Prediction of 3D Protein Structure Based on The Mutation of AKAP3 and PLOD3 Genes in The Case of Non-Obstructive Azoospermia

Ajit Kumar Saxena; Meenakshi Tiwari; Mukta Agarwal; Aprajita Aniket Kumar

doi:10.22074/ijfs.2020.6028

Prediction of 3D Protein Structure Based on The Mutation of AKAP3 and PLOD3 Genes in The Case of Non-Obstructive Azoospermia

Int J Fertil Steril. 2020 Jul;14(2):102-109. doi: 10.22074/ijfs.2020.6028. Epub 2020 Jul 15.

Authors

Ajit Kumar Saxena¹, Meenakshi Tiwari², Mukta Agarwal³, Aprajita Aniket Kumar²

Affiliations

¹ Department of Pathology/Laboratory Medicine, All India Institute of Medical Sciences, Bihar, India. Electronic Address: draksaxena1@rediffmail.com.
² Department of Pathology/Laboratory Medicine, All India Institute of Medical Sciences, Bihar, India.
³ Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, Bihar, India.

Abstract

Background: The present study has been designed with the aim of evaluating A-kinase anchoring proteins 3 (AKAP3) and Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 (PLOD3) gene mutations and prediction of 3D protein structure for ligand binding activity in the cases of non-obstructive azoospermic male.

Materials and methods: Clinically diagnosed cases of non-obstructive azoospermia (n=111) with age matched controls (n=42) were included in the present case-control study for genetics analysis and confirmation of diagnosis. The sample size was calculated using Epi info software version 6 with 90 power and 95% confidence interval. Genomic DNA was isolated from blood (2.0 ml) and a selected case was used for whole exome sequencing (WES) using Illumina Hiseq for identification of the genes. Bioinformatic tools were used for decode the amino acid sequence from biological database (www.ncbi.nlm.nih.gov/protein). 3D protein structure of AKAP3 and PLOD3 genes was predicted using I-TASSER server and binding energy was calculated by Ramachandran plot.

Results: Present study revealed the mutation of AKAP3 gene, showing frameshift mutation at rs67512580 (ACT → -CT) and loss of adenine in homozygous condition, where, leucine changed into serine. Similarly, PLOD3 gene shows missense mutation in heterozygous condition due to loss of guanine in the sequence AGG→A-G and it is responsible for the change in post-translational event of amino acid where arginine change into lysine. 3D structure shows 8 and 4 pockets binding site in AKAP3 and PLOD3 gene encoded proteins with MTX respectively, but only one site bound to the receptor with less binding energy representing efficient model of protein structure.

Conclusion: These genetic variations are responsible for alteration of translational events of amino acid sequences, leading to protein synthesis change following alteration in the predicted 3D structure and functions during spermiogenesis, which might be a causative "risk" factor for male infertility.

Keywords: AKAP3; Infertility; Iterative Threading ASSEmbly Refinement; PLOD3 gene; Whole Exome Sequencing.