Structure and flexibility within proteins as identified through small angle X-ray scattering.
Structure and flexibility within proteins as identified through small angle X-ray scattering.
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DOI：
10.4149/gpb_2009_02_174
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发表时间：
2009-06
影响因子：
1.5
通讯作者：
Hammel M
中科院分区：
文献类型：
--
作者：
Pelikan M;Hura GL;Hammel M
蛋白质结构域之间的灵活性通常对功能至关重要。这些具有大范围柔性的运动和蛋白质通常不容易接受传统的结构分析，如X射线结晶学、核磁共振或电子显微镜。一旦确定了高分辨率结构，结晶学项目的一个常见发展就是假设可能的灵活性。在这里，我们描述了一种分析工具，使用相对便宜的小角X射线散射(SAXS)测量来确定灵活性并验证构建的最小模型集成，这些模型表示溶液中的高填充构象。这些结果的分辨率足以解决所提出的问题：结构域在溶液中采样哪些类型的构象？在我们的刚体建模策略BILBOMD中，分子动力学(MD)模拟用于探索构象空间。一种常见的策略是在非常高的温度下对域连接进行MD模拟，在这种情况下，额外的动能防止分子陷入局部极小。分子动力学模拟提供了一系列分子模型，计算了SAXS曲线，并与实验曲线进行了比较。使用遗传算法来确定最适合实验数据所需的最小集成(最小集成搜索，MES)。我们在几个模型和四个实验实例中演示了MES的使用。
Flexibility between domains of proteins is often critical for function. These motions and proteins with large scale flexibility in general are often not readily amenable to conventional structural analysis such as X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR) or electron microscopy. A common evolution of a crystallography project, once a high resolution structure has been determined, is to postulate possible sights of flexibility. Here we describe an analysis tool using relatively inexpensive small angle X-ray scattering (SAXS) measurements to identify flexibility and validate a constructed minimal ensemble of models, which represent highly populated conformations in solution. The resolution of these results is sufficient to address the questions being asked: what kinds of conformations do the domains sample in solution? In our rigid body modeling strategy BILBOMD, molecular dynamics (MD) simulations are used to explore conformational space. A common strategy is to perform the MD simulation on the domains connections at very high temperature, where the additional kinetic energy prevents the molecule from becoming trapped in a local minimum. The MD simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. A genetic algorithm is used to identify the minimal ensemble (minimal ensemble search, MES) required to best fit the experimental data. We demonstrate the use of MES in several model and in four experimental examples.
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影响因子：
5.6
作者：
Foerster, Friedrich;Webb, Benjamin;Krukenberg, Kristin A.;Tsuruta, Hiro;Agard, David A.;Sali, Andrej
通讯作者：
Sali, Andrej
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通讯作者：
Pop, M
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作者：
Gilbert, Hannah E.;Asokan, Rengasamy;Perkins, Stephen J.
通讯作者：
Perkins, Stephen J.
影响因子：
5.6
作者：
Gilbert, HE;Eaton, JT;Perkins, SJ
通讯作者：
Perkins, SJ