Abstract
SHANK3, a member of SH3 and multiple ankyrin repeat domains (SHANK) proteins, plays a crucial role in synaptic development and functions. Mutations in SHANK3 have been linked to a number of neuropsychiatric and neurodevelopmental disorders, including autism spectrum disorder. In this study, the functional and structural impacts of non-synonymous single-nucleotide polymorphisms (SNPs) on SHANK3 were predicted. Various databases were used to extract 16,894 non-redundant SNPs, out of which 1179 were annotated as missense variants. Missense variants were categorized as deleterious or non-deleterious. Twenty-nine missense variants were unanimously recognized as deleterious and subjected to structural and stability analyses. Mutations, including L47P, G54W, G172D, G250C/D, and G627E, which posed drastic effects on the secondary structure of SHANK3, were modeled. Stability analyses introduced L47P, G54W, and G250D as the most destabilizing mutations, thus they were subjected to molecular dynamics simulation. Simulation revealed significant changes in intramolecular interactions and high fluctuations in residues of 1–350 that significantly affect the ANK functional domain. G250C/D and G635R consensus deleterious mutations were found in the first and second binding domains of SHANK3, and none were found in the post-translational modification sites. This study suggests L47P, G54W, and G250C/D deleterious mutations as priorities for future studies on SHANK3.
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Acknowledgments
Research reported in this publication was supported by the Elite Researcher Grant Committee under award number 963461 from the National Institutes for Medical Research Development (NIMAD), Tehran, Iran, to Y. Ghasemi.
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Figure S1
a) Functional domains of the SHANK3 protein, retrieved by CDD. b) 3D-structure of SHANK3 functional domains, retrieved from the Protein Data Bank. (PNG 1473 kb)
Figure S2
Structural property of the SHANK3 protein. The first line displays the SHANK3 sequence. Second and third lines display 3-state and 8-state secondary structure prediction in which H, E, and C stand for helix, β-sheet, and coil, respectively. The fourth line displays solvent accessibility in which E, M, and B stands for exposed, medium, and buried, respectively. Last line shows order/disorder region with * indicating disorder. (JPG 1947 kb)
Figure S3
Positions of the target residues for MD simulation in the crystallography structure of the N-terminus part of SHANK3 protein with the PDB ID of 5G4X. (PNG 631 kb)
Figure S4
Superimposition of residues 1–100 of the crystallography structure (yellow) over residues 1–100 of model protein obtained at the end of MD simulation time related to: (a) wild type, (b) L47P, (c) G54D, and (d) G250D. (PNG 2940 kb)
Table S1
Different types of SNPs in SHANK3 gene, retrieved from dbSNP, OMIM, HGMD, and GWAS databases. (XLS 1447 kb)
Table S2
Functional impact of missense SNPs predicted by various tools. (XLS 261 kb)
Table S3
Affected motifs and potential structural effects predicted by MutPred 2. Information (XLS 59 kb)
Table S4
I-TASSER results for top five models of each mutant and wild protein. (XLS 98 kb)
Table S5
Evaluation of wild-type and mutant protein models by five different tools. (XLS 71 kb)
Table S6
Ligand binding sites of SHANK3 protein, retrieved by RaptorX binding server. (DOCX 115 kb)
Table S7
Post-translational modification sites retrieved from different servers. (DOCX 65 kb)
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Owji, H., Eslami, M., Nezafat, N. et al. In Silico Elucidation of Deleterious Non-synonymous SNPs in SHANK3, the Autism Spectrum Disorder Gene. J Mol Neurosci 70, 1649–1667 (2020). https://doi.org/10.1007/s12031-020-01552-5
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DOI: https://doi.org/10.1007/s12031-020-01552-5