蛋白质结构预测,原子模型构建和验证使用B型肝炎病毒球形亚病毒粒子的冷EM密度图
Nadia DiNunno1, Emily N Bianchini1, Haitao Liu1
1Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
Bio-protocol
|July 27, 2023
概括
研究人员使用冷电子显微镜以6.3 Å的精度解决了乙型肝炎病毒 (HBV) 球形亚病毒粒子 (SVP) 结构. 一个新的协议将AlphaFold2与冷EM数据相结合,用于可靠的3DHBV SVP建模.
科学领域:
- 结构生物学 结构生物学
- 病毒学 病毒学
- 生物物理学的生物物理.
背景情况:
- 乙型肝炎病毒 (HBV) 感染是全球重要的健康问题.
- 慢性HBV感染包括在球形亚病毒颗粒 (SVP) 中过度产生免疫性小表面抗原.
- 之前对HBV SVP的结构研究产生了低分辨率 (12-30 Å) 和相互矛盾的架构细节.
研究的目的:
- 为了确定HBV球形SVP的高分辨率结构.
- 通过将AlphaFold2预测与冷电子显微镜 (cryo-EM) 数据相结合,开发并介绍一个可靠的HBV SVP3D模型的强大协议.
- 建立适用于各种冷电磁数据集的工作流程.
主要方法:
- 使用冷电子显微镜 (cryo-EM) 和3D图像重建来解决HBV球形SVP结构.
- 开发了一种结合AlphaFold2预测与中等分辨率冷EM密度图的新方案.
- 该协议涉及3D模型预测,评估,刚体配件,灵活配件,真实空间改进,验证和调整,使用标准的冷EM软件.
主要成果:
- HBV 球形 SVP 的 3D 结构得到了 6.3 Å 的分辨率.
- 通过将AlphaFold2预测与冷EM数据集成,成功构建了HBV球形SVP的可靠3D模型.
- 提交的协议证明了其在生成高质量的结构模型中的有效性.
结论:
- 这项研究提供了HBV球形SVP的高分辨率结构,进步了我们对HBV的理解.
- 描述了一种经过验证的计算协议,用于使用组合AlphaFold2和冷EM数据构建病毒颗粒的准确3D模型.
- 该协议可用于分析中度和高分辨率的冷EM数据集,为结构病毒学提供了有价值的工具.
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