Siddiqa Amnah, Ahmad Jamil, Ali Amjad, Paracha Rehan Zafar, Bibi Zurah, Aslam Babar
Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
Comput Biol Chem. 2016 Apr;61:210-20. doi: 10.1016/j.compbiolchem.2016.01.009. Epub 2016 Jan 25.
Angiopoietin-like protein 8 (ANGPTL8) (also known as betatrophin) is a newly identified secretory protein with a potential role in autophagy, lipid metabolism and pancreatic beta-cell proliferation. Its structural characterization is required to enhance our current understanding of its mechanism of action which could help in identifying its receptor and/or other binding partners. Based on the physiological significance and necessity of exploring structural features of ANGPTL8, the present study is conducted with a specific aim to model the structure of ANGPTL8 and study its possible interactions with Lipoprotein Lipase (LPL). To the best of our knowledge, this is the first attempt to predict 3-dimensional (3D) structure of ANGPTL8. Three different approaches were used for modeling of ANGPTL8 including homology modeling, de-novo structure prediction and their amalgam which is then proceeded by structure verification using ERRATT, PROSA, Qmean and Ramachandran plot scores. The selected models of ANGPTL8 were further evaluated for protein-protein interaction (PPI) analysis with LPL using CPORT and HADDOCK server. Our results have shown that the crystal structure of iSH2 domain of Phosphatidylinositol 3-kinase (PI3K) p85β subunit (PDB entry: 3mtt) is a good candidate for homology modeling of ANGPTL8. Analysis of inter-molecular interactions between the structure of ANGPTL8 and LPL revealed existence of several non-covalent interactions. The residues of LPL involved in these interactions belong from its lid region, thrombospondin (TSP) region and heparin binding site which is suggestive of a possible role of ANGPTL8 in regulating the proteolysis, motility and localization of LPL. Besides, the conserved residues of SE1 region of ANGPTL8 formed interactions with the residues around the hinge region of LPL. Overall, our results support a model of inhibition of LPL by ANGPTL8 through the steric block of its catalytic site which will be further explored using wet lab studies in future.
血管生成素样蛋白8（ANGPTL8）（也称为β-促胰岛素分泌素）是一种新发现的分泌蛋白，在自噬、脂质代谢和胰腺β细胞增殖中具有潜在作用。需要对其进行结构表征，以加深我们目前对其作用机制的理解，这有助于识别其受体和/或其他结合伙伴。基于探索ANGPTL8结构特征的生理意义和必要性，本研究旨在构建ANGPTL8的结构模型，并研究其与脂蛋白脂肪酶（LPL）的可能相互作用。据我们所知，这是首次预测ANGPTL8三维（3D）结构的尝试。采用三种不同方法对ANGPTL8进行建模，包括同源建模、从头结构预测及其合并，然后使用ERRATT、PROSA、Qmean和拉氏图评分进行结构验证。使用CPORT和HADDOCK服务器对所选的ANGPTL8模型进行进一步评估，以分析其与LPL的蛋白质-蛋白质相互作用（PPI）。我们的结果表明，磷脂酰肌醇3激酶（PI3K）p85β亚基的iSH2结构域（PDB编号：3mtt）的晶体结构是ANGPTL8同源建模的良好候选对象。对ANGPTL8和LPL结构之间分子间相互作用的分析揭示了几种非共价相互作用的存在。参与这些相互作用的LPL残基来自其盖子区域、血小板反应蛋白（TSP）区域和肝素结合位点，这表明ANGPTL8在调节LPL的蛋白水解、运动性和定位方面可能发挥作用。此外，ANGPTL8的SE1区域的保守残基与LPL铰链区域周围的残基形成了相互作用。总体而言，我们的结果支持ANGPTL8通过空间位阻其催化位点来抑制LPL的模型，未来将通过湿实验室研究进一步探索这一模型。
