Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University Lyon1, 7 passage du Vercors, 69007 Lyon, France.
Biochim Biophys Acta Biomembr. 2023 Apr;1865(4):184133. doi: 10.1016/j.bbamem.2023.184133. Epub 2023 Feb 3.
Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. In order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.
冷冻电镜观察生物样本可以可视化样本的异质性，这种异质性可以表现为离散状态，也可以表现为局部蛋白质运动导致的连续异质性，在闪光冷冻之前。对这种连续异质性的可变性分析描述了粒子堆栈和体积之间的差异，并生成了一系列图谱，描述了样品在粒子堆栈中经历的各种步骤。虽然这种观察结果令人惊叹，但很难将结构细节精确定位到图谱的元素上。为了弥合观察和解释之间的差距，我们设计了一种工具，可以将结构集合细化为可变性分析的所有图谱。使用这个结构束，很容易发现结构的可变部分，以及不运动的部分。与分子动力学模拟的比较突出了这样一个事实，即运动遵循相同的方向，尽管幅度不同。也可以使用这种方法研究配体。可变性细化可在 Phenix 软件套件中使用，在程序名为 phenix.varref 的项下可用。
