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YiiP is a homodimer [https://en.wikipedia.org/wiki/Protein_dimer (protein dimer)], with each monomer consisting of 238 residues with TransMembrane (<scene name='69/694236/Realtmd1/1'>TMD</scene>) and C-Terminal (<scene name='69/694236/Realctd1/1'>CTD</scene>) domains (colored blue) that are connected via a charge interlocking mechanism located on a flexible loop. In total, the Yiip protein has three Zn²⁺ <scene name='69/694236/Bindingsiteswcolor/2'>binding sites</scene>, site A, B, and C. Site A is located in the <scene name='69/694236/Bindingsiteswcolor/3'>TMD</scene> of the protein, highlighted in purple, site C is located in the <scene name='69/694236/Bindingsiteswcolor/4'>CTD</scene>, now seen in purple, and site B is located at the junction of the two domains. The TMD, where Zn²⁺ binding site A resides, consists of 6 transmembrane (TM) helices, 4 of which, <scene name='69/694236/Tmlabels/1'>TM1,TM2,TM4, and TM5</scene> (labeled on only one monomer, but present on both), pivot about the ion binding site A. The remaining two helices, <scene name='69/694236/Tm3tm6/2'>TM3 and TM6</scene>, are oriented <scene name='69/694236/Tm3tm6antiparallel/1'>antiparallel</scene> to the bundle. Movement of these helices plays a role in the function of Zn²⁺ transport.  

[[Image:ElectrostaticV2.png|250px|right|thumb|Figure 1. 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 2. 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 3.]]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 the TM2-TM3 loop 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.

YiiP's ability to export Zn²⁺ from the cytoplasm is best described as an alternating access mechanism with Zn²⁺/H⁺ antiport. YiiP has 2 major structural conformations as shown by the crystallized structures [http://proteopedia.org/wiki/index.php/3h90 3H90] and [http://proteopedia.org/wiki/index.php/3j1z 3J1Z] <ref>PMID:23341604</ref> (a YiiP homolog derived from ''Shewanella oneidensis''). 3H90 shows YiiP in its outward-facing conformation with Zn²⁺ present and 3J1Z which shows the YiiP homolog in an inward-facing conformation where there is no Zn²⁺ present.

Zinc induced conformation changes in the TMD and CTD leads to the major <scene name='69/694236/Outward-facinggreen/1'>outward-facing</scene> and <scene name='69/694236/Inward-facinggreen/1'>inward-facing conformations</scene>. [[Image:InwardVsOutward.png|300px|right|thumb| Figure 6. Side by side comparison of one monomer for the the outward-facing conformation of 3H90 and the inward-facing conformation of 3J1Z. TM1, TM2, TM4, and TM5 (yellow) pivot around TM3 and TM6 (green). The helices of the other half of the homodimer (blue) function identically.  

]]

It is believed that the energy for TMD conformation change comes from energy of binding each substrate. Changing to the outward from the inward-facing conformation causes a shift in the <scene name='69/694236/Shorttm5/1'>TM5 helix</scene> which disrupts the tetrahedral geometry of active site A. This in turn decreases binding affinity site A has for Zn²⁺ making export to the periplasm possible. After Zn²⁺ is exported and site A is either empty or bound to H⁺, the protein's conformation changes to the favored inward-facing conformation.

In contrast the main purpose of conformation change in the CTD is to stabilize the YiiP dimer and to act as a Zn²⁺ sensor.  

This is possible because of the flexible loop that links the TMD and the CTD. This loop harbors the <scene name='75/756372/Bestsaltbridgetransparent/1'>salt bridge</scene> which serves as a hinge that allows movement of the CTD. Using [https://en.wikipedia.org/wiki/F%C3%B6rster_resonance_energy_transfer FRET] to measure the distance between the CTD of each monomer fluorescence quenching was observed as the concentration Zn²⁺ increased, which supports that idea that Zn²⁺ induces a stabilizing conformation change in the CTD.<ref>PMID:19749753</ref> CTD of both monomers were measured to be closer together when saturated with Zn²⁺.

<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