Phase retrieval in protein crystallography.

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-02-07 DOI:10.1107/S0108767311053815

Zhong Chuan Liu, Rui Xu, Yu Hui Dong

引用次数: 25

Abstract

Solution of the phase problem is central to crystallographic structure determination. An oversampling method is proposed, based on the hybrid input-output algorithm (HIO) [Fienup (1982). Appl. Opt. 21, 2758-2769], to retrieve the phases of reflections in crystallography. This method can extend low-resolution structures to higher resolution for structure determination of proteins without additional sample preparation. The method requires an envelope of the protein which divides a unit cell into the density region where the proteins are located and the non-density region occupied by solvents. After a few hundred to a few thousand iterations, the correct phases and density maps are recovered. The method has been used successfully in several cases to retrieve the phases from the experimental X-ray diffraction data and the envelopes of proteins constructed from structure files downloaded from the Protein Data Bank. It is hoped that this method will greatly facilitate the ab initio structure determination of proteins.

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蛋白质晶体学中的相位检索。

相问题的解决是晶体学结构确定的核心。提出了一种基于混合输入输出算法(HIO)的过采样方法[Fienup(1982)]。达成。光学学报，21 (2)，2758-2769 [j]。该方法可以将低分辨率结构扩展到更高分辨率，用于蛋白质的结构测定，而无需额外的样品制备。该方法需要一个蛋白质包膜，该包膜将单个细胞分为蛋白质所在的密度区和溶剂占据的非密度区。在几百到几千次迭代之后，就可以恢复正确的相位和密度图。该方法已成功地用于从实验x射线衍射数据中检索相和从蛋白质数据库下载的结构文件中构建的蛋白质包膜。希望该方法能极大地促进蛋白质从头计算结构的测定。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Acta Crystallographica Section A 化学-晶体学

自引率

11.10%

发文量

审稿时长

3 months

期刊介绍： Acta Crystallographica Section A: Foundations and Advances publishes articles reporting advances in the theory and practice of all areas of crystallography in the broadest sense. As well as traditional crystallography, this includes nanocrystals, metacrystals, amorphous materials, quasicrystals, synchrotron and XFEL studies, coherent scattering, diffraction imaging, time-resolved studies and the structure of strain and defects in materials. The journal has two parts, a rapid-publication Advances section and the traditional Foundations section. Articles for the Advances section are of particularly high value and impact. They receive expedited treatment and may be highlighted by an accompanying scientific commentary article and a press release. Further details are given in the November 2013 Editorial. The central themes of the journal are, on the one hand, experimental and theoretical studies of the properties and arrangements of atoms, ions and molecules in condensed matter, periodic, quasiperiodic or amorphous, ideal or real, and, on the other, the theoretical and experimental aspects of the various methods to determine these properties and arrangements.