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1. Allosterism in the PDZ Family

   https://doi.org/10.3390/ijms23031454  

   Stevens, Amy O.; He, Yi (February 2022, International Journal of Molecular Sciences)

   Dynamic allosterism allows the propagation of signal throughout a protein. The PDZ (PSD-95/Dlg1/ZO-1) family has been named as a classic example of dynamic allostery in small modular domains. While the PDZ family consists of more than 200 domains, previous efforts have primarily focused on a few well-studied PDZ domains, including PTP-BL PDZ2, PSD-95 PDZ3, and Par6 PDZ. Taken together, experimental and computational studies have identified regions of these domains that are dynamically coupled to ligand binding. These regions include the αA helix, the αB lower-loop, and the αC helix. In this review, we summarize the specific residues on the αA helix, the αB lower-loop, and the αC helix of PTP-BL PDZ2, PSD-95 PDZ3, and Par6 PDZ that have been identified as participants in dynamic allostery by either experimental or computational approaches. This review can serve as an index for researchers to look back on the previously identified allostery in the PDZ family. Interestingly, our summary of previous work reveals clear consistencies between the domains. While the PDZ family has a low sequence identity, we show that some of the most consistently identified allosteric residues within PTP-BL PDZ2 and PSD-95 PDZ3 domains are evolutionarily conserved. These residues include A46/A347, V61/V362, and L66/L367 on PTP-BL PDZ2 and PSD-95 PDZ3, respectively. Finally, we expose a need for future work to explore dynamic allostery within (1) PDZ domains with multiple binding partners and (2) multidomain constructs containing a PDZ domain. 

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2. Adeno-associated viral overexpression of neuroligin 2 in the mouse hippocampus enhances GABAergic synapses and impairs hippocampal-dependent behaviors.

   https://doi.org/10.1016/j.bbr.2018.12.052  

   Van Zandt, M; Weiss, E; Almyasheva, A; Lipior, S; Maisel, S; Naegele, J. (January 2019, Behavioural brain research)

   null (Ed.)

   The cell adhesion molecule neuroligin2 (NLGN2) regulates GABAergic synapse development, but its role inneural circuit function in the adult hippocampus is unclear. We investigated GABAergic synapses and hippo-campus-dependent behaviors following viral-vector-mediated overexpression of NLGN2. Transducing hippo-campal neurons with AAV-NLGN2 increased neuronal expression of NLGN2 and membrane localization ofGABAergic postsynaptic proteins gephyrin and GABAARγ2, and presynaptic vesicular GABA transporter protein(VGAT) suggesting trans-synaptic enhancement of GABAergic synapses. In contrast, glutamatergic postsynapticdensity protein-95 (PSD-95) and presynaptic vesicular glutamate transporter (VGLUT) protein were unaltered.Moreover, AAV-NLGN2 significantly increased parvalbumin immunoreactive (PV+) synaptic boutons co-loca-lized with postsynaptic gephyrin+puncta. Furthermore, these changes were demonstrated to lead to cognitiveimpairments as shown in a battery of hippocampal-dependent mnemonic tasks and social behaviors. 

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3. NMDAR-dependent long-term depression is associated with increased short term plasticity through autophagy mediated loss of PSD-95

   https://doi.org/10.1038/s41467-021-23133-9  

   Compans, Benjamin; Camus, Come; Kallergi, Emmanouela; Sposini, Silvia; Martineau, Magalie; Butler, Corey; Kechkar, Adel; Klaassen, Remco V.; Retailleau, Natacha; Sejnowski, Terrence J.; et al (December 2021, Nature Communications)

   null (Ed.)

   Abstract Long-term depression (LTD) of synaptic strength can take multiple forms and contribute to circuit remodeling, memory encoding or erasure. The generic term LTD encompasses various induction pathways, including activation of NMDA, mGlu or P2X receptors. However, the associated specific molecular mechanisms and effects on synaptic physiology are still unclear. We here compare how NMDAR- or P2XR-dependent LTD affect synaptic nanoscale organization and function in rodents. While both LTDs are associated with a loss and reorganization of synaptic AMPARs, only NMDAR-dependent LTD induction triggers a profound reorganization of PSD-95. This modification, which requires the autophagy machinery to remove the T19-phosphorylated form of PSD-95 from synapses, leads to an increase in AMPAR surface mobility. We demonstrate that these post-synaptic changes that occur specifically during NMDAR-dependent LTD result in an increased short-term plasticity improving neuronal responsiveness of depressed synapses. Our results establish that P2XR- and NMDAR-mediated LTD are associated to functionally distinct forms of LTD. 

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4. Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation

   https://doi.org/10.1093/nar/gkab874  

   Chen, Wei; Lu, Wei; Wolynes, Peter G; Komives, Elizabeth A (October 2021, Nucleic Acids Research)

   Abstract Binding and unbinding of transcription factors to DNA are kinetically controlled to regulate the transcriptional outcome. Control of the release of the transcription factor NF-κB from DNA is achieved through accelerated dissociation by the inhibitor protein IκBα. Using single-molecule FRET, we observed a continuum of conformations of NF-κB in free and DNA-bound states interconverting on the subseconds to minutes timescale, comparable to in vivo binding on the seconds timescale, suggesting that structural dynamics directly control binding kinetics. Much of the DNA-bound NF-κB is partially bound, allowing IκBα invasion to facilitate DNA dissociation. IκBα induces a locked conformation where the DNA-binding domains of NF-κB are too far apart to bind DNA, whereas a loss-of-function IκBα mutant retains the NF-κB conformational ensemble. Overall, our results suggest a novel mechanism with a continuum of binding modes for controlling association and dissociation of transcription factors. 

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5. Socially induced plasticity of the posterior tuberculum and motor behavior in zebrafish ( Danio rerio )

   https://doi.org/10.1242/jeb.248148  

   Heagy, Faith K; Clements, Katie N; Adams, Carrie L; Blain, Elena; Issa, Fadi A (October 2024, Journal of Experimental Biology)

   Social dominance is prevalent throughout the animal kingdom. It facilitates the stabilization of social relationships and allows animals to divide resources according to social rank. Zebrafish form stable dominance relationships that consist of dominants and subordinates. Although social-status-dependent differences in behavior must arise due to neural plasticity, mechanisms of how neural circuits are reconfigured to cope with social dominance are poorly described. Here, we describe how the posterior tuberculum nucleus (PT), which integrates sensory social information to modulate spinal motor circuits, is morphologically and functionally influenced by social status. We combined non-invasive behavioral monitoring of motor activity (startle escape and swim) and histological approaches to investigate how social dominance affects the morphological structure, axosomatic synaptic connectivity, and functional activity of the PT in relation to changes in motor behavior. We show that dopaminergic cell number significantly increases in dominants compared to subordinates, while PT synaptic interconnectivity, demonstrated with PSD-95 expression, is higher in subordinates compared to dominants. Secondly, these socially induced morphological differences emerge after one week of dominance formation and correlate with differences in cellular activities illustrated with higher phosphor-S6 ribosomal protein expression in dominants compared to subordinates. Thirdly, these morphological differences are reversible as the social environment evolves and correlates with adaptations in startle escape and swim behaviors. Our results provide new insights of the neural bases of social behavior that may be applicable to other social species with similar structural and functional organization. 

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