Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.
Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.
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DOI：
10.1371/journal.pcbi.1009970
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发表时间：
2022-03
影响因子：
4.3
通讯作者：
Flechsig H
中科院分区：
文献类型：
--
作者：
Amyot R;Marchesi A;Franz CM;Casuso I;Flechsig H
原子力显微镜（AFM）可以可视化在接近生理条件下的单个生物分子的动力学。然而，扫描尖端仅探测具有有限分辨率的分子表面，缺少仅从成像完全推断功能机制所需的细节。为了克服这些缺点，我们开发了一个计算框架，从AFM表面扫描重建三维原子结构，采用模拟AFM和自动拟合实验图像。我们提供的应用范围从单分子机器，蛋白质丝，大规模组装的二维蛋白质晶格的AFM图像，并展示了如何获得完整的原子信息超越原来的地形AFM图像的分子理解。我们表明，模拟AFM进一步允许定量分子特征分配内测得的AFM形貌。将开发的方法应用到BioAFMviewer软件的多功能交互式界面中，可在www.bioafmviewer.com上免费获得，这为广泛的Bio-AFM社区提供了利用大量现有结构和建模数据来促进分辨率受限AFM图像解释的机会。原子力显微镜（AFM）允许可视化单个生物分子在其活动期间的动力学。然而，所有的观察都局限于扫描过程中相当大的探测头可以到达的区域。因此，AFM仅以有限的空间分辨率对生物分子表面进行成像，错过了详细了解所观察到的现象所需的重要信息。我们采用模拟原子显微镜（sAFM），计算模拟实验扫描，自动适应现有的生物分子结构到实验AFM图像。这允许从实验AFM表面扫描获得3D原子分子结构。对于从单分子机器，蛋白质丝，蛋白质晶格组装的应用程序，我们展示了如何全面的原子信息超越实验图像的分子理解。所开发的计算方法嵌入在用户友好的BioAFMviewer交互式软件界面中，为Bio-AFM社区使用模拟AFM更好地理解实验结果提供了方便的平台。
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, the scanning tip probes only the molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework to reconstruct 3D atomistic structures from AFM surface scans, employing simulation AFM and automatized fitting to experimental images. We provide applications to AFM images ranging from single molecular machines, protein filaments, to large-scale assemblies of 2D protein lattices, and demonstrate how the obtained full atomistic information advances the molecular understanding beyond the original topographic AFM image. We show that simulation AFM further allows for quantitative molecular feature assignment within measured AFM topographies. Implementation of the developed methods into the versatile interactive interface of the BioAFMviewer software, freely available at www.bioafmviewer.com, presents the opportunity for the broad Bio-AFM community to employ the enormous amount of existing structural and modeling data to facilitate the interpretation of resolution-limited AFM images. Atomic force microscopy (AFM) allows to visualize the dynamics of single biomolecules during their activity. All observations are, however, restricted to regions accessible by a fairly big probing tip during scanning. Hence, AFM images only the biomolecular surface with limited spatial resolution, missing important information required for a detailed understanding of the observed phenomena. We employ simulation atomic microscopy (sAFM), computationally emulating experimental scanning, to automatically fit available biomolecular structures into experimental AFM images. This allows to obtain 3D atomistic molecular structures from experimental AFM surface scans. For applications ranging from single molecular machines, protein filaments, to assemblies of protein lattices, we demonstrate how the full atomistic information advances the molecular understanding beyond experimental images. The developed computational methods are embedded within the user-friendly BioAFMviewer interactive software interface, providing the convenient platform for the Bio-AFM community to employ simulation AFM to better understand experimental results.
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BioAfmViewer：用于模拟生物分子结构和动力学的AFM扫描的交互式界面。
影响因子：
4.3
作者：
Amyot R;Flechsig H
通讯作者：
Flechsig H
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通讯作者：
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