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厌氧固定靶标串行晶体学

Anaerobic fixed-target serial crystallography.

作者信息

Rabe Patrick, Beale John H, Butryn Agata, Aller Pierre, Dirr Anna, Lang Pauline A, Axford Danny N, Carr Stephen B, Leissing Thomas M, McDonough Michael A, Davy Bradley, Ebrahim Ali, Orlans Julien, Storm Selina L S, Orville Allen M, Schofield Christopher J, Owen Robin L

机构信息

Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.

Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.

出版信息

IUCrJ. 2020 Aug 21;7(Pt 5):901-912. doi: 10.1107/S2052252520010374. eCollection 2020 Sep 1.

Abstract

Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitro-gen cryo-stream at 100 K) enable, is data collection of di-oxy-gen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for di-oxy-gen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the 'sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent l-arginine hy-droxy-lase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics.

摘要

低温X射线衍射是用于对包括加氧酶和氧化酶在内的酶进行晶体学研究的强大工具。低温条件(通常在100 K下采用氮气低温流)带来的诸多好处之一是能够收集对双氧敏感的样品的数据。尽管并非严格厌氧,但在低温下,玻璃态冰的条件会严重限制氧气扩散进入和/或穿过蛋白质晶体。低温条件限制化学反应活性,包括需要显著构象变化的反应。相比之下,室温下的数据收集对扩散和反应活性的限制较少;因此,室温串行方法在同步加速器和X射线自由电子激光装置中变得越来越普遍。然而,对于同步辐射光源的室温串行数据收集,尚未探索如何为依赖双氧的酶维持厌氧环境。这项工作描述了一种方法,该方法采用了“片上片”样品架的改进形式,适用于在同步辐射光源下对厌氧样品进行低剂量室温数据收集。该方法的特点是在厌氧手套箱中易于制备样品、对晶体的操作轻柔、样品消耗低以及在实验时间尺度(<5分钟)内保持局部厌氧环境。用三种对X射线辐射敏感的含铁(II)模型酶的研究突出了该方法的实用性:2-酮戊二酸依赖性L-精氨酸羟化酶VioC和DNA修复酶AlkB,以及参与所有青霉素和头孢菌素抗生素生物合成的氧化酶异青霉素N合酶(IPNS)。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c80/7467159/38c71734f864/m-07-00901-fig1.jpg

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