Mental retardation (MR)/ intellectual disability (ID) is a neuro-developmental disorder characterized by a low
intellectual quotient (IQ) and deficits in adaptive behavior related to everyday life tasks such as delayed language
acquisition, social skills or self-help skills with onset before age 18. To date, a few genes (PRSS12, CRBN, CC2D1A,
GRIK2, TUSC3, TRAPPC9, TECR, ST3GAL3, MED23, MAN1B1, NSUN1) for autosomal-recessive forms of non
syndromic MR (NS-ARMR) have been identified and established in various families with ID. The recently reported
candidate gene TRAPPC9 was selected for computational analysis to explore its potentially important role in pathology as
it is the only gene for ID reported in more than five different familial cases worldwide.
YASARA (12.4.1) was utilized to generate three dimensional structures of the candidate gene TRAPPC9. Hybrid structure
prediction was employed. Crystal Structure of a Conserved Metalloprotein From Bacillus Cereus (3D19-C) was selected
as best suitable template using position-specific iteration-BLAST. Template (3D19-C) parameters were based on E-value,
Z-score and resolution and quality score of 0.32, -1.152, 2.30°A and 0.684 respectively. Model reliability showed 93.1%
residues placed in the most favored region with 96.684 quality factor, and overall 0.20 G-factor (dihedrals 0.06 and
covalent 0.39 respectively). Protein-Protein docking analysis demonstrated that TRAPPC9 showed strong interactions of
the amino acid residues S253, S251, Y256, G243, D131 with R105, Q425, W226, N225, S233, its functional partner 1KBKB.
Protein-protein interacting residues could facilitate the exploration of structural and functional outcomes of wild type and
mutated TRAPCC9 protein. Actively involved residues can be used to elucidate the binding properties of the protein, and
to develop drug therapy for NS-ARMR patients.