Srp20-Human Alternative Splicing Factor: Difference between revisions

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Neel Bhagat

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 ==== RNA Recognition Motif ====
-The SRp20 RRM (aa 1-86) contains a βαββαβ <scene name='78/786034/Imager1/2'>pattern</scene>, common of many other RRMs. To explore substrate binding, researchers used a 4 base RNA ligand with sequence CAUC, which matches the SRp20 recognition sequence found in the corresponding H2A histone mRNA. The RNA bases each <scene name='78/786034/Imager2/2'>stack</scene> onto an aromatic side chain protruding from one of the SRp20 β-sheets, forming the primary interactions that allow the substrate to bind to the protein. In particular, C1 <scene name='78/786034/Imager3/1'>stacks</scene> on Y13 in β1, <scene name='78/786034/Imager4/1'>A2</scene> stacks on F50 in β3, and F48 of β3 sits in between the sugar rings of C1 and A2. It should also be noted that A2 adopts an irregular <scene name='78/786034/Imager5/1'>syn</scene> conformation when bound to the RRM, something that was previously observed only for guanine in the 2 position. U3 <scene name='78/786034/Imager8/1'>stacks</scene> onto F48 in β3, as W40 and A42 in β2.  However, when bound, U3 <scene name='78/786034/Imager9/2'>bulges</scene> out of line in comparison to the rest of the substrate. C4 partially stacks over <scene name='78/786034/Imager6/1'>A2</scene>, and also forms hydrogen <scene name='78/786034/Imager7/1'>bonds</scene> between the C4 amino group, A2 2’ oxygen, and a main chain phosphate oxygen.
+The SRp20 RRM (aa 1-86) contains a βαββαβ <scene name='78/786034/Imager1/2'>pattern</scene>, common of many other RRMs. To explore substrate binding, researchers used a 4 base RNA ligand with sequence CAUC, which matches the SRp20 recognition sequence found in the corresponding H2A histone mRNA. The RNA bases each <scene name='78/786034/Imager2/2'>stack</scene> onto an aromatic side chain protruding from one of the SRp20 β-sheets, forming the primary interactions that allow the substrate to bind to the protein. In particular, C1 <scene name='78/786034/Imager3/1'>stacks</scene> on Y13 in β1, <scene name='78/786034/Imager4/1'>A2</scene> stacks on F50 in β3, and F48 of β3 sits in between the sugar rings of C1 and A2. It should also be noted that A2 adopts an irregular <scene name='78/786034/Imager5/2'>syn</scene> conformation when bound to the RRM, something that was previously observed only for guanine in the 2 position. U3 <scene name='78/786034/Imager8/1'>stacks</scene> onto F48 in β3, as W40 and A42 in β2.  However, when bound, U3 <scene name='78/786034/Imager9/2'>bulges</scene> out of line in comparison to the rest of the substrate. C4 partially stacks over <scene name='78/786034/Imager6/1'>A2</scene>, and also forms hydrogen <scene name='78/786034/Imager7/1'>bonds</scene> between the C4 amino group, A2 2’ oxygen, and a main chain phosphate oxygen.
 While all 4 bases form a number of hydrophobic stacking interactions, alteration to the last 3 bases of the substrate sequence does not significantly impact binding affinity, while the C to G mutation of C1 results in a 10-fold decrease in binding affinity. This suggests that C1 interacts specifically with the protein, while positions 2-4 interact nonspecifically. The SRp20 RRM is able to recognize C1 with high specificity primarily through 4 <scene name='78/786034/Imager10/1'>hydrogen bonds</scene>: from the C1 amino protons to Leu80 backbone carbonyl oxygen and to Glu79 side-chain carboxyl oxygen, from C1 N3 to Asn82 amide, and from C1 O2 to Ser81 side chain hydroxyl group.
 The semi-specific RNA recognition is a mechanism which reduces evolutionary pressure on bound mRNA by increasing the number of possible RNA recognition sequences. As a result, tolerance for possible mutation in the RNA sequence is increased, meaning SRp20 can bind a diverse range of substrates, or even to original substrates that were mutated during replication (eg. H2A mRNA with a point mutation).  Therefore, this mechanism increases organism survival chance by reducing the probability of physiological impact as a result of certain mutations<ref name="Hargous">PMID:17036044</ref>.