Computational analysis of non-synonymous single nucleotide polymorphism in the bovine <i>PKLR</i> gene

Pyruvate kinase (PKLR) is a potential candidate gene for milk production traits in cows. The main aim of this work is to investigate the potentially deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the <i>PKLR</i> gene by using several computational tools. <i>In silico</i> tools including SIFT, Polyphen-2, SNAP2 and Panther indicated only 18 nsSNPs out of 170 were considered deleterious. The analysis of proteins’ stability change due to amino acid substitution performed by the use of the I-mutant, MUpro, CUPSTAT, SDM and Dynamut confirmed that 9 nsSNPs decreased protein stability. ConSurf analysis predicted that all 18 nsSNPs were evolutionary moderately or highly conserved. Two different domains of PKLR protein were revealed by the InterPro tool with 12 nsSNPs positioned in the Pyruvate Kinase barrel domain and 6 nsSNP present in the Pyruvate Kinase C Terminal. The PKLR 3D model was predicted by MODELLER software and validated <i>via</i> Ramachandran plot and Prosa which indicated a good quality model. The analysis of energy minimizations for the native and mutated structures was performed by SWISS PDB viewer with GROMOS 96 program and showed that 3 structural and 4 functional residues had total energy higher than the native model. These findings indicate that these mutant structures (rs441424814, rs449326723, rs476805413, rs472263384, rs474320860, rs475521477, rs441633284) were less stable than the native model. Molecular Dynamics simulations were performed to confirm the impact of nsSNPs on the protein structure and function. The present study provides useful information about functional SNPs that have an impact on PKLR protein in cattle. Communicated by Ramaswamy H. Sarma

丙酮酸激酶（Pyruvate kinase, PKLR）是奶牛产奶性状的潜在候选基因。本研究旨在利用多种计算工具，探究PKLR基因中潜在有害的非同义单核苷酸多态性（non-synonymous single nucleotide polymorphisms, nsSNPs）。通过SIFT、Polyphen-2、SNAP2及Panther等计算机模拟（in silico）工具分析显示，170个nsSNPs中仅18个被判定为有害。利用I-mutant、MUpro、CUPSTAT、SDM及Dynamut对氨基酸替换引发的蛋白质稳定性变化开展分析，证实其中9个nsSNPs可降低蛋白质稳定性。ConSurf分析预测，该18个nsSNPs均处于进化中度或高度保守区域。InterPro工具揭示PKLR蛋白存在两个不同结构域：12个nsSNPs位于丙酮酸激酶桶状结构域，剩余6个nsSNPs存在于丙酮酸激酶C端结构域。本研究利用MODELLER软件预测PKLR的三维结构模型，并通过拉马钱德兰图（Ramachandran plot）与ProSA进行验证，结果显示模型质量优异。搭载GROMOS 96程序的SWISS-PDB查看器对野生型与突变体结构开展能量最小化分析，结果表明3个结构相关残基与4个功能相关残基的总能量高于野生型模型。上述结果表明，这些突变体结构（rs441424814、rs449326723、rs476805413、rs472263384、rs474320860、rs475521477、rs441633284）的稳定性低于野生型模型。本研究通过分子动力学模拟（Molecular Dynamics simulations）验证了nsSNPs对蛋白质结构与功能的影响。本研究可为影响奶牛PKLR蛋白功能的SNPs提供极具价值的参考信息。本文由Ramaswamy H. Sarma转交。

搜集汇总

背景与挑战

背景概述

该数据集通过计算工具分析牛PKLR基因中的非同义单核苷酸多态性（nsSNPs），旨在识别影响蛋白质稳定性和功能的有害突变。研究发现，在170个nsSNPs中，18个被预测为有害，其中9个会降低蛋白质稳定性，且这些突变位于进化保守区域。研究还通过3D建模和分子动力学模拟验证了突变对蛋白质结构的影响，为牛牛奶生产性状的遗传研究提供了关键数据。