雞低密度脂蛋白計算模型之建立與研究

報告時間：2025-6-20
報告地點：407
指導老師：辛坤鎰
學生：招重君

雞胚之發育過程仰賴脂質作為主要能量來源，且需要有效地將脂質轉運至蛋黃；此過程涉及一特定靶向蛋黃之極低密度脂蛋白（very-low-density lipoproteins targeting the yolk, VLDLy），其由中性脂質核心、載脂蛋白B-100（apoB100）以及載脂蛋白VLDL-II（apoVLDL-II）組成；其中，apoVLDL-II僅存在於VLDLy中。由於apoVLDL-II的存在，VLDLy顆粒之尺寸比血漿中的VLDL顯著較小（分別為27.9 nm與72.3 nm），儘管兩者在結構組成上非常相似。在血液循環系統中，VLDL會被代謝為低密度脂蛋白（LDL），其直徑（19–25 nm）與VLDLy（25–44 nm）相當，顯示非交換性的apoB100在兩者中的結構可能相似。由於人類LDL與apoB100與心血管疾病密切相關，其已被廣泛研究，並以電腦模擬方式建立3D立體結構之模型，以協助了解apoB100之結構特徵與功能。人類與雞隻的apoB100經比對後，整體序列同一性為50.52%，殘基相似性為55.82%。次級結構分析（PSI-Blast based secondary structure prediction, PSIPRED）顯示兩者在α-螺旋（31.43%與31.74%）、β-摺疊（33.95%與33.02%）與捲曲結構（34.63%與35.24%）方面具高度相似性。這些結果顯示，人類apoB100可作為建模雞apoB100的適當模板。本研究旨在應用人類相關脂蛋白模型為參考，模擬並建立雞之LDL與apoB100結構模型，作為了解蛋雞VLDLy的第一步。本研究之LDL脂質核心由POPC （1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine）、溶血磷脂酰膽鹼（Lysophosphatidylcholine, lysoPC）、膽固醇、膽固醇油酸酯與三油酸酯組成，並以粗粒化分子動態模擬方法建立模型。經過1.3微秒模擬後，脂質核心結構達到穩定，平均壓力為2.46 bar，溫度為310.01 K。至於apoB100區段，本研究嘗試多種同源建模與機械學習之類神經網路方法；其中，MODELLER（同源建模）與AlphaFold2（AF2，深度學習預測）產生之模型精確度高於其他軟體，其Ramachandran分析之蛋白質中骨幹的旋轉角度允許區域分數分別為93.4%與90.1%，不允許區域僅為0.3%與0.4%。相較於人類apoB100，MODELLER與AF2模型中N端結構域的RMSD分別為1.393 Å與7.240 Å。AF2亦成功以中等準確度預測了尚未解析的apoVLDL-II結構（其中70%結構的predicted local distance difference test (pLDDT) > 70）。本研究應用高速運算及in-silico分子模擬方法建構了一個包含脂質核心與apoB100的雞隻LDL初步模型；該模型為後續模擬雞隻VLDL與VLDLy以及apoVLDL-II結構奠定了基礎，有助於釐清蛋雞體內VLDL、apoB100與apoVLDL-II之間的交互作用。

關鍵字: 雞胚、計算模型、低密度脂蛋白
參考文獻
  • Abraham, M. J., T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, and E. Lindahl. 2015. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 1-2:19–25.
  • Berndsen, Z. T., and C. K. Cassidy. 2024. The structure of apolipoprotein B100 from human low-density lipoprotein. Nature.
  • Boyle-Roden, E., and R. L. Walzem. 2005. Integral apolipoproteins increase surface-located triacylglycerol in intact native apoB-100-containing lipoproteins. Journal of Lipid Research. 46:1624–1632.
  • Feingold, K. R. 2022. Lipid and Lipoprotein Metabolism. Endocrinology and Metabolism Clinics of North America. 51:437–458.
  • Jeiran, K., S. M. Gordon, D. O. Sviridov, A. M. Aponte, A. Haymond, G. Piszczek, D. Lucero, E. B. Neufeld, I. I. Vaisman, L. Liotta, A. Baranova, and A. T. Remaley. 2022. A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking. International Journal of Molecular Sciences. 23:11480.
  • Jumper, J., R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Žídek, A. Potapenko, A. Bridgland, C. Meyer, S. A. A. Kohl, A. J. Ballard, A. Cowie, B. Romera-Paredes, S. Nikolov, R. Jain, J. Adler, and T. Back. 2021. Highly Accurate Protein Structure Prediction with Alphafold. Nature. 596:583–589.
  • McGuffin, L. J., K. Bryson, and D. T. Jones. 2000. The PSIPRED protein structure prediction server. Bioinformatics. 16:404–405.
  • Murtola, T., T. A. Vuorela, M. T. Hyvönen, S.-J. Marrink, M. Karttunen, and I. Vattulainen. 2011. Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids. Soft Matter. 7:8135.
  • Perry, M. M., H. D. Griffin, and A. B. Gilbert. 1984. The binding of very low density and low density lipoproteins to the plasma membrane of the hen’s oocyte. Experimental Cell Research. 151:433–446.
  • Pettersen, E. F., T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin. 2004. UCSF Chimera--a visualization system for exploratory research and analysis. Journal of Computational Chemistry. 25:1605–1612.
  • Reimund, M., A. D. Dearborn, G. Graziano, H. Lei, and J. Marcotrigiano. 2024. Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor. Nature. 1–7.
  • Robert, X., and P. Gouet. 2014. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research. 42:W320–W324.
    Šali, A., and T. L. Blundell. 1993. Comparative Protein Modelling by Satisfaction of Spatial Restraints. Journal of Molecular Biology. 234:779–815.
  • Schneider, W., R. Carroll, D. Severson, and J. Nimpf. 1990. Apolipoprotein VLDL-II inhibits lipolysis of triglyceride-rich lipoproteins in the laying hen. Journal of Lipid Research. 31:507–513.
  • Walzem, R. L., R. J. Hansen, D. L. Williams, and R. L. Hamilton. 1999. Estrogen Induction of VLDLy Assembly in Egg-Laying Hens. The Journal of Nutrition. 129:467S472S.