Abstract
Specific interactions between scaffold protein SH3 and multiple ankyrin repeat domains protein 3 (Shank3) and synapse-associated protein 90/postsynaptic density-95–associated protein (SAPAP) are essential for excitatory synapse development and plasticity. In a bunch of human neurological diseases, mutations on Shank3 or SAPAP are detected. To investigate the dynamical and thermodynamic properties of the specific binding between the N-terminal extended PDZ (Post-synaptic density-95/Discs large/Zonaoccludens-1) domain (N-PDZ) of Shank3 and the extended PDZ binding motif (E-PBM) of SAPAP, molecular dynamics simulation approaches were used to study the complex of N-PDZ with wild type and mutated E-PBM peptides. To compare with the experimental data, 974QTRL977 and 966IEIYI970 of E-PBM peptide were mutated to prolines to obtain the M4P and M5P system, respectively. Conformational analysis shows that the canonical PDZ domain is stable while the βN extension presents high flexibility in all systems, especially for M5P. The high flexibility of βN extension seems to set up a barrier for the non-specific binding in this area and provide the basis for specific molecular recognition between Shank3 and SAPAP. The wild type E-PBM tightly binds to N-PDZ during the simulation while loss of binding is observed in different segments of the mutated E-PBM peptides. Energy decomposition and hydrogen bonds analysis show that M4P mutations only disrupt the interactions with canonical PDZ domain, but the interactions with βN1′ remain. In M5P system, although the interactions with βN1′ are abolished, the binding between peptide and the canonical PDZ domain is not affected. The results indicate that the interactions in the two-binding site, the canonical PDZ domain and the βN1′ extension, contribute to the binding between E-PBM and N-PDZ independently. The binding free energies calculated by MM/GBSA (Molecular Mechanics/Generalized Born Surface Area) are in agreement with the experimental binding affinities. Most of the residues on E-PBM contribute considerably favorable energies to the binding except A963 and D964 in the N-terminal. The study provides information to understand the molecular basis of specific binding between Shank3 and SAPAP, as well as clues for design of peptide inhibitors.
Highlights
Scaffold proteins are highly abundant in dendritic spine and synapses
The root mean square fluctuations (RMSF) values of the extended PDZ binding motif (E-PDZ binding motif (PBM)) C terminal residues in M5P system were as low as those in the WT system, especially for the QTRL parts. It seems the mutations only affected the binding of the N terminal part of E-PBM to βN hairpin, not the binding of C terminal residues to the canonical PDZ domain
SCc-i.b2a0s1e9d, 20e,x2p24eriments showed that the IEIWI (966–970) to prolines weakened the bindi4nogf 17 between shank N-PDZ and synapse-associated protein 90/postsynaptic density-95–associated protein (SAPAP) E-PBM to approximately five-fold, a value comparable to the ligands only binding to the canonical PDZ domain [11]
Summary
Scaffold proteins are highly abundant in dendritic spine and synapses. Specific interactions between the scaffold proteins play critical roles in the dendritic spine and synapse formation, maturation and maintenance [1]. The gene deletions of Shank cause the development of 22q13 deletion syndrome (Phelan-Mcdermid syndrome) and autism spectrum disorders (ASD) [4,5,6,7]. The disruption of the Shank gene in mice models directly leads to the genesis of the autistic-like behaviors [8,9]. The overexpression of Shank leads to hyperkinetic neuropsychiatric disorder [10]. A proper dosage of Shank is critical for normal brain function
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