Dynamical Aspects of Biomacromolecular Multi-resolution Modelling Using the UltraScan Solution Modeler (US-SOMO) Suite
Dynamical Aspects of Biomacromolecular Multi-resolution Modelling Using the UltraScan Solution Modeler (US-SOMO) Suite
复制标题
使用 UltraScan Solution Modeler (US-SOMO) 套件进行生物大分子多分辨率建模的动力学方面
DOI：
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发表时间：
2014
期刊：
影响因子：
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通讯作者：
E. Brookes
中科院分区：
文献类型：
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作者：
M. Rocco;E. Brookes
尽管目前的高分辨率方法（X射线晶体学/NMR）不断取得技术进步，但列出每个相关生物结构及其与每个伴侣的复合物的详尽清单仍然是一个遥不可及的目标。此外，动力学方面，从局部或大规模的灵活性，构象变化后的相互作用/结合，超分子结构的形成，是不容易服从高分辨率分析。然而，许多中等分辨率的技术可用于补充更高分辨率的数据，如低温电子显微镜和电子断层扫描，而小角X射线散射（SAXS）和小角中子散射（SANS）也能够监测溶液中结构变化的演变。由于上述技术可以以~10-20 A的分辨率提供3D包络，因此典型的任务涉及将组分的原子结构放置在包络内或优化其布置以拟合实验散射数据。由低分辨率技术提供的单值参数，如回转半径R g、平移扩散系数D t、沉降系数s、斯托克斯半径R s、旋转相关时间τ c和特性粘度（η），也可以用于筛选/确认模块/结构域的潜在空间排列，或监测它们的总体构象变化。UltraScan Solution MOdeler（US-SOMO）计算机程序套件的开发用于从其原子分辨率结构开始计算生物大分子的溶液性质，并将其与实验数据进行比较。在这篇简短的评论中，它的使用方面的动态多分辨率建模，包括构象变化和灵活性的问题，进行了讨论。
Notwithstanding the continuous technological advancements in the current high-resolution methods (X-ray crystallography/NMR), an exhaustive list of every relevant biological structure and of its complexes with every partner remains a far fetched goal. Furthermore, dynamical aspects, from local or large scale flexibility, to conformational changes following interactions/binding, to supramolecular structures formation, are not easily amenable to high-resolution analysis. A host of intermediate-resolution techniques are, however, available to complement the higher resolution data, like cryo-electron microscopy and electron tomography, while small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are in addition capable to monitor the evolution of structural changes in solution. Since the above-mentioned techniques can provide 3D envelopes at ~10–20 A resolution, a typical task involves placing the atomic structures of the components inside the envelope or to optimize their arrangement to fit experimental scattering data. Single-valued parameters provided by low-resolution techniques, such as the radius of gyration R g , the translational diffusion coefficient D t , the sedimentation coefficient s, the Stokes radius R s , the rotational correlation time τ c , and the intrinsic viscosity (η), can be also utilized to screen/confirm potential spatial arrangements of modules/domains, or to monitor their overall conformational changes. The UltraScan SOlution MOdeler (US-SOMO) suite of computer programs was developed for the computation of the solution properties of biomacromolecules starting from their atomic resolution structures, and their comparison with experimental data. In this brief review, its use with respect to dynamical aspects in multi-resolution modeling, including conformational variation and flexibility issues, is discussed.
影响因子：
5.7
作者：
Topf, Maya;Lasker, Keren;Sali, Andrej
通讯作者：
Sali, Andrej
影响因子：
5.7
作者：
Rocco, Mattia;Rosano, Camillo;Hantgan, Roy R.
通讯作者：
Hantgan, Roy R.
影响因子：
16
作者：
Zhu, Jianghai;Luo, Bing-Hao;Xiao, Tsan;Zhang, Chengzhong;Nishida, Noritaka;Springer, Timothy A.
通讯作者：
Springer, Timothy A.