Characterizing the polymorphism K232A of the diacylglycerol-acyltransferase-1 lipogenic enzyme of bovine Bos taurus using in silico comparative protein prediction analyses

Abstract

(With 1 figure) The diacylglycerol-acyltransferase-1 lipogenic enzyme (DGAT1) is a multi-pass transmembrane protein that catalyzes the conversion of diacylglycerol and fatty acyl CoA to triacylglycerol or retinol (LIU et al., 2012). The lysine to alanine polymorphism in the DGAT1 (K232A) is directly associated with 50% of the genetic variation in milk-fat percentage and exerts a strong effect on milk fatty acid composition (Schennink et al., 2008). Within this perspective, this study aimed to predict potential structural and functional effects of the polymorphism K232A on DGAT1 protein sequences of bovine Bos taurus using in silico comparative modelling prediction analyses.Two sequences of the DGAT1 protein of bovine Bos taurus were analyzed in this study: the non-polymorphic DGAT1 sequence (ID:Q8MK44) searched and selected from a non-redundant protein sequence database UniProtKB/ Swiss-Prot, and polymorphic DGAT1 sequence harboring the mutation K232A. Functional predictions of these proteins were evaluated using SIFT and PolyPhen-2 tools that infer the effect of an amino acid substitution on the structure and function of a protein using sequence homology (Kumar et al., 2009;Adzhubei et al., 2010). The prediction of differences in the protein stability due to mutation was also estimated from Gibbs free energy change (DDG) using I-Mutant version 2.0 (Capriotti et al., 2005). In silico comparative modelling prediction analyses of the tertiary and quaternary structures of the non-polymorphic and polymorphic DGAT-1 proteins were predicted using Phyre2 (Kelley et al., 2015) and Swiss-Model (Biasini et al., 2014) servers that build 3D theoretical models for protein fold recognition based on evolutionary related proteins and homology modelling. All computational biology tools selected in current study have been largely described in the literature as sufficient and reliable evaluative tools for in silico characterization of multiple target proteins.The SIFT and PolyPhen-2 results demonstrated that the mutation K232A was predicted to be tolerated with a score of 0.19 and benign with a score to 0.001, 0.99 sensitivity and 0.15 specificity. Furthermore, DDG value resulting of the polymorphism K232A was 0.78, indicating an increase in the structural stability of the polymorphic DGAT1. In Phyre2 analyses the modelling prediction for the non-polymorphic DGAT1 sequence targeted directly to Chain A of the membrane channel protein WSK3, a watersoluble analogue of the potassium channel KcsA, modelling 96 residues (20% of the sequence) with 23.9% confidence ( Figure 1A). Values of the global modelling quality estimation (GMQE and QMEAN) of the target-template alignment were 0.06 and -3.57, respectively. Notably, the modelling prediction for the polymorphic DGAT1 sequence matched to Chain A of a stromal interaction molecule 2, modelling 21 residues (4% of the sequence) with 23.0% confidence ( Figure 1B), and 0.04 GMQE and -6.27 QMEAN values. According to Kelley et al. (2015), 3D structure protein modellings may be very useful as ...

Predicting the effects of the single nucleotide polymorphism A122V on CXC chemokine receptor type 1 of Bos taurus (Artiodactyla: Bovidae) cattle by in silico analyses

“…Two sequences of CXCR1 protein of B. taurus were selected from the non-redundant protein sequence database UniProtKB/Swiss-Prot (BOUTET et al, 2007): a) a non-polymorphic sequence (A7KWG0), containing the alanine (A) at position 122, and b) a polymorphic sequence harboring the causal polymorphism A122V with the substitution by valine (V) at the same position. Analyses of the primary and secondary structures of the amino acid residues of both protein sequences were carried out using the ProtParam program and Chou & Fasman Protein Secondary Structure Prediction CFSSP algorithm, as described in detail by Costa et al (2013) and Costa et al (2018). Theoretical isoelectric point (pI), estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) were some of the biochemical parameters determined under these experimental conditions.…”