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Figure 5 | Journal of Clinical Bioinformatics

Figure 5

From: Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitroby Phosphoproteomic and Bioinformatic tools

Figure 5

Effect of the phosphorylation of Ser-48 in the stability of the dimmer structure of the first RNA recognition motif of HuR. [A] Crystal structure of HuR dimmer (Protein Data Bank code: 3HI9, chains B and D) indicating the position of Ser-48, Glu-47 and Lys-50 in the dimmerization surface. [B] Relative spatial position of the two HuR monomers after 10ns of unrestricted Molecular Dynamics (MD) simulation of both non-phosphorylated (red structure, left) and phosphorylated (green structure, right) states of Ser-48. Position of initial dimmer structure, prior to the MD simulation, is included for comparison (in gray). Note the large displacement of the non-phosphorylated state in contrast to the stability exhibited by the dimmer in presence of phosphoSer48. Respective positions of Ser-48 and phosphoSer-48 are indicated. [C] Left: RMSD values measured for HuR dimmer (red) monomer A (blue) and monomer B (green) during the 10 ns trajectory of the unrestricted MD simulation of the dimmer in presence of non-phosphorylated Ser-48 (HUR plot, top panel) or phosphorylated pSer-48 (HURP plot, lower panel). Right: continuous measurement of Cα Cα distances between residues E47(A)-K50(B) (red), S48(A)-S48(B) (blue) and E47(A)-K50(B) (green), during the MD trajectory. Distortion of the HuR dimmer in the presence of Ser-48 (HUR plot, top panel) when compared to the phosphorylated state of the protein (HURP plot, lower panel) is patent in both RMSD and Cα-Cα measurements. Structure plots were generated as in Figure 4.

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