User:Jacob Holt/Sandbox 1: Difference between revisions

[[Image:SCD1_rxn.png|500 px|right|thumb|Figure 1. Overall reaction completed by the SCD1 enzyme. It introduces a double bond between carbons 9 and 10 on the ligand Stearoyl CoA, converting it into Oleoyl CoA.]]Stearyol CoA Desaturase (SCD1) functions as a lipogenic enzyme which is essential for fatty acid metabolism. SCD1 desaturates the sigma bond, within the 18-carbon acyl-CoA ligand, that attaches carbons 9 and 10<ref name="Bai">PMID: 26098370 </ref>.  The primary role of SCD1 is to catalyze the biosynthesis of monounsaturated fatty acids (MUFAs) via saturated [https://en.wikipedia.org/wiki/Acyl-CoA acyl-CoAs] with an acyl chain length of 14-19 carbons<ref name="Paton">PMID: 19066317 </ref><ref name="Shen">PMID: 32470559 </ref>. Variations of the monounsaturated fatty acids function as precursors for the biosynthesis of [https://en.wikipedia.org/wiki/Phospholipid phospholipids], [https://en.wikipedia.org/wiki/Cholesteryl_ester cholesteryl esters], and [https://en.wikipedia.org/wiki/Triglyceride triglycerides]; therefore, SCD1 is a promising candidate for drug targeting<ref name="Bai" />.

 

 

[[Image:colorful2.jpg|352 px|thumb|right|Figure 3. Hydrophobicity of each of the 12 helices found in SCD.  red, blue, yellow, and green represent helices found in the transmembrane region.  Orange helices represent helices found on the surface of the membrane.  Pale yellow helices represent the hydrophilic helices.]]SCD1 is a [https://en.wikipedia.org/wiki/Transmembrane transmembrane protein] (4 helices in membrane, 8 helices in cytoplasm, shown in Figures 2 and 3) that acquires electrons via an electron transport chain which includes [https://en.wikipedia.org/wiki/Cytochrome_b5_reductase cytochrome b5 reductase] and [https://en.wikipedia.org/wiki/Cytochrome_b5 cytochrome b5].  The electrons are transferred via a ternary complex and accepted by SCD1 by the iron metal ions<ref name="Shen" />.  SCD1 has 4 helices that are hydrophobic, 8 helices that are hydrophilic, and 3 helices that are amphipathic<ref name="Bai" /><ref name="Shen" />(Figure 2).There are two Fe2+ metal ions within the structure of SCD1 that were determined by x-ray fluorescence chromatography [https://en.wikipedia.org/wiki/X-ray_fluorescence x-ray fluorescense]<ref name="Shen" />.  These ions are believed to be the activators of the catalytic molecule to allow for the desaturation reaction to occur within the enzyme.

The ligand binding pocket is a narrow tunnel that extends approximately 24 Å into the mostly hydrophobic interior of the protein. The ligand is stabilized by bending into a kinked conformation which creates a tight fit in the binding pocket tunnel, and by a hydrogen bond that occurs between the <scene name='87/877552/W258/3'>W 258</scene> side chain and the acyl carbonyl<ref name="Bai" />. The kink in the tunnel is formed by the conserved residues, <scene name='87/877552/Desaturation_site/10'>T 257 and W 149</scene> which are stabilized by the hydrogen bond shared with Q143<ref name="Bai" />. There are <scene name='87/877552/Substrate_orientation_w_fe/7'>two Fe2+ ions</scene> that interact with the substrate; the Fe2+ ions are coordinated by <scene name='87/877552/Histidine_coordination/8'>9 invariant histidine residues</scene>.  <scene name='87/877552/Substrate_oreintation_fe_90deg/5'>When rotated 90 degrees</scene> the ligand is seen to be in a eclipsed position, indicating it is in its post-reaction form.  One metal ion is coordinated by 4 histidines residues and a water molecule, and the other metal ion is coordinated by 5 histidine residues<ref name="Bai" />.  The histidine residues position the metal ions 6.4 Å apart<ref name="Bai" />.

The ligand is desaturated at carbons 9 and 10<ref name="Shen" />.  The desaturation site of the ligand takes place inside the active site tunnel which enforces correct positioning of the substrate<ref name="Bai" />.  Before the reaction occurs, the ligand is in a gauche conformation at the desaturation site. This was determined by accidental usage of <scene name='87/877552/Pre_reaction_substrate_zn/3'>Zn+ ions</scene> which allowed for binding of the substrate but prevented the reaction<ref name="Shen" />.  The product is in a cis conformation post-reaction. The product structure was determined using Fe2+ metal ions which allowed for the full reaction to take place<ref name="Shen" />.  The difference between the <scene name='87/877552/Overlay_of_ligands/6'>substrate and product</scene> is the creation of a double bond, and the positioning of carbon 9 and 10 into a eclipsed position

The two conserved residues of the active site cap are <scene name='87/877552/Active_site_cap/8'>Y 104 and G 287</scene>.  These two residues form a hydrogen bond creating a rigid barrier at the end of the active site to keep the ligand from moving during the reaction<ref name="Bai" />.  The active site cap is also used in determining the substrate length when entering the active site<ref name="Bai" />.   

== Proposed Mechanism ==

[[Image:SCD1_New.jpeg|450 px|right|thumb|Figure 4: A proposed mechanism for SCD1 desaturase. The catalytic water molecule reacts with Fe2+ and O2 to create oxygen radicals on the iron ions. Electrons are brought in via an electron transport chain; this lowers the oxidation state of the iron ions and forms the reactive species. The first hydrogen is abstracted creating a radical intermediate that is then deprotonated again to make the final desaturated product. Electrons are transferred in again to allow for the iron ions to go back to their original oxidation state because enzymes must end a reaction in the same state, they started it. Figure was a modification of scheme 1 proposed by Yu M. and Chen S.5.]]

'''Step 1''': Addition of O2 and H2O which react with the Fe2+ ions to create oxygen radicals on the iron ions (Figure 4).  

'''Step 2''': Electron/proton pair is brought in via the electron transport chain; this increases the oxidation of both iron ions, gets rid of the radicals, and creates an active Fe-oxyl molecule (Figure)<ref name="Yu" />. Fe-oxyl molecule is reactive enough, due to the change in the oxidation state, to pull off the first hydrogen on carbon 9 (Figure 4).   

'''Step 3''': An unstable radical intermediate of the 18-carbon acyl-CoA ligand is formed which reacts with the other Fe-O molecule, in the +3 state, to pull of the second hydrogen and form the final product (Figure 4)<ref name="Yu" />.  

'''Step 4''': Another electron/proton pair is brought in to create three H2O molecules and to take the Fe ions back down to their original oxidation state of +2 (Figure 4)<ref name="Yu" />.  

[[Image:scd_in_membrane.jpeg|500 px|thumb|Figure 5. Position of SCD within the biological membrane.  The protein is part of an electron transport chain involving cytochrome b5 reductase (PDB: 5GV8) and cytochrome b5 (PDB: 3NER) to allow for the activation of the catalytic molecule coordinated by the two ions in the center of SCD.  SCD is colored according to the hydrophobicities of each helix, shown in figures 2 and 3.]]The electron transport chain allows for the mechanism of SCD1 to be carried out by providing electrons via either a Cytochrome B5 electron shuttle or an exchange through a [https://en.wikipedia.org/wiki/Ternary_complex#:~:text=A%20ternary%20complex%20can%20be,type%20of%20enzyme%2Dcatalyzed%20reactions ternary complex]<ref name="Shen" />.  The electrons will be shuttled from complex to complex and then eventually be accepted by the SCD1 enzyme which will allow for activation of the catalytic molecule (Figure 5). The placement of SCD1 in the ER membrane is believed to prevent inhibition by allowing better flow of products/side products to their later pathways<ref name="Shen" />.

Absence or a deficit of SCD1 in the body is associated with obesity and insulin resistance which is a main cause of [https://en.wikipedia.org/wiki/Type_2_diabetes type 2 diabetes]<ref name="Shen" />. Cancer sites in the body tend to show a much higher expression rate of SCD1<ref name="Shen" />.  Focusing on SCD1 as a drug target could lead to advancements in treatment of obesity, diabetes, and other metabolic diseases<ref name="Bai" />.

The SCD1 enzyme can be down regulated or slightly inhibited by low-carbohydrate diets, low glucose levels, low insulin levels, and a low cholesterol diet. SCD1 is also regulated by <scene name='87/877552/Leptin/1'>leptin</scene>; a protein that is created by fat cells<ref name="Ntambi" />.  When the [https://en.wikipedia.org/wiki/Leptin leptin] signaling pathway is fully functioning, the SCD1 enzyme is regulated in its ability to create MUFAs. SCD1 being associated with obesity could directly be tied to errors in the signaling pathways of the leptin protein<ref name="Ntambi" />.