Sandbox Reserved 1069: Difference between revisions

[[Image:ElectrostaticV2.png|250px|right|thumb|Figure 2. Electrostatic Charge Distribution]]<scene name='69/694236/Electrostaticv2/1'>Charge Distribution</scene> along the exterior surface of the protein, shown in Figure 1, is primarily neutral (white) for the TMDs, but transitions to positive (blue) near the location of the <scene name='69/694236/Electrostaticv2salt/2'>salt bridge</scene> and interior side of the cell membrane. This positive section is characteristic of trans-membrane proteins as a means of achieving proper orientation within the cell membrane. <scene name='69/694236/Electrostaticbsc/2'>Binding sites</scene> A, B, and C, as well as the CTDs of both monomers, all possess a high negative charge (red) relative to the other charges present, facilitating the binding and releasing of Zn²⁺ ions. The two CTDs are held together by the charge interlock and hydrophobic interactions of the TMDs, despite their electrostatic repulsion. Upon the release of Zn²⁺ ions, the CTDs undergo alterations to electronegativity, which enables domain separation.

The <scene name='75/756372/Bestsaltbridgetransparent/1'>salt bridge</scene> formation between Lys77 and Asp207 of each domain of YiiP forms an interlocking interaction that acts as the pivot point of the conformational change that drives the function of YiiP as shown in Figure 2. Interlocking interactions are disrupted when Zn²⁺ is bound, due to movement of the antiparallel helices, causing a conformational shift in YiiP. The salt bridge also aids in holding the two monomers together, where [[Image:Saltbridge.png|200px|left|thumb|Figure 3. Lys77 and Asp207 Salt Bridges]]<scene name='75/756372/Besthydrophobiczoom1/1'>hydrophobic</scene> residues around the salt bridge further stabilize the two domains in the v-shaped void where the domains connect. This prevents degradation of the protein's interlock via interactions with the environment.

[[Image:activesites.png|thumb|right|Figure 4. Binding sites A, B, and C]]Each Yiip monomer contains three Zn²⁺ <scene name='69/694236/Bindingsiteswcolor/2'>binding sites</scene>. There is an active site (Site A), and two cytoplasmic binding sites (Site B and C) depicted in Figure 3. It was found that only site A and C are conserved, while the function of Site B is not well defined, though it is believed that it plays a role in subunit dimerization.

<scene name='69/694236/Bsc/1'>Binding site C</scene> has vastly opposite properties from what is seen in binding site A. It is located on a random coil between the two C-terminus domain interfaces. Here, there is a binuclear coordination of Zn²⁺ between the Asp285 residue that <scene name='69/694236/Bsc/2'>bridges</scene> the Zn²⁺ ions together and the four <scene name='69/694236/Bsc/3'>coordinating</scene> residues (His232, His248, His283, His161). The Asp285 residue does not have outer shell constraints, however, the same cannot be said for the four histidine residues. These constraints consist of hydrogen bonds to the residues surrounding the binding site allowing bidentate bond formation, or hydrogen bonding to a metal in two places. Formation of bidentate bonds creates an extensive network of interactions at the CTD interface, which allow for stability and strengthening of the CTD-CTD association.

== Other 3d structures of Yiip ==

[http://proteopedia.org/wiki/index.php/3j1z (3j1z)], [http://proteopedia.org/wiki/index.php/3byp (3byp)]

'''Structure of Yiip'''

[http://proteopedia.org/wiki/index.php/2qfi (2qfi)]

<ref>"Protein Page: YiiP." Protein Page: YiiP. National Center for Biotechnology Information, n.d. Web. 24 Feb. 2017.</ref>  

<ref>"Laboratory of David Stokes." NYUSOM. NYU School of Medicine, n.d. Web. 24 Feb. 2017.</ref>

https://www.bnl.gov/isd/documents/71335.pdf