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首页> 外文期刊>Journal of Applied Crystallography >PSX, Protein-Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates
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PSX, Protein-Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates

机译：PSX，蛋白质溶剂交换：用于计算蛋白质坐标的小角中子散射测量中的氘交换效果的软件

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摘要

Recent developments in neutron scattering instrumentation and sample handling have enabled studies of more complex biological samples and measurements at shorter exposure times. The experiments are typically conducted in D2O-based buffers to emphasize or diminish scattering from a particular component or to minimize background noise in the experiment. To extract most information from such experiments it is thus desirable to determine accurate estimates of how and when closely bound hydrogen atoms from the biomolecule exchange with the deuterium in the solvent. This article introduces and documents software, PSX, for exploring the effect of hydrogen-deuterium exchange for proteins solubilized in D2O as well as the underlying bioinformatical models. The software aims to be generally applicable for any atomistic structure of a protein and its surrounding environment, and thus captures effects of both heterogenous exchange rates throughout the protein structure and varying the experimental conditions such as pH and temperature. The paper concludes with examples of applications and estimates of the effect in typical scenarios emerging in small-angle neutron scattering on biological macromolecules in solution. The analysis presented here suggests that the common assumption of 90% exchange is in many cases an overestimate with the rapid sample handling systems currently available, which leads to fitting and calibration issues when analysing the data. Source code for the presented software is available from an online repository in which it is published under version 3 of the GNU publishing licence.
机译：最近的中子散射仪表和样品处理的发展使得能够在更短的曝光时间下进行更复杂的生物样品和测量。实验通常在基于D2O的缓冲液中进行，以强调或减少来自特定组件的散射，或者最小化实验中的背景噪音。因此，从这些实验中提取大多数信息，因此期望确定如何以及当与溶剂中的氘相交的生物分子交换紧密结合的氢原子的准确估计。本文介绍和文件软件PSX，用于探讨氢氘交换对D2O中溶解的蛋白质的影响以及潜在的生物信息模型。该软件旨在通常适用于蛋白质及其周围环境的任何原子结构，从而捕获在整个蛋白质结构中的异构交换率的影响，并改变pH和温度等实验条件。本文与溶液中生物大分子生物大分​​子散射出现的典型情景效应的应用和估计的施工和估算。此处提出的分析表明，90％交换的共同假设是许多情况下，许多情况下与当前可用的快速样品处理系统高估，这导致分析数据时拟合和校准问题。呈现软件的源代码可从在线存储库中获取，其中它在GNU发布许可证的版本3下发布。

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