Luo Xubo, Seidler Morgan, Lee Yen Jea, Yu Tianyi, Zuckermann Ronald N, Balsara Nitash P, Abel Brooks A, Prendergast David, Jiang Xi
Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Macromol Rapid Commun. 2025 Jan;46(1):e2400589. doi: 10.1002/marc.202400589. Epub 2024 Sep 12.
Cryogenic transmission electron microscopy (cryo-TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA-reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo-TEM 3D reconstructions of self-assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. These findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.
低温透射电子显微镜（cryo-TEM）与单颗粒分析（SPA）相结合是一种新兴的软材料成像方法。然而，由于纳米结构潜在的堆积异质性，SPA重建的纳米结构的准确性，尤其是由合成聚合物形成的纳米结构的准确性，仍然不确定。在本研究中，分子动力学（MD）模拟和图像模拟相结合，用于验证自组装聚肽纤维纳米结构的低温TEM三维重建的准确性。使用CryoSPARC软件进行图像模拟、二维分类、从头重建和均匀细化。通过将结果与原子模型进行比较，评估分子细节的恢复情况，识别异质结构，并评估提取位置对重建的影响。这些发现证实了单颗粒分析在准确解析复杂结构特征和异质结构方面的保真度，展示了其作为合成聚合物和软材料详细结构分析的宝贵工具的潜力。
