Koch Michel H, Vachette Patrice, Svergun Dmitri I
European Molecular Biology Laboratory-Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.
Q Rev Biophys. 2003 May;36(2):147-227. doi: 10.1017/s0033583503003871.
A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies--on ribosomes and on the allosteric protein aspartate transcarbamoylase--illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.
本文给出了溶液中生物大分子X射线和中子散射图谱解释的主要概念和方法的自包含介绍，包括对X射线和中子散射基础的回顾以及现代仪器相关方面的简要概述。对于单分散溶液，实验数据可得出大分子的散射强度，其取决于溶剂与颗粒之间的对比度以及它们的形状和内部散射密度波动，还有与大分子间相互作用相关的结构因子。在简要分析散射强度的信息内容后，介绍了两种用于模拟大分子形状和/或结构的主要方法以及计算中使用的全局最小化方案。第一种方法在其更高级版本中基于球谐函数近似，依赖较少参数，而第二种方法使用具有数千个参数的珠子模型。珠子建模的扩展可用于模拟高分辨率结构中的结构域结构和缺失部分。讨论了从原子模型计算散射图谱的方法，包括水合壳的贡献，并给出了示例，这些示例还表明晶体结构和溶液结构有时存在显著差异。在某些情况下，这些差异可以用结构部分的刚体运动来解释。两项广泛研究的结果——关于核糖体和变构蛋白天冬氨酸转氨甲酰酶——说明了各种方法的应用。基于结构因子分析和最近关于组装和蛋白质折叠的时间分辨研究，通过对分子间相互作用（包括结晶）的建模，说明了散射技术在平衡结构与热力学或动力学方面之间提供的独特桥梁。
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