In Silico Evaluation of the ATP7B Protein: Insights from the Role of Rare Codon Clusters and Mutations that Affect Protein Structure and Function

Background: Wilson’s disease is a rare autosomal recessive genetic disorder of copper metabolism, which is characterized by hepatic and neurological disease. ATP7B encodes a transmembrane protein ATPase (ATP7B), which functions as a copper-dependent P-type ATPase. The mutations in the gene ATP7B (on chromosome 13) lead to Wilson’s disease and is highly expressed in the liver, kidney, and placenta. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as the rare codons of the ATP7B gene were evaluated by online software, including a rare codon calculator (RCC), ATGme, LaTcOm, and Sherlocc program. Additionally, the multiple sequence alignment of this enzyme was studied. Finally, for evaluation of the effects of rare codons, the 3D structure of ATP7B was modeled in the Swiss Model and I-TASSER web server. Results: The results showed that the ATP7B gene has 35 single rare codons for Arg. Additionally, RCC detected two rare codons for Leu, 13 single rare codons for Ile and 28 rare codons for the Pro. ATP7B gene analysis in minmax and sliding_window algorithm resulted in the identification of 16 and 17 rare codon clusters, respectively, indicating the different features of these algorithms in the detection of RCCs. Analyzing the 3D model of ATP7B protein showed that Arg816 residue constitutes hydrogen bonds with Glu810 and Glu816. Mutation of this residue to Ser816 cause these hydrogen bonds not to be formed and may interfere in the proper folding of ATP7B protein. Furthermore, the side chain of Arg1228 does not form any bond with other residues. By mutation of Arg1228 to Thr1228, a new hydrogen bond is formed with the side chain of Arg1228. The addition and deletion of hydrogen bonds alter the proper folding of ATP7B protein and interfere with the proper function of the ATP7B position. On the other hand, His1069 forms the hydrogen bonds with the His880 and this hydrogen bond adhere two regions of the protein together, which is critical in the final structural folding of ATP7B protein. Conclusion: Previous studies show that synonymous and silent mutations have been linked to numerous diseases. Given the importance of synonymous and silent mutations in diseases, the aim of this study was to investigate the rare codons (synonymous codons) in the structure of ATP7B enzyme. By these analyses, a new understanding was developed and our findings can further be used in some fields of the clinical and industrial biotechnology.