Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.
Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.
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通过 iSPOT 进行多蛋白复合物的理论建模：小角度 X 射线散射、羟基自由基足迹和计算对接的集成。
DOI：
10.1016/j.jsb.2016.08.001
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发表时间：
2016-12
影响因子：
3
通讯作者：
Yang, Sichun
中科院分区：
文献类型：
--
作者：
Huang, Wei;Ravikumar, Krishnakumar M.;Parisien, Marc;Yang, Sichun
蛋白质-蛋白质复合物（例如多域核受体）的结构测定对于高分辨率结构技术来说一直具有挑战性。在这里，我们提出了多种生物物理方法的组合使用，称为 iSPOT，整合了来自小角度 X 射线散射 (SAXS) 的形状信息、通过羟基自由基足迹探测的保护因子，以及来自刚体或分子动力学 (MD) 模拟的大量计算对接构象。经过在两个模型系统上的专门测试，iSPOT 的功能被证明可以根据复合物各个成分的结构准确预测大型蛋白质-蛋白质复合物 (TGFβ-FKBP12) 和多域核受体同二聚体 (HNF-4α) 的结构。虽然单独使用 SAXS 或足迹法都无法为每个复合体生成明确的图像，但将两者无缝集成到 iSPOT 中，可以缩小最佳拟合结构的范围，在 RMSD 中分别与相应的晶体结构相比约为 3.3 Å 和 4.2 Å。此外，这项基于从可用晶体结构综合得出的数据的原理验证研究表明，iSPOT（使用刚体或基于 MD 的柔性对接）能够克服独立计算方法的缺点，特别是对于 HNF-4α。通过利用基于 SAXS 的形状信息和基于足迹的保护/可访问性以及计算对接的集成，该 iSPOT 平台将成为对许多具有挑战性的多蛋白复合物进行精确集成建模的强大方法。
Structural determination of protein-protein complexes such as multidomain nuclear receptors has been challenging for high-resolution structural techniques. Here, we present a combined use of multiple biophysical methods, termed iSPOT, an integration of shape information from small-angle X-ray scattering (SAXS), protection factors probed by hydroxyl radical footprinting, and a large series of computationally docked conformations from rigid-body or molecular dynamics (MD) simulations. Specifically tested on two model systems, the power of iSPOT is demonstrated to accurately predict the structures of a large protein-protein complex (TGFβ-FKBP12) and a multidomain nuclear receptor homodimer (HNF-4α), based on the structures of individual components of the complexes. Although neither SAXS nor footprinting alone can yield an unambiguous picture for each complex, the combination of both, seamlessly integrated in iSPOT, narrows down the best-fit structures that are about 3.3 Å and 4.2 Å in RMSD from their corresponding crystal structures, respectively. Furthermore, this proof-of-principle study based on the data synthetically derived from available crystal structures shows that the iSPOT—using either rigid-body or MD-based flexible docking—is capable of overcoming the shortcomings of standalone computational methods, especially for HNF-4α. By taking advantage of the integration of SAXS-based shape information and footprinting-based protection/accessibility as well as computational docking, this iSPOT platform is set to be a powerful approach towards accurate integrated modeling of many challenging multiprotein complexes.
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影响因子：
2.9
作者：
KARPEN, ME;TOBIAS, DJ;BROOKS, CL
通讯作者：
BROOKS, CL
影响因子：
16.8
作者：
Lou, Xiaohua;Toresson, Gudrun;Gustafsson, Jan-Ake
通讯作者：
Gustafsson, Jan-Ake
影响因子：
2.7
作者：
Grishaev, Alexander;Tugarinov, Vitali;Bax, Ad
通讯作者：
Bax, Ad
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：
--
作者：
Chambon, P
通讯作者：
Chambon, P