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提高数据质量,并扩大生物小角 X 射线散射实验至低分子量和低浓度蛋白质样品。

Improving data quality and expanding BioSAXS experiments to low-molecular-weight and low-concentration protein samples.

机构信息

Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain.

DESY Photon Science, Notkestrasse 85, 08290 Hamburg, Germany.

出版信息

Acta Crystallogr D Struct Biol. 2020 Oct 1;76(Pt 10):971-981. doi: 10.1107/S2059798320010700. Epub 2020 Sep 16.

DOI:10.1107/S2059798320010700
PMID:33021499
Abstract

The addition of compounds to scavenge the radical species produced during biological small-angle X-ray scattering (BioSAXS) experiments is a common strategy to reduce the effects of radiation damage and produce better quality data. As almost half of the experiments leading to structures deposited in the SASBDB database used scavengers, finding potent scavengers would be advantageous for many experiments. Here, four compounds, three nucleosides and one nitrogenous base, are presented which can act as very effective radical-scavenging additives and increase the critical dose by up to 20 times without altering the stability or reducing the contrast of the tested protein solutions. The efficacy of these scavengers is higher than those commonly used in the field to date, as verified for lysozyme solutions at various concentrations from 7.0 to 0.5 mg ml. The compounds are also very efficient at mitigating radiation damage to four proteins with molecular weights ranging from 7 to 240 kDa and pH values from 3 to 8, with the extreme case being catalase at 6.7 mg ml, with a scavenging factor exceeding 100. These scavengers can therefore be instrumental in expanding BioSAXS to low-molecular-weight and low-concentration protein samples that were previously inaccessible owing to poor data quality. It is also demonstrated that an increase in the critical dose in standard BioSAXS experiments leads to an increment in the retrieved information, in particular at higher angles, and thus to higher resolution of the model.

摘要

在生物小角 X 射线散射(BioSAXS)实验中添加化合物以清除自由基是减少辐射损伤并获得更好质量数据的常用策略。由于导致在 SASBDB 数据库中沉积结构的实验中几乎有一半使用了清除剂,因此找到有效的清除剂对许多实验都将是有利的。这里介绍了四种化合物,三种核苷和一种含氮碱基,它们可以作为非常有效的自由基清除添加剂,将临界剂量提高 20 倍,而不会改变测试蛋白质溶液的稳定性或降低对比度。这些清除剂的功效比迄今为止在该领域中常用的清除剂更高,这在从 7.0 到 0.5mg/ml 的各种浓度的溶菌酶溶液中得到了验证。这些化合物还非常有效地减轻了四种分子量从 7 到 240 kDa 且 pH 值从 3 到 8 的蛋白质的辐射损伤,其中极端情况是在 6.7mg/ml 的过氧化氢酶中,清除因子超过 100。因此,这些清除剂可以帮助将 BioSAXS 扩展到低分子量和低浓度的蛋白质样品,这些样品以前由于数据质量差而无法获得。还证明了标准 BioSAXS 实验中临界剂量的增加会导致检索到的信息增加,特别是在更高的角度,从而提高模型的分辨率。

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A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies.基于小角 X 射线散射的方法来合理评估自由基清除剂 - 旨在消除溶液和晶体学研究中的辐射损伤。
J Synchrotron Radiat. 2021 Sep 1;28(Pt 5):1309-1320. doi: 10.1107/S1600577521004045. Epub 2021 Aug 9.
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Radiation damage to biological samples: still a pertinent issue.
生物样本的辐射损伤:仍是一个相关问题。
J Synchrotron Radiat. 2021 Sep 1;28(Pt 5):1278-1283. doi: 10.1107/S1600577521008845.