Schematic structural diagrams of the RNA dissociation processes from RRMs, RBD, and SUMO2/RBD.

For the RRMs and the RBD, the RNA dissociation is a two-step process: RNA dissociation from RRM2 is followed by its dissociation from RRM1. For the SUMO2/RBD complex, RNA must dissociate from the two RRMs simultaneously.</p

RNA dissociation pathway I from RRMs shown in Fig 5B.

(MP4)</p

Binding energy of canonical SIM/SUMO2 complex structure when scanning the sequence of full length CPEB3 over the SIM peptide.

The x axis is the residue index of the first amino acid in each CPEB3 peptide. The black line shows the binding energy for the original SIM peptide in the PDB structure (ID: 6JXW). The two green shaded regions highlighted peptides containing the predicted SIMs in CPEB3 via bioinformatic search (V273-V283; P484-W489). (EPS)</p

Introduction to the AWSEM-3SPN2 force field.

Binding energy for SIM/SUMO2 complex. Additional potentials. Simulation methods: Equilibrum simulation of free RRMs; Equilibrum simulation of full length RBD; Structural prediction to the SUMO2/RBD complex; Free energy profiles for RNA dissociation; Free energy profiles for the closure motion of RRMs. Efficiency of the shift of RNA-binding equilibration. (PDF)</p

RNA dissociation pathway I from RBD shown in S7 Fig.

(MP4)</p

RNA dissociation pathway II from SUMO2/RBD complex shown in Fig 5B.

(MP4)</p

Fig 8 -

A. The two potential SUMOylated sites on CPEB3 are highlighted using two SUMO2 labels (pink). B. The complete negative feedback loop between CPEB3 and SUMO2: ① An external signal stimulates the synapses and triggers the deSUMOylation of basal CPEB3. ② CPEB3 exposes its prion-like domain (PRD) and actin-binding domain (ABD) and aggregates upon binding with actin filaments (F-actin). ③ CPEB3 fibers form local translation factory assembly lines to activate the translation of its target mRNAs, which includes SUMO2 mRNA. ④ Newly synthesized SUMO2 proteins are then used for the SUMOylation of monomeric CPEB3. ⑤ A shift of mRNAs from binding with CPEB3 fibers to binding with SUMOylated CPEB3 occurs due to the RNA-binding affinity difference. ⑥ SUMOylated CPEB3 binds with target mRNAs and recruits them into P bodies for translational repression. A legend is shown at the upper-right corner. C. Sketches of the CPEB3 regulation mechanism for target mRNA activity in synapses. The active mRNA level during one feedback cycle, in response to one synaptic stimulation pulse, is illustrated in the left panel. The protein levels of different CPEB3 states in response to several stimulation pulses are sketched in the right panel. Following each stimulations pulse, synapses return to a new basal state where the CPEB3 fiber level has been risen. We see that a sequence of stimulation events acts as a ratchet, increasing the basal level of CPEB3 fibers in steps. Stimulation steps are labeled by grey arrows.</p

Fig 2 -

A. A diagram of the CPEB3 subdomains including a prion-like domain (PRD), an actin-binding domain (ABD), and an RNA-binding domain (RBD). The RBD consists of two RNA recognition motifs, RRM1 and RRM2 (colored in blue and red hereinafter), and one Zinc-finger domain (ZnF, colored in grey). B. The NMR structure of CPEB1 ZnF (Zinc ions are shown in purple). C. The NMR structure of CPEB4 RRMs binding with target mRNA (shown in orange). D. The NMR structure of free CPEB4 RRMs. E. The histogram for the distribution of first principal component, PC0, sampled during 20 equilibrium simulation trajectories of CPEB3 RRMs. Embedded: Variance contributed by the first five principal components from the principal component analysis. The PC0 values for the NMR structures of the RNA-bound state and the free state are shown by green and yellow dashed lines, respectively.</p

The two RNA dissociation pathways from RBD.

These correspond with the pathway I and pathway II shown in Fig 5B. The starting point of the dissociation pathways is marked by a white star. (EPS)</p

The conformational changes of CPEB3 provide a mechanism for the switchable translational control in dendritic spines.

In a basal state, monomeric CPEB3 (shown in red) is colocalized with P-bodies and represses the translation of its target mRNAs. In response to a stimulation signal, CPEB3 monomers are released from P-bodies and then aggregate into CPEB3 fibers (shown in green). CPEB3 fibers (using the vectorial channeling mechanism) activate the local translation of synaptic proteins, including the actin proteins which are the molecular basis for the growth of the spines. The stability of the remaining prion-like CPEB3 aggregates would raise a problem of how the translational activation is turned down after a stimulation pulse. SUMO binding provides a route to return to the new basal state. A legend is shown at the upper-right corner.</p