Super-resolution biomolecular crystallography with low-resolution data.
Super-resolution biomolecular crystallography with low-resolution data.
复制标题
作者：
X 射线衍射通过揭示蛋白质、核酸及其复合物的原子结构，在理解生物系统方面发挥着关键作用，最近人们对核糖体等非常大的组装体产生了浓厚的兴趣。由于此类大型组件的晶体通常衍射较弱（分辨率低于 4 Å），因此我们需要在如此低分辨率下工作的方法。在大分子组装体中，某些组分可能以高分辨率已知，而另一些组分则未知：当前的细化方法失败，因为它们需要整个复合物的高分辨率起始结构。确定此类复合物通常具有关键的生物学重要性，原则上应该是可能的，因为分辨率低于 5 Å 的独立衍射强度的数量通常超过自由度的数量。在这里，我们介绍一种新方法，该方法添加来自已知同源结构的特定信息，但允许这些同源模型的全局和局部变形。我们的方法利用了这样的观察：随着序列和功能的进化，局部蛋白质结构趋于保守。与 Rfree 的交叉验证确定同源模型的最佳变形和影响。对于具有高分辨率已知结构的 3.5 – 5 Å 分辨率的测试用例，我们的方法在模型坐标精度、二级结构的定义和电子密度图的质量方面比传统的细化方法有了显着的改进。对于 PDB 中具有代表性的 19 个低分辨率晶体结构的重新细化，我们发现了类似的改进。因此，从低分辨率衍射数据导出的结构可以具有与高分辨率结构相似的质量。我们的方法适用于使用 X 射线微衍射以及来自新 X 射线光源的数据来研究弱衍射晶体。同源信息的使用并不局限于 X 射线晶体学和冷冻电子显微镜：随着光学成像技术进步到亚纳米分辨率，它可以使用类似的工具。
X-ray diffraction plays a pivotal role in understanding of biological systems by revealing atomic structures of proteins, nucleic acids, and their complexes, with much recent interest in very large assemblies like the ribosome. Since crystals of such large assemblies often diffract weakly (resolution worse than 4 Å), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, while others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution below 5 Å generally exceed the number of degrees of freedom. Here we introduce a new method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with Rfree determines the optimum deformation and influence of the homology model. For test cases at 3.5 – 5 Å resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model coordinate accuracy, the definition of secondary structure, and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the PDB, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to studying weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X-ray crystallography and cryo-electron microscopy: as optical imaging advances to sub-nanometer resolution, it can use similar tools.
登录
查看更多内容
影响因子：
64.8
作者：
Raines, Kevin S.;Salha, Sara;Miao, Jianwei
通讯作者：
Miao, Jianwei
DOI：
10.1073/pnas.58.2.420
发表时间：
1967-01-01
影响因子：
11.1
作者：
GIBSON, KD;SCHERAGA, HA
通讯作者：
SCHERAGA, HA
影响因子：
5.7
作者：
Davies, Jason M.;Brunger, Axel T.;Weis, William I.
通讯作者：
Weis, William I.
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
影响因子：
3.5
作者：
PEARL, L;BLUNDELL, T
通讯作者：
BLUNDELL, T