Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
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DOI：
10.1529/biophysj.107.115949
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发表时间：
2008-03-01
影响因子：
3.4
通讯作者：
Thorpe, M. F.
中科院分区：
文献类型：
--
作者：
Jolley, Craig C.;Wells, Stephen A.;Thorpe, M. F.
最近在低温电子显微镜（cryo-EM）中产生密度图的实验进展对理论家提出了挑战，要求他们开发改进的技术来提供与数据一致的结构模型，并保留与生物分子相关的所有局部立体化学。我们开发了一种新技术，在每个拟合阶段保持局部几何和化学。几何模拟是用来驱动结构从一个适当的起点（附近的实验结构或模型结构）向实验密度，通过一组小的增量运动。在拟合过程中，当初始结构与实验密度对齐时，结构图案（如a-螺旋）可以保持刚性。在对腺苷酸激酶和乳铁蛋白的模拟数据进行验证后，我们展示了如何使用起始x射线晶体结构适合两种不同GroEL结构的低温电镜数据。我们表明，通过在建模中加入正确的局部立体化学，可以获得有效分辨率的结构，其有效分辨率明显高于标称低温电镜分辨率的预期。
Recent experimental advances in producing density maps from cryo-electron microscopy (cryo-EM) have challenged theorists to develop improved techniques to provide structural models that are consistent with the data and that preserve all the local stereochemistry associated with the biomolecule. We develop a new technique that maintains the local geometry and chemistry at each stage of the fitting procedure. A geometric simulation is used to drive the structure from some appropriate starting point (a nearby experimental structure or a modeled structure) toward the experimental density, via a set of small incremental motions. Structural motifs such as a-helices can be held rigid during the fitting procedure as the starting structure is brought into alignment with the experimental density. After validating this procedure on simulated data for adenylate kinase and lactoferrin, we show how cryo-EM data for two different GroEL structures can be fit using a starting x-ray crystal structure. We show that by incorporating the correct local stereochemistry in the modeling, structures can be obtained with effective resolution that is significantly higher than might be expected from the nominal cryo-EM resolution.