Wang Edina, Chinni Suresh, Bhore Subhash Janardhan
Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia.
Bioinformation. 2014 Mar 19;10(3):130-7. doi: 10.6026/97320630010130. eCollection 2014.
The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken.
The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools.
The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated.
The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate.
The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates.
植物油的脂肪酸组成决定了其性质和营养价值。从非洲油棕[油棕（Elaeis guineensis Jacq.（Tenera））]中提取的棕榈油含有44%的棕榈酸（C16:0），但从美洲油棕[油棕（Elaeis oleifera）]中提取的棕榈油仅含有25%的C16:0。部分原因是，β-酮脂酰-[酰基载体蛋白]合酶II（KASII）[酶编号：2.3.1.179]蛋白导致了非洲油棕来源的棕榈油中C16:0含量较高。为了更深入了解油棕KASII（EgKASII）和油棕KASII（EoKASII）蛋白，了解其结构至关重要。因此，开展了本研究。
本研究的目的是使用分子建模工具预测EgKASII和EoKASII蛋白的三维（3D）结构。
从美国国家生物技术信息中心（NCBI）的蛋白质数据库中检索KASII蛋白的氨基酸序列。使用蛋白质结构预测的同源建模和从头预测技术方法对两种蛋白的3D结构进行预测。进行分子动力学（MD）模拟以优化预测结构。对预测的结构模型进行评估，并计算均方根偏差（RMSD）和均方根波动（RMSF）值。
同源建模显示，EgKASII和EoKASII蛋白分别与肺炎链球菌KASII和布鲁氏菌KASII有78%和74%的相似性。使用从头预测技术方法预测的EgKASII和EoKASII结构与其通过同源建模预测的结构分别有6%和9%的偏差。结构优化和验证证实预测结构是准确的。
预测了EgKASII和EoKASII蛋白的3D结构。然而，要了解EgKASII和EoKASII蛋白与其底物的相互作用，还需要进一步研究。
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