Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module
Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module
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DOI：
10.1107/s0021889813027751
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发表时间：
2013-12-01
影响因子：
6.1
通讯作者：
Rocco, Mattia
中科院分区：
文献类型：
--
作者：
Brookes, Emre;Perez, Javier;Rocco, Mattia
纤维蛋白原是一种大的异质性聚集/降解倾向蛋白质，在血液凝固和相关病理学中起核心作用，其结构尚未完全解析。当通过尺寸排阻高效液相色谱/小角X射线散射（HPLC-SAXS）分析高分子量组分时，出现几个复合峰，并且由于纤维蛋白原的粘性，分析因严重的毛细污染而变得复杂。新的SAS分析工具开发的UltraScan解决方案建模（US-SOMO; http：//somo.uthscsa.edu/），一个开源套件的工具，具有先进的图形用户界面，其最初的目标是生物大分子的流体动力学建模的一部分，实施和应用于这个问题。它们包括校正由于SAXS毛细管壁上材料的积累而引起的基线漂移，以及非基线分辨HPLC-SAXS洗脱峰的高斯分解。因此，可以在纤维蛋白原主要单体峰下分离至少两种共洗脱物质（可能由柱内降解产生），并在低聚物峰下分离另外两种物质。使用US-SOMO SAS模块中可用的手动或半自动程序确定所有物质的总体和横截面回转半径、分子量和质量/长度比。单体物种和线性和侧向低聚物之间的差异，从而确定和合理化。这个新的US-SOMO版本还包含几个计算和图形工具，实现了一些功能，例如对P（r）特定区域的残基进行映射，以及一个高级模块，用于将初级I（q）与q数据与从原子水平结构或珠模型计算的模型曲线进行比较。它应该是很大的帮助，在多分辨率的研究，涉及流体力学，溶液散射和结晶/NMR数据。
Fibrinogen is a large heterogeneous aggregation/degradation-prone protein playing a central role in blood coagulation and associated pathologies, whose structure is not completely resolved. When a high-molecular-weight fraction was analyzed by size-exclusion high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS), several composite peaks were apparent and because of the stickiness of fibrinogen the analysis was complicated by severe capillary fouling. Novel SAS analysis tools developed as a part of the UltraScan Solution Modeler (US-SOMO; http://somo.uthscsa.edu/), an open-source suite of utilities with advanced graphical user interfaces whose initial goal was the hydrodynamic modeling of biomacromolecules, were implemented and applied to this problem. They include the correction of baseline drift due to the accumulation of material on the SAXS capillary walls, and the Gaussian decomposition of non-baseline-resolved HPLC-SAXS elution peaks. It was thus possible to resolve at least two species co-eluting under the fibrinogen main monomer peak, probably resulting from in-column degradation, and two others under an oligomers peak. The overall and cross-sectional radii of gyration, molecular mass and mass/length ratio of all species were determined using the manual or semi-automated procedures available within the US-SOMO SAS module. Differences between monomeric species and linear and sideways oligomers were thus identified and rationalized. This new US-SOMO version additionally contains several computational and graphical tools, implementing functionalities such as the mapping of residues contributing to particular regions of P(r), and an advanced module for the comparison of primary I(q) versus q data with model curves computed from atomic level structures or bead models. It should be of great help in multi-resolution studies involving hydrodynamics, solution scattering and crystallographic/NMR data.