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拉曼显微镜法动力学晶体学

Kinetic crystallography by Raman microscopy.

作者信息

Carey Paul R, Chen Yuanyuan, Gong Bo, Kalp Matthew

机构信息

Case Western Reserve University, Department of Biochemistry, 10900 Euclid Avenue, Cleveland, OH 44106, USA.

出版信息

Biochim Biophys Acta. 2011 Jun;1814(6):742-9. doi: 10.1016/j.bbapap.2010.08.006. Epub 2010 Aug 23.

Abstract

Raman spectra, obtained using a Raman microscope, offer a unique and incisive approach to follow interactions and reactions inside a single crystal under soak-in or soak-out conditions. The utility of this approach derives from the finding that the Raman spectra from single macromolecular crystals, under normal (non-resonance) conditions, are extremely stable, with a low "light background," and provide ideal platforms for Raman difference spectroscopy. In turn, this allows the interrogation of sub-molecular changes in very large and complex macromolecular environments. There is often great synergy with X-ray crystallography, with the Raman spectroscopist providing crystallography colleagues with the best soak-in conditions to generate a targeted intermediate for flash freezing and X-ray analysis. On the other hand, X-ray structures at points along a reaction pathway provide invaluable benchmarks for interpreting the Raman data from populations seen by Raman to be changing in real-time. These principles will be illustrated by two reactions: the first involves a complex, branching reaction pathway underlying the inhibition of β-lactamases by clinically important pharmaceutical compounds, where different combinations of drug and enzyme function in different regions of the pathway. The second shows how temporal data can be derived for several events in the initiation step of RNA synthesis-more specifically, when one GTP molecule is joined to one ATP molecule to form a G∙A dimer in the active site of a 115,000 Dalton crystalline RNA polymerase. Finally, we will summarize the extension of Raman microscopy to nucleic acid crystals and the information that has been obtained for RNA-based enzymes. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

摘要

使用拉曼显微镜获得的拉曼光谱,为追踪单晶在浸泡或浸泡出条件下的相互作用和反应提供了一种独特而深刻的方法。这种方法的实用性源于以下发现:在正常(非共振)条件下,单个大分子晶体的拉曼光谱极其稳定,具有低“光背景”,并为拉曼差示光谱提供了理想平台。反过来,这使得在非常大且复杂的大分子环境中研究亚分子变化成为可能。它与X射线晶体学通常有很大的协同作用,拉曼光谱学家为晶体学同事提供最佳的浸泡条件,以生成用于快速冷冻和X射线分析的目标中间体。另一方面,反应途径上各点的X射线结构为解释拉曼光谱实时观察到的群体变化数据提供了宝贵的基准。这些原理将通过两个反应来说明:第一个涉及临床重要药物化合物抑制β-内酰胺酶背后的复杂分支反应途径,其中药物和酶的不同组合在途径的不同区域起作用。第二个展示了如何在RNA合成起始步骤中的几个事件中获取时间数据——更具体地说,当一个GTP分子与一个ATP分子在一个115,000道尔顿的结晶RNA聚合酶活性位点结合形成G∙A二聚体时。最后,我们将总结拉曼显微镜技术在核酸晶体方面的扩展以及从基于RNA的酶中获得的信息。本文是名为:晶体状态下的蛋白质结构与功能的特刊的一部分。

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5
Raman crystallography of RNA.
Methods. 2009 Oct;49(2):101-11. doi: 10.1016/j.ymeth.2009.04.016. Epub 2009 May 4.
7
Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.
Mol Cell. 2008 Dec 5;32(5):707-17. doi: 10.1016/j.molcel.2008.11.010.
8
Carbapenems and SHV-1 beta-lactamase form different acyl-enzyme populations in crystals and solution.
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10
A novel method for detection of selenomethionine incorporation in protein crystals via Raman microscopy.
Acta Crystallogr D Biol Crystallogr. 2008 Feb;64(Pt 2):167-71. doi: 10.1107/S0907444907058416. Epub 2008 Jan 16.

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