Facing the phase problem.
Facing the phase problem.
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作者：
本文综述了高分子晶体学中的相评价。它伴随着2023年埃瓦尔德奖讲座在第26届IUCr大会，致敬保罗埃瓦尔德的深远影响。X射线晶体学的神奇之处在于从衍射图样中推断出的原子结构的美丽和精确。由于这些图案只记录振幅，因此还必须评估衍射波的相位，以便系统地确定结构。因此，我们把相位问题作为一个核心的复杂问题，无论是在理论上还是在实践中，对于许多分析都是如此。在这里，我讨论了我们-我自己，我的实验室和衍射社区-如何面对相位问题，考虑到结构生物学发展到今天的相位评估方法的演变。在大分子晶体学的爆炸性增长过程中，衍射分析的实践从普遍依赖于同晶置换发展到最终主导的异常衍射从头结构测定。随着蛋白质数据库（PDB）的发展和蛋白质之间的家族关系变得清晰，分子置换取代了所有其他定相方法;然而，实验定相对于没有明显先例的分子仍然是必不可少的，多波长和单波长异常衍射（MAD和SAD）占主导地位。虽然基于分子生物学的直接方法已被证明不适用于典型的大分子，但它们在硒甲硫酰蛋白的SAD分析中恢复了对大量硒亚结构的裂解。利用生物分子固有的S和P原子的天然SAD已成为常规。硒亚甲基SAD和MAD是结构基因组学的主要工作，以填充PDB与新的蛋白质。最近，PDB训练的人工智能方法在蛋白质结构预测方面取得了成功。目前，使用AlphaFold模型进行分子替换通常可以避免实验阶段评估的需要。由于多种原因，我们现在不受相位问题的困扰。冷冻电镜分析是一个有吸引力的替代晶体学的许多应用所面临的今天的结构生物学家。它只是精细的相位问题，然而，衍射分析的原则和程序仍然是相关的，并采用单粒子冷冻EM研究的生物分子。
This article reviews phase evaluation in macromolecular crystallography. It accompanies the 2023 Ewald Prize lecture at the 26th IUCr Congress, paying tribute to Paul Ewald’s far-reaching influence. The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. Since these patterns record only amplitudes, phases for the diffracted waves must also be evaluated for systematic structure determination. Thus, we have the phase problem as a central complication, both intellectually for the field and practically so for many analyses. Here, I discuss how we – myself, my laboratory and the diffraction community – have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. During the explosive growth of macromolecular crystallography, practice in diffraction analysis evolved from a universal reliance on isomorphous replacement to the eventual domination of anomalous diffraction for de novo structure determination. As the Protein Data Bank (PDB) grew and familial relationships among proteins became clear, molecular replacement overtook all other phasing methods; however, experimental phasing remained essential for molecules without obvious precedents, with multi- and single-wavelength anomalous diffraction (MAD and SAD) predominating. While the mathematics-based direct methods had proved to be inadequate for typical macromolecules, they returned to crack substantial selenium substructures in SAD analyses of selenomethionyl proteins. Native SAD, exploiting the intrinsic S and P atoms of biomolecules, has become routine. Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. Currently, molecular replacement with AlphaFold models often obviates the need for experimental phase evaluation. For multiple reasons, we are now unfazed by the phase problem. Cryo-EM analysis is an attractive alternative to crystallography for many applications faced by today’s structural biologists. It simply finesses the phase problem; however, the principles and procedures of diffraction analysis remain pertinent and are adopted in single-particle cryo-EM studies of biomolecules.
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DOI：
10.1073/pnas.2218630120
发表时间：
2023-01-03
影响因子：
11.1
作者：
Gong, Zhen;Wang, Wei;El Omari, Kamel;Lebedev, Andrey A.;Clarke, Oliver B.;Hendrickson, Wayne A.
通讯作者：
Hendrickson, Wayne A.
影响因子：
5.7
作者：
Collins, Mark N.;Hendrickson, Wayne A.
通讯作者：
Hendrickson, Wayne A.
影响因子：
2.9
作者：
Cheung, Jonah;Le-Khac, Matthew;Hendrickson, Wayne A.
通讯作者：
Hendrickson, Wayne A.
DOI：
10.1016/j.nimb.2016.12.005
发表时间：
2017-11-15
期刊：
Nuclear instruments & methods in physics research. Section B, Beam interactions with materials and atoms
影响因子：
--
作者：
Aurelius O;Duman R;El Omari K;Mykhaylyk V;Wagner A
通讯作者：
Wagner A
DOI：
10.1007/s10969-010-9094-7
发表时间：
2010-09
期刊：
Journal of structural and functional genomics
影响因子：
--
作者：
Love, James;Mancia, Filippo;Shapiro, Lawrence;Punta, Marco;Rost, Burkhard;Girvin, Mark;Wang, Da-Neng;Zhou, Ming;Hunt, John F;Szyperski, Thomas;Gouaux, Eric;MacKinnon, Roderick;McDermott, Ann;Honig, Barry;Inouye, Masayori;Montelione, Gaetano;Hendrickson, Wayne A
通讯作者：
Hendrickson, Wayne A