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J Biomed Phys Eng. 2019 Feb 1;9(1):105-120. eCollection 2019 Feb.

In-silico Evaluation of Rare Codons and their Positions in the Structure of ATP8b1 Gene.

M Z1,2, S M D3, F E3, M R F3, M M4, S M B T5.

Author information

1
MD, PhD, Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
2
MD, PhD, legal medicine research center, legal medicine organization, Tehran , iran.
3
MD, Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
4
PhD, Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran.
5
MD, Genetic Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.

Abstract

Background:

Progressive familial intrahepatic cholestases (PFIC) are a spectrum of autosomal progressive liver diseases developing to end-stage liver disease. ATP8B1 deficiency caused by mutations in ATP8B1 gene encoding a P-type ATPase leads to PFIC1. The gene for PFIC1 has been mapped on a 19-cM region of 18q21-q22, and a gene defect in ATP8B1 can cause deregulations in bile salt transporters through decreased expression and/or activity of FXR. Point mutations are the most common, with the majority being missense or nonsense mutations. In addition, approximately 15% of disease-causing ATP8B1 mutations are annotated as splicing disrupting alteration given that they are located at exon-intron borders.

Objective:

Here, we describe the hidden layer of computational biology information of rare codons in ATP8B1, which can help us for drug design.

Methods:

Some rare codons in different locations of ATP8b1 gene were identified using several web servers and by in-silico modelling of ATP8b1 in Phyre2 and I-TASSER server, some rare codons were evaluated.

Results:

Some of these rare codons were located at special positions which seem to have a critical role in proper folding of ATP8b1 protein. Structural analysis showed that some of rare codons are related to mutations in ATP8B1 that are responsible for PFIC1 disease, which may have a critical role in ensuring the correct folding.

Conclusion:

Investigation of such hidden information can enhance our understanding of ATP8b1 folding. Moreover, studies of these rare codons help us to clarify their role in rational design of new and effective drugs.

KEYWORDS:

ATP8b1; Bioinformatics Analysis; Rare Codon; Progressive Familial Intrahepatic Cholestasis

PMID:
30881940
PMCID:
PMC6409373

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