In silico prediction of the functional and structural consequences of the non-synonymous single nucleotide polymorphism A122V in bovine CXC chemokine receptor type 1.

A F Guzzi,P F Tavares-Filho,F S L Oliveira,M M S Amaro,J E Gabriel

doi:10.1590/1519-6984.188655

Abstract

The current study aimed to assess whether the A122V causal polymorphism promotes alterations in the functional and structural proprieties of the CXC chemokine receptor type 1 protein (CXCR1) of cattle Bos taurus by in silico analyses. Two amino acid sequences of bovine CXCR1 was selected from database UniProtKB/Swiss-Prot: a) non-polymorphic sequence (A7KWG0) with alanine (A) at position 122, and b) polymorphic sequence harboring the A122V polymorphism, substituting alanine by valine (V) at same position. CXCR1 sequences were submitted as input to different Bioinformatics' tools to examine the effects of this polymorphism on functional and structural stabilities, to predict eventual alterations in the 3-D structural modeling, and to estimate the quality and accuracy of the predictive models. The A122V polymorphism exerted tolerable and non-deleterious effects on the polymorphic CXCR1, and the predictive structural model for polymorphic CXCR1 revealed an alpha helix spatial structure typical of a receptor transmembrane polypeptide. Although higher variations in the distances between pairs of amino acid residues at target-positions are detected in the polymorphic CXCR1 protein, more than 97% of the amino acid residues in both models were located in favored and allowed conformational regions in Ramachandran plots. Evidences has supported that the A122V polymorphism in the CXCR1 protein is associated with increased clinical mastitis incidence in dairy cows. Thus, the findings described herein prove that the replacement of the alanine by valine amino acids provokes local conformational changes in the A122V-harboring CXCR1 protein, which could directly affect its post-translational folding mechanisms and biological functionality.

Highlights

The CXC chemokine receptor type 1 (CXCR1) characterizes as a class-A, rhodopsin-like G-protein-coupled receptor, the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors
Several studies have concluded that Sorting Intolerant From Tolerant (SIFT) and PolyPhen are useful to prioritize changes associated with loss of protein function, and their low specificity to predict gain of protein function should be interpreted with caution to support/refute pathogenicity or functionality of a missense variant (Gnad et al, 2013; Miosge et al, 2015)
Findings revealing great stability of the polymorphic CXCR1 protein using Bioinformatics’ tools are not sufficient to validate the empirical effects of the A122V polymorphism on its structural and functional stability, since previous report in the literature have described that this polymorphism is yet associated with higher susceptibility to clinical mastitis in dairy cows (Pokorska et al, 2016)

Summary

Introduction

The CXC chemokine receptor type 1 (CXCR1) characterizes as a class-A, rhodopsin-like G-protein-coupled receptor, the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors. Several genetic polymorphisms in the CXCR1 gene have suggested that this gene is a potential marker of susceptibility to mastitis in dairy cows. The SNP c.365C>T located in exon II of the CXCR1 gene resulted in a non-synonymous mutation [GCC (Ala) > GTC (Val)], which suggests its possible negative effect on the host response against mastitis (Zhou et al, 2013). According to Pokorska et al (2016), a non-synonymous mutation c.+365T>C in the bovine CXCR1 gene provoked a change in the coded protein [GCC (Ala) to GTC (Val) at the 122nd amino acid], demonstrating stronger association with susceptibility of Polish Holstein-Friesian cows to clinical mastitis

Methods

Results

Conclusion