Institute of Applied Mechanics, University of Stuttgart, Stuttgart, Germany; Stuttgart Research Centre for Simulation Technology (SimTech), Stuttgart, Germany.
Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
Acta Biomater. 2018 Mar 15;69:206-217. doi: 10.1016/j.actbio.2018.01.020. Epub 2018 Jan 31.
Traditionally, protein structures have been described by the secondary structure architecture and fold arrangement. However, the relatively novel method of 3D confocal microscopy of fluorescent-protein-tagged networks in living cells allows resolving the detailed spatial organization of these networks. This provides new possibilities to predict network functionality, as structure and function seem to be linked at various scales. Here, we propose a quantitative approach using 3D confocal microscopy image data to describe protein networks based on their nano-structural characteristics. This analysis is constructed in four steps: (i) Segmentation of the microscopic raw data into a volume model and extraction of a spatial graph representing the protein network. (ii) Quantifying protein network gross morphology using the volume model. (iii) Quantifying protein network components using the spatial graph. (iv) Linking these two scales to obtain insights into network assembly. Here, we quantitatively describe the filamentous temperature sensitive Z protein network of the moss Physcomitrella patens and elucidate relations between network size and assembly details. Future applications will link network structure and functionality by tracking dynamic structural changes over time and comparing different states or types of networks, possibly allowing more precise identification of (mal) functions or the design of protein-engineered biomaterials for applications in regenerative medicine.
Protein networks are highly complex and dynamic structures that play various roles in biological environments. Analyzing the detailed spatial structure of these networks may lead to new insight into biological functions and malfunctions. Here, we propose a tool set that extracts structural information at two scales of the protein network and allows therefore to address questions such as "how is the network built?" or "how networks grow?".
传统上，蛋白质结构是通过二级结构架构和折叠排列来描述的。然而，在活细胞中使用荧光蛋白标记的网络的三维共聚焦显微镜相对新颖的方法允许解析这些网络的详细空间组织。这为预测网络功能提供了新的可能性，因为结构和功能似乎在各个尺度上都有联系。在这里，我们提出了一种使用三维共聚焦显微镜图像数据的定量方法，根据蛋白质网络的纳米结构特征来描述它们。该分析分为四个步骤：（i）将微观原始数据分割成体积模型，并提取表示蛋白质网络的空间图。（ii）使用体积模型量化蛋白质网络的总形态。（iii）使用空间图量化蛋白质网络组件。（iv）将这两个尺度联系起来，以深入了解网络组装。在这里，我们定量描述了苔藓Physcomitrella patens 的丝状温度敏感 Z 蛋白网络，并阐明了网络大小与组装细节之间的关系。未来的应用将通过随时间跟踪动态结构变化并比较不同状态或类型的网络，将网络结构和功能联系起来，从而可能更精确地识别（异常）功能或设计用于再生医学应用的蛋白质工程生物材料。
蛋白质网络是高度复杂和动态的结构，在生物环境中发挥着各种作用。分析这些网络的详细空间结构可能会为生物功能和功能障碍提供新的见解。在这里，我们提出了一套工具集，可提取蛋白质网络两个尺度的结构信息，因此可以解决“网络如何构建？”或“网络如何增长？”等问题。
