD patients.The affinity of PBT2 to Cu and Zn is higher than the affinity of AB to the metal, therefore it is cable to inhibit the AB/metal interactions by sequestering the metal ions. The affinity of PBT2 to Cu or Zn is greater outside the cell, however once transported into the cell, the affinity decreases and the metals become bioavailable and can dissociate from PBT2.

Cofactors in the folding of Azurin:

Many proteins need to coordinate to cofactors to attain their activity. These cofactors are usually metal ions and they interact with the appropriate protein. Azurin is a blue copper protein and is able to coordinate to cofactors, Cu1+, Cu2+, and Zn2+. These metal ions can bind to unfolded apo-azurin and form folded holo-azurin, its native state.

Folded holo-azurin, also known as the active form of the protein and folded apo-azurin, known as the inactive form of the protein. Apo azurin requires the coordination to a metal ion to produce the active form of azurin (holo azurin).

Azurin folding can be depicted in two different pathways: 1) copper coordinating to the unfolded apo-azurin followed by the protein folding into its native state; 2) unfolded apo-azurin folds into the folded apo-azurin form followed by the coordination of the copper ion in order to fold into its native state.

The fastest way to activate functional azurin is via copper coordination before the folding of the polypeptide. This means that Azurin folding is much more rapid when the metal ion (copper) binds to the unfolded polypeptide chain rather than the folded-apo azurin.

Topics and subtopics:

Multicopper oxidases

- L-ascorbate oxidase article

-Nitrite reductase reaction equation for nitrite reduction + reaction mechanism

Nitrogenase

Nitrogenase reduction is dependent on a supply of a low-potential reductant, MgATP, an anaerobic environment, and $H^{+}$. The Nitrogenase reaction involves a series of reductions. $N_{2}$ is reduced with hydrogen to form a diimine, which is further reduced to produce a hydrazine molecule and finally the hydrazine is reduced to produce 2 $NH_{3}$ molecules.

Blue copper proteins

-azurin structure

-role of cofactors in folding of Azurin

Many proteins need to coordinate to co factors in order to attain their activity. These co factors are usually metal ions and they interact with the appropriate protein. Azurin is a blue copper protein and is able to coordinate to co factors, Cu1+, Cu2+, and Zn2+. These metal ions can bind to unfolded apo-azurin and form folded holo-azurin, its native state. Folded holo-azurin, also known as the active form of the protein and folded apo-azurin, known as the inactive form of the protein . apo azurin requires the coordination to a metal ion to produce the active form of azurin (holo azurin). Azurin folding can be depicted in two different pathways: 1) copper coordinating to the unfolded apo-azurin followed by the protein folding into its native state; 2) unfolded apo-azurin  folds into the folded apo-azurin form followed by the coordination of the copper ion in order to fold into its native state.

Metal Chaperones

Metallochaperones bind to specific metals and guide them towards their specific binding site in the appropriate protein. Free forms of certain metals can be toxic to the cell so metallochaperones are used to transport these metals to their appropriate protein, safely. Metallochaperones are present at different locations inside the cell including the cytoplasm, Golgi apparatus, and the mitochondria. An example of an intermembrane space chaperone is COX17. This Cu chaperone is used to transport copper to its appropriate protein.

Different types of metal chaperones:

ATX1 or ATOX1:

Atox1 is a metal chaperone that  is able to coordinate to copper in the cytosol and deliver it to its appropriate protein, ATP7B. This protein is a membrane transporter that distributes copper to biosynthetic pathways as well as regulate copper levels in the liver, brain and other tissues. Copper binding to ATP7B is crucial in the P-type ATPase catalytic cycle because it allows the formation of the phosphorylated enzyme intermediate. The absence of Atox1 would result in a excess of copper in the body and the inability to activate ATP7B which leads to a fatal hepatoneurologic disorder, Wilson's disease.

LYS7

Lys7 is a copper metallochaperone that is used to bind copper in the cytoplasm of the cell and deliver it to the apoprotein Cu/Zn superoxide dismutase.

Fe Metallochaperones

The toxicity of Iron to cells is like that of copper, hence, homeostatic control mechanisms can be put in place to ensure very low levels of toxic free Iron in the cell. Therefore, Iron metallochaperones exist to prevent any damage to the cell by binding to and directing Iron to its corresponding protein.

CCS:

These copper chaperones are used to transport Cu into the CU and Zn requiring SOD1. the SOD1 is used to guard the cell against oxidation damage by collecting toxic superoxide anion radicals.

PBT2:

Bioinorganic Chemistry

-Entatic state principle elaboration

Iron transport and storage

-Transferrin receptor

References:

Bertini, I., Gray, Steifel, & Valentine. (2007). Biological inorganic chemistry: Structure and reactivity. Sausalito, CA: University Science Books.

Hoffman, B. M., Lukoyanov, D., Yang, Z. Y., Dean, D. R., & Seefeldt, L. C. (2014). Mechanism of nitrogen fixation by nitrogenase: the next stage. Chemical reviews, 114(8), 4041-62.

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== Nitrate Reductase (Types) ==

Prokaryotic

Assimilatory bacterial nitrate reductase/Cytoplasmic assimilatory nitrate reductase

This group of nitrate reductases contain 2 NRases contained in bacteria: ferredoxin/flavodoxin-dependent Nas and NADH-dependent Nas. These two classes differ from one another based on their cofactor structure.

Ferredoxin/ flavodoxin-dependent Nas

Ferredoxin-dependent Nas consists of a Mo-co active center and Fe-S clusters. The amino acid sequence contains a cysteine at the N-terminus of the protein. A.chroococcum, Clostridium perfringens, and Ectothiorhodospira shaposhnikovii are examples of bacteria that consist of ferredoxin-dependent nitrate reductases. The Ferredoxin Nas structure resembles that of cyanobacteria, eukaryotic algae and vascular plants which contain cysteine residue to bind the iron Sulphur and siroheme cofactors.

NADH-dependent Nas

NADH-dependent nitrate reductases are heterodimers which consist of a molybdenum cofactor and [4Fe-4S] center along with 2 subunits, a FAD containing subunit (45kD) and a catalytic subunit (95kD). This type of NRases are found in Klebsiella oxytoca and Rhodobacter capsulatus bacteria. Klebsiella oxytoca NRases has an extra [2Fe-2S] center coordinated to the C-terminal cluster on the cysteine residues. This unique coordination is what makes the two classes of assimilatory bacterial NRases different.

Membrane-bound respiratory nitrate reductase

These bacterial enzymes are commonly found in E. coli bacteria and three subunits make up the enzyme; α, β, and γ subunits. Subunits α and β are located in the cytoplasm while subunit γ is located in the membrane. Subunit γ acts as an anchor and anchors subunits α and β to the internal membrane. Subunit γ is a hydrophobic protein in which the N-terminus is localized in the periplasm and the C-terminus is localized in the cytoplasm and is made up of 2 b-type hemes. Electrons from Quinone are transferred from subunit γ to subunit β using b-hemes via histidine ligand chains. This forms a transmembrane electrochemical gradient where ATP formation takes place using ATP synthase. Nitrate reduction occurs on subunit α, which is made up of [4Fe-4S] cluster and a molybdenum cofactor.

Periplasmic dissimilatory nitrate reductase

Periplasmic dissimilatory nitrate reductases catalyze the denitrification process in prokaryotes. These NRases are heterodimers which involve 2 subunits. A catalytic subunit, which consists of a molybdenum cofactor and a [4Fe-4S] center and another subunit which consists of two heme cytochrome c. This type of NRases are found in H. influenza, Shewanella putrefaciens, salmonella typhimurium,etc.

Eukaryotic

Assimilatory eukaryotic nitrate reductase (Euk-NRase)

Eukaryotic assimilatory nitrate NRases consists of a molybdenum center coordinated to two sulfur atoms. These NRases are active when they are present as a homodimer. The nitrogen reductase monomer consists of 3 subunits; the molybdenum center, the Fe-heme of cytochrome b₅ domain and the C-terminus with the FAD cofactor.

Catalytic mechanism for nitrate reductase

Nitrate reductase catalytic mechanism

Types of NRases

Types of nitrate reductases

Catalytic cycle for CuZnSOD

Catalytic cycle for CuZnSOD

Metal binding site represented by a reduced model.

CuZnSOD metal binding site represented by a reduced model

Metal binding site represented by an oxidized model.

Carbonic Anhydrase Mechanism

Carbonic Anhydrase Mechanism

Nitrate Reductase

• Different types of NRases
• Catalytic Mechanism diagram
• References

Carbonic Anhydrase

• Mechanism diagram
• Reference

Superoxide Dismutase

• Mechanism diagram
• CuZnSOD active site diagram
• Reference

Week3 Tasks- Info for Potassium Oxalate Monohydrate

Properties of Potassium Oxalate Monohydrate

• Molecular formula: $C_{2}H_{2}K_{2}O_{5}$
• Molar mass: 184.23
• m.p. -
• b.p. -
• solubility in water: soluble 0.1M

Potassium Oxalate Monohydrate

Potassium Oxalate Monohydrate

The Sigma-Aldrich catalog entry for Potassium Oxalate Monohydrate

For further information visit oxalates.

Properties
Molecular formula	$C_{2}H_{2}K_{2}O_{5}$
Molar mass	184.23
m.p.	-
b.p.	-
Solubility in water	soluble 0.1M

$2x^{2}+2x+{24 \over 2}=4^{2}$

Nitrogenase gene diversity and microbial community structure: a cross-system comparison

Nitrogenase and biological nitrogen fixation

Photoinhibition of Photosystem II. Inactivation, protein damage and turnover

References:

MursalSadat/sandbox

Names
IUPAC name dipotassium;oxalate;hydrate
Identifiers
CAS Number	6487-48-5 Y
PubChem CID	2724193
UNII	6S7F3685W2 Y
Properties
Chemical formula	$C_{2}H_{2}K_{2}O_{5}$
Molar mass	184.23
Appearance	Crystalline powder
Solubility in water	Soluble in cold water
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Infobox references