Naveed et al., J Appl Bioinforma Comput Biol 2016, 5:2 DOI: 10.4172/2329-9533.1000127 Journal of Applied Bioinformatics & Computational Biology Research Article a SciTechnol journal social, practical adaptive skills and conceptual, originating before 18 Computational Analysis and years [1] and intellectual functioning (I.Q below 70%). It is observed that 1- 3% of general population is affected with MR [2]. Because large Polymorphism study of Tumor numbers of X-linked MR genes are involved in mental retardation which gives ratio between mentally retarded males and females which Suppressor Candidate Gene-3 seem to be quite high at 1.4-:1 to 1.6:1 [3]. Intellectual disability has a very diverse etiology [4]. The causes of ID that affect the development for Non Syndromic Autosomal and functioning of CNS prenatally or postnatally can involve both Recessive Mental Retardation genetic and environmental factors [5]. Muhammad Naveed*, Syeda Khushbakht Kazmi, Fiza Anwar, Prenatal causes of mental retardation include congenital Fatima Arshad, Tehreem Zafar Dar and Muddassar Zafar infections such as cytomegalovirus, toxoplasmosis, syphilis, rubella, herpes and human immunodeficiency virus; prolonged maternal fever in the first trimester; disclosure to alcohol or anticonvulsants; Abstract and untreated maternal phenylketonuria (PKU). Complications of prematurity especially in exceptionally low-birth-weight infants or Mental Retardation (MR) is regarded as a neuronal malfunction certain postnatal exposure can lead to mental retardation/ID [6]. characterized by a low Intellectual Quotient (IQ). To date, few genes (GRIK2, TUSC3, TRAPPC9, TECR, ST3GAL3, MED23, MAN1B1, Genetic causes of MD include genomic disorders, chromosome NSUN1 PRSS12, CRBN, CC2D1A) for autosomal-recessive non structural abnormalities, monogenic diseases and chromosome syndromic MR (NS-ARMR) have been identified and established aneusomies. Such causes account for more than 50% of moderate in various families with MR. The recently reported candidate gene to severe MR, whereas environmental factors (e.g. malnutrition, “Tumor Suppressor Candidate Gene-3 (TUSC3)” was selected for cultural deficit) account for 5-13% and play an essential part in the computational analysis to explore its potential role in pathology pathogenesis of mild ID [7]. as it is the only gene for MR reported in more than five different familial cases worldwide. TUSC3 gene located at chromosome Mental retardation is classified on the basis of transmitted 8p22 contains 11 exons and encodes a protein involved in the genes, either to present on sex chromosome or autosomes. If mental vertebrate plasma membrane magnesium ion transport system. retardation is inherited through autosomes it is called as autosomal Three dimensional structures of the candidate gene TUSC3 MR and if it is related with the X chromosome it is said to be X-linked and its mutated structure with Q55X were generated. Template MR. Phenotypic appearance (dominant or recessive) and mode of parameters were based on Z-score, E value, resolution and quality. inheritance (X-linked and autosomal) are the key determinants of Present study demonstrates the reliability of 3D model which satisfies the overall quality of the model constructed, employing autosomal syndromic and non-syndromic mental retardation. The both physiochemical and statistical model evaluation. Previously identification/recognition of autosomal dominant genes involved in a homozygous 163C-T transition in exon 2 of the TUSC3 gene, MR is quite difficult owing to the low accessibility of large families; resulting in a gln55-to-ter (Q55X) substitution has been reported. suffered individuals rarely reproduce. Up till now, no gene for And here we predicted by PHD-SNP that X could be either proline autosomal dominant non-syndromic MR has been reported other (P) or Aspartic acid (D) causing deleterious effect. As mutation at than several vulnerable genes involved in autosomal dominant MR 55 position was responsible for non-syndromic autosomal recessive have been identified during mapping of chromosomal breakpoints mental retardation, so it was assumed that mutation was either by in patients with balanced chromosomal aberrations [8]. Genotyping proline or aspartic acid. Further, MUPRO, PROVEAN, I-Mutant, Predict SNP, Meta SNP, Panther, SIFT, SNPs 3D confirmed that via microarray analysis has contributed considerably and numerous deleterious mutation was Q55P transition. loci and genes (PRSS12, CRBN, CC2D1A, GRIK2, TRAPPC9, TECR, ST3GAL3, MED23, MAN1B1, and NSUN1) responsible for autosomal Keywords recessive non- syndromic MR (AR-NSMR) have been identified. Mental retardation; Computational analysis; Polymorphism of Tumor suppressor candidate gene 3 is 11 exons gene that encodes TUSC3; Structure prediction; Deleterious mutation; SNP predictor; 348 amino acid protein. I-Mutant The foremost aim of the present study is to perform computational analysis of the gene TUSC3. The three dimensional structure of Introduction TUSC3 has not been identified by NMR and X-ray crystallography. Mental retardation (MR) is a complex phenotype distinguished by We have applied relative modeling to generate the 3D structure suboptimal functioning of the central nervous system (CNS) resulting of TUSC3 The ancestral relationships of TUSC3 were predicted in considerable restrictions in both adaptive behavior as articulated in using homologous genes to construct an ancestral hierarchy of the candidate protein profile. Materials and Methods *Corresponding author: Muhammad Naveed, Department of Biochemistry and Molecular Biology, University of Gujrat, Pakistan 50700, Tel: 00923015524624; The amino acid sequence of TUSC3 was retrieved from the E-mail: [email protected] Universal Protein Resource (UniProt) with accession number Received: July 11, 2016 Accepted: October 15, 2016 Published: October 18, Q13454.1. The sequence was subjected to the 03 position-specific 2016 iteration-Basic local alignment search tool (PSI-BLAST) to All articles published in Journal of Applied Bioinformatics & Computational Biology are the property of SciTechnol, and is International Publisher of Science, protected by copyright laws. Copyright © 2016, SciTechnol, All Rights Reserved. Technology and Medicine Citation: Naveed M, Kazmi SK, Anwar F, Arshad F, Dar TZ, et al. (2016) Computational Analysis and Polymorphism study of Tumor Suppressor Candidate Gene-3 for Non Syndromic Autosomal Recessive Mental Retardation. J Appl Bioinforma Comput Biol 5:2. doi: 10.4172/2329-9533.1000127 extort a position- specific scoring matrix (PSSM) from UniRef90 was carried out using ERRAT (Figure 2) and PROSA web servers [9] and then against the protein databank (PDB) [10] with (Figure 3) and PROCHECK (Table 2) for the validation of model 0.5 cutoff. The protein sequence of TUSC3 was subjected to quality and overall quality through VERIFY 3D [16]. RAMPAGE secondary structure analysis using PSI-PRED. I-TESSER was output for Ramachadran plot (Figure 4). used to generate 3D-models for TUSC3 and mutated (Q55X). Phylogenetic analysis Physiochemical information about the predicted wild model and mutated model of TUSC3 was evaluated by PROCHECK [11] and The Molecular Evolutionary Genetic Algorithm (MEGA 5) was statistical analysis was carried out using ERRAT (http://services.mbi. employed on. A distance-based approach was selected to conclude ucla.edu/ERRAT) PROSA web servers and RAMPAGE. And the the ancestral history. The (Neighbor-Joining method) NJ was used to overall quality of proposed model was predicted by VERIFY-3D [12]. build a phylogenetic tree. The interior branch method and bootstrap In order to predict physiochemical properties, ProtParam server was value were implemented to validate the ancestral relationships used; this computes various physical and chemical parameters, i.e., (Figure 5). amino acid composition, atomic composition, estimated half-life, Mutational analysis instability index, molecular weight, theoretical pI, aliphatic index and grand average of hydropathicity (GRAVY) for a particular protein. Software used for mutational analysis of Q55X was explained in Table 3. Phylogenetic analysis PhD-SNP The (Molecular Evolutionary Genetic Algorithm) MEGA 5 [13] was employed on. A distance-based approach was selected to PhD-SNP, [17] a SVM based classifier, classifies substitutions at conclude the ancestral history. The (Neighbor-Joining method) specified position of amino acid in protein sequence and check for NJ was executed to build a phylogenetic tree. The interior branch each possible amino acid replacement and on the base of sequence method and bootstrap value were then implemented for verifying the and profile based prediction, it classifies the mutation as neutral or ancestral relationships. deleterious polymorphism. For TUSC3, PhD-SNP confirmed Q55P and Q55D transitions as disease-related polymorphisms. Mutational analysis MUPRO In literature, it has been reported that Q at 55 position was replaced by X which could be any amino acid. And here we predicted Mupro [18] based on the Support Vector Machines (SVM) and by PHD-SNP that X could be either proline (P) or Aspartic acid (D) neural network calculates the sign of energy change and predicts the causing deleterious effect. As mutation at 55 position was responsible structure stability for mutation. The confidence score between -1 and for non-syndromic autosomal recessive mental retardation, so it 1 is used to measure the confidence of the prediction. was assumed that mutation