Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan.
J Chem Theory Comput. 2020 Feb 11;16(2):1349-1358. doi: 10.1021/acs.jctc.9b00991. Epub 2020 Jan 22.
High-speed (HS) atomic force microscopy (AFM) is a prominent imaging technology that observes large-scale structural dynamics of biomolecules near the physiological condition, but the AFM data are limited to the surface shape of specimens. Rigid-body fitting methods were developed to obtain molecular structures that fit to an AFM image, without accounting for conformational changes. Here, we developed a method to fit flexibly a three-dimensional (3D) biomolecular structure into an AFM image. First, we describe a method to produce a pseudo-AFM image from a given 3D structure in a differentiable form. Then, using a correlation function between the experimental AFM image and the computational pseudo-AFM image, we developed a flexible fitting molecular dynamics (MD) simulation method by which we obtain protein structures that well fit to the given AFM image. We first test it with a twin experiment; using an AFM image produced from a protein structure different from its native conformation as a reference, we performed the flexible fitting MD simulations to sample conformations that fit well the reference AFM image, and the method was confirmed to work well. Then, parameter dependence in the protocol was discussed. Finally, we applied the method to a real experimental HS-AFM image for a flagellar protein FlhA, demonstrating its applicability. We also test the rigid-body fitting of a molecular structure to an AFM image. Our method will be a general tool for dynamic structure modeling based on HS-AFM images and is publicly available through the CafeMol software.
高速原子力显微镜（HS-AFM）是一种杰出的成像技术，可在接近生理条件下观察生物分子的大尺度结构动力学，但 AFM 数据仅限于标本的表面形状。刚体拟合方法被开发出来，以获得适合 AFM 图像的分子结构，而不考虑构象变化。在这里，我们开发了一种将三维（3D）生物分子结构灵活拟合到 AFM 图像中的方法。首先，我们描述了一种从给定的 3D 结构中以可微形式生成伪 AFM 图像的方法。然后，使用实验 AFM 图像和计算伪 AFM 图像之间的相关函数，我们开发了一种灵活的拟合分子动力学（MD）模拟方法，通过该方法可以获得与给定 AFM 图像很好拟合的蛋白质结构。我们首先通过双胞胎实验进行了测试；使用与其天然构象不同的蛋白质结构产生的 AFM 图像作为参考，我们进行了灵活拟合 MD 模拟，以采样与参考 AFM 图像很好拟合的构象，该方法被证实效果良好。然后，讨论了协议中的参数依赖性。最后，我们将该方法应用于鞭毛蛋白 FlhA 的真实实验 HS-AFM 图像，证明了其适用性。我们还测试了分子结构对 AFM 图像的刚体拟合。我们的方法将成为基于 HS-AFM 图像的动态结构建模的通用工具，并通过 CafeMol 软件公开提供。
