User:Ethan Kitt/Sandbox 1: Difference between revisions

=Human Poly(A) Binding Protein (1CVJ)=

<StructureSection load='1B7F' size='350' frame='true' side='right' caption='Sex lethal (PDB: 1B7F)' scene='78/782600/Opening_image/2'>

The <scene name='78/782616/Subunits_of_pabp/3'>Components of PABP</scene> are categorized into two RRMs: the n-terminus RRM1 (red) and c-terminus RRM2 (blue) are shown accordingly. The two RRMs are linked via an alpha-helix linker (green) that maintains the RRM1/2 complex that is the biological assembly and active form of PABP. Each RRM has a four-stranded antiparallel beta sheet backed by two corresponding alpha helices. <ref name="Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein">Deo, Rahul C, et al. “Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein.” Cell 98:6. (1999) 835-845. Print. </ref> mRNA poly-adenosine recognition is due to the presence of the conserved residues within the beta-sheet surface <ref name="The Poly(A)-Binding Protein and an mRNA Stability Protein Jointly Regulate an Endoribonuclease Activity.">Wang, Zuoren and Kiledjian, Megerditch. “The Poly(A)-Binding Protein and an mRNA Stability Protein Jointly Regulate an Endoribonuclease Activity.” Molecular and Cellular Biology 20.17 (2000): 6334–6341. Print.</ref> , which forms a <scene name='78/782616/Trough2/1'>trough</scene>-like pocket for the mRNA to bind. The beta-sheet flooring present in PABP interacts with the 3’ mRNA tail via a combination of van der Waals, aromatic stacking, and Hydrogen bonding. Through these interactions, PABP binds to 3’ Poly (A) tail with a KD of 2-7 nM. <ref name="Roles of Cytoplasmic Poly(A)-Binding Proteins">Gorgoni, Barbra, and Gray, Nicola. “The Roles of Cytoplasmic Poly(A)-Binding Proteins in Regulating Gene Expression: A Developmental Perspective.” Briefings in Functional Genomics and Proteomics, vol. 3, no. 2, 1 Aug. 2004, pp. 125–141., doi:10.1093/bfgp/3.2.125.</ref> [[Image:Hydrophobicity (1).png|200px|right|thumb| "Figure 1:" Surface hydrophobicity shown in presence of mRNA]]  

Further, the RRM1/2 complex interacts with the mRNA's sugar-phosphate backbone, where 4 of the 8 mRNA adenosines interact electrostatically.<ref name="Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein">Deo, Rahul C, et al. “Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein.” Cell 98:6. (1999) 835-845. Print. </ref> Upon closer examination of the PABP structure, the protein contains loop-like domains that form the walls of the beta-sheet trough. Although these <scene name='78/782616/Walls_of_trough/3'>loop walls</scene> are present, no interaction occurs between the mRNA and these regions. We propose that these loops only keep unwanted cellular elements out of the binding pocket via hydrophobic and hydrophilic interactions, maintaining the protein's selectivity for mRNA (Figure 1). The structural elements highlighted consist of the RRM1/2 subunits, the linker domain, and the Poly(A) mRNA binding trough.  

===Adenosine Recognition Interactions===                

<tr id='Nucleotide'><td class="sblockLbl"><b>Nucleotide</b></td><td class="sblockDat">PABP residue</td><td class="sblockDat">Atom on PABP residue</td>

<tr id='A2'><td class="sblockLbl"><b>A2</b></td><td class="sblockDat"><scene name='78/782616/Asn105_a2/2'>Asn105</scene></td><td class="sblockDat">side chain amine</td>

<tr id='A3'><td class="sblockLbl"><b>A3</b></td><td class="sblockDat"><scene name='78/782616/Lys174-a3/2'>Lys174</scene></td><td class="sblockDat">amine</td></tr>

<tr id='A4'><td class="sblockLbl"><b>A4</b></td><td class="sblockDat"><scene name='78/782616/Asn100-a4/2'>Asn100</scene></td><td class="sblockDat">side chain amine and carbonyl</td></tr>

<tr id='A4'><td class="sblockLbl"><b>A4</b></td><td class="sblockDat"><scene name='78/782616/Ser127-a4/2'>Ser127</scene></td><td class="sblockDat">side chain and N-term amine</td></tr>

<tr id='A5'><td class="sblockLbl"><b>A5</b></td><td class="sblockDat"><scene name='78/782616/His144-a5/2'>His144</scene></td><td class="sblockDat">pyrimidine π-amine </td></tr>

<tr id='A6'><td class="sblockLbl"><b>A6</b></td><td class="sblockDat"><scene name='78/782616/Gln88-a6/2'>Gln88</scene></td><td class="sblockDat">N-term amine and C-term OH</td></tr>

<tr id='A6'><td class="sblockLbl"><b>A6</b></td><td class="sblockDat"><scene name='78/782616/Trp86-a6/2'>Trp86</scene></td><td class="sblockDat">N-term amine</td></tr>

<tr id='A7'><td class="sblockLbl"><b>A7</b></td><td class="sblockDat"><scene name='78/782616/Tyr54-ribose_a7/1'>Trp54</scene></td><td class="sblockDat">side chain OH</td></tr>

<tr id='A7'><td class="sblockLbl"><b>A7</b></td><td class="sblockDat"><scene name='78/782616/Asp45-a7/2'>Asn45</scene></td><td class="sblockDat">side chain OH</td></tr>

<tr id='A7'><td class="sblockLbl"><b>A7</b></td><td class="sblockDat"><scene name='78/782616/Met46-a7/2'>Met46</scene></td><td class="sblockDat">C-term carbonyl</td></tr>

<tr id='A8'><td class="sblockLbl"><b>A8</b></td><td class="sblockDat"><scene name='78/782616/Tyr54-a8/2'>Tyr54</scene></td><td class="sblockDat">side chain OH</td></tr>

<tr id='A9'><td class="sblockLbl"><b>A9</b></td><td class="sblockDat"><scene name='78/782616/Arg44-a9/2'>Arg44</scene></td><td class="sblockDat">side chain τ-amine</td></tr>

Upon mRNA Poly(A) recognition, PABP and the bound mRNA stimulate the initiation of translation by interacting with initiation factor eIF4G. Protein eIF4G actually interacts with PABP's dorsal side (under the trough) hydrophobic and acidic residues that stimulate the interaction between the two proteins. These specific residues are phylogenetically conserved among all PABPs, and therefore significant in the protein's function and interaction with eIF4G.

PABP and mRNA complex aids in translation initiation under two proposed mechanisms. Within the two mechanisms, studies have highlighted the presence  The “Closed Loop” Model entails the recognition of the 5’ 7-methyl-Guanosine cap by [https://en.wikipedia.org/wiki/Eukaryotic_initiation_factor_4F eIF4F], which is a ternary complex made up of a cap-binding protein [https://en.wikipedia.org/wiki/EIF4E (eIF4E)] and RNA helicase [https://en.wikipedia.org/wiki/EIF4A (eIF4A)] connected by the bridging protein (eIF4G) (Figure 2).¹ Translation initiation is stimulated by the PABP bound to the poly(A) tail and its association with eIF4G.<ref name="Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein">Deo, Rahul C, et al. “Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein.” Cell 98:6. (1999) 835-845. Print. </ref> The 5’ UTR is unwound by the elF4F complex, and ribosomes are recruited to create the initiation complex. The eIF4G protein then guides the 40S subunit to the start codon (AUG), which is followed by the binding 60S ribosomal subunit, creating the 80S initiation complex.<ref name="Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein">Deo, Rahul C, et al. “Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein.” Cell 98:6. (1999) 835-845. Print. </ref> The association of the PABP and eIF4G gave rise to the name “closed loop.”<ref name="Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein">Deo, Rahul C, et al. “Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein.” Cell 98:6. (1999) 835-845. Print. </ref> Mutations of Arg→Ala and Lys→Ala in human eIF4G and in yeast extracts decrease the rate of translation initiation and destabilizing the interactions with PABP, indicating that basic residues are essential to the interaction with PABP.<ref name="Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein">Deo, Rahul C, et al. “Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein.” Cell 98:6. (1999) 835-845. Print. </ref>

[[Image:closedlooper.png|300px|right|thumb| "Figure 2:" Closed loop model of the eIF4F complex and PABP creating a loop out of the mRNA ]]