Ab initio protein modelling for automated X-ray crystal structure solution

用于自动 X 射线晶体结构解决方案的从头算蛋白质建模

• 批准号: BB/H013652/1
• 负责人: Martyn Winn
• 金额: $ 4.25万
• 依托单位: Science and Technology Facilities Council
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FH013652%2F1
• 关键词: Ab; initio; protein; modelling; automated

Proteins make up the functional machinery of all living beings. Their particular roles depend on their 3-dimensional structures which allow given proteins to interact specifically with other molecules in their environment. Some proteins - enzymes - go further and can transform certain compounds into others. To understand better how proteins work and be able to use them in industry and medicine, scientists are greatly interested in figuring out their 3-dimensional structures. There are various ways to do this, but the dominant technique is X-ray crystallography. In this, an intense beam of X-rays is fired at a protein crystal. The X-rays are diffracted when passing through the crystal, producing a pattern of rays that is characteristic of the protein under study. In order to elucidate the structure of the protein, information derived from multiple diffraction patterns obtained from the same protein but under different conditions must be drawn together. The acquisition of such extra diffraction patterns can be time consuming, expensive, and commonly involves hazardous chemicals. A technique exists, however, where computers substitute the additional experiments by estimating equivalent information from available structures of proteins similar to that under study. In this way, protein structures can be solved from one single diffraction pattern. This technique - called Molecular Replacement (MR) - is fast, economical, clean and often uncomplicated. However, since MR relies on pre-existing structures, it is not applicable to many proteins of interest, for which similar structures are simply not available. For many years, scientists have tried to develop computer methods to predict the structure of proteins, purely based on their sequences. These methods are generally called ab initio modelling methods. Over the past decade, these efforts have started to bear fruit. These predicted models are unlikely to substitute for crystal structures any time soon since they typically contain errors, but recent work has shown that they are sometimes close enough to the real structure for them to be used in the MR process. This is the main idea behind this proposal - to adapt current ab initio modelling procedures to the specific needs of MR. With ab initio modelling, it is generally the case that the more detailed (i.e. the longer) the computer calculation, the better the model you can make. Unfortunately, achieving the best models is so demanding that it often requires extensive calculation times or access to supercomputers or other vast computer resources. Few crystallographers have access to these facilities, making the modelling method impractical. We therefore propose a different approach, making efficient use of simpler models that can be easily obtained on typical computers. In our preliminary work, we have already proven that this approach can work successfully for MR. What we want to do now is find the best way to produce optimal models and to do this automatically. This effectively means adapting the method to meet the demands of modern X-ray crystallography, making it fast so that it can be used as a routine approach and accessible to other crystallographers without specialist knowledge of ab initio modelling. We then want to include the method in the MrBUMP program, which is a well-established package allowing for easy, automated MR. MrBUMP can be added to a software package called CCP4i that is widely used by crystallographers. By incorporating our processing method in a familiar program, we expect it to become widely used across the world. We expect that by extending the MR computational approach we will enable protein structures to be determined more quickly and cheaply. In this way, research in all sorts of areas that depend on protein structure information, like drug design, will proceed faster.

蛋白质构成了所有生物的功能机器。它们的特殊作用取决于它们的 3 维结构，这些结构允许给定的蛋白质与其环境中的其他分子发生特异性相互作用。一些蛋白质（酶）更进一步，可以将某些化合物转化为其他化合物。为了更好地了解蛋白质的工作原理并能够在工业和医学中使用它们，科学家们对弄清楚它们的 3 维结构非常感兴趣。有多种方法可以做到这一点，但占主导地位的技术是 X 射线晶体学。在此过程中，向蛋白质晶体发射强烈的 X 射线束。 X 射线穿过晶体时会发生衍射，产生所研究蛋白质特有的射线图案。为了阐明蛋白质的结构，必须将从同一蛋白质但在不同条件下获得的多个衍射图案中获得的信息汇总在一起。获取此类额外的衍射图案可能非常耗时、昂贵，并且通常涉及危险化学品。然而，存在一种技术，计算机通过从与所研究的蛋白质相似的可用蛋白质结构中估计等效信息来替代额外的实验。通过这种方式，可以从一个衍射图解出蛋白质结构。这种技术称为分子替代 (MR)，快速、经济、清洁且通常并不复杂。然而，由于 MR 依赖于预先存在的结构，因此它不适用于许多感兴趣的蛋白质，因为这些蛋白质根本没有类似的结构。多年来，科学家们一直试图开发计算机方法来纯粹根据蛋白质的序列来预测蛋白质的结构。这些方法通常称为从头开始建模方法。过去十年，这些努力已开始取得成果。这些预测模型不太可能很快取代晶体结构，因为它们通常包含错误，但最近的工作表明，它们有时足够接近真实结构，可以在 MR 过程中使用。这是该提案背后的主要思想 - 使当前的从头开始建模程序适应 MR 的特定需求。对于从头建模，通常情况下，计算机计算越详细（即越长），您可以制作出越好的模型。不幸的是，实现最佳模型的要求如此之高，以至于通常需要大量的计算时间或访问超级计算机或其他大量计算机资源。很少有晶体学家能够使用这些设施，使得建模方法不切实际。因此，我们提出了一种不同的方法，有效地利用可以在典型计算机上轻松获得的更简单的模型。在我们的前期工作中，我们已经证明这种方法可以成功地应用于 MR。我们现在要做的是找到生成最佳模型并自动执行此操作的最佳方法。这实际上意味着调整该方法以满足现代 X 射线晶体学的需求，使其快速，以便可以用作常规方法，并且无需从头建模的专业知识的其他晶体学家也可以使用。然后，我们希望将该方法包含在 MrBUMP 程序中，这是一个完善的软件包，可以实现简单、自动化的 MR。 MrBUMP 可以添加到晶体学家广泛使用的名为 CCP4i 的软件包中。通过将我们的处理方法整合到一个熟悉的程序中，我们期望它能够在世界各地广泛使用。我们期望通过扩展 MR 计算方法，我们将能够更快、更便宜地确定蛋白质结构。这样，依赖蛋白质结构信息的各种领域的研究（例如药物设计）将进展得更快。

项目成果

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement.

应用 AMPLE 簇截断方法对 NMR 结构进行分子替换。

• DOI: http://dx.10.1107/s0907444913018453
• 发表时间: 2013
• 期刊: Acta crystallographica. Section D, Biological crystallography
• 作者: Bibby J

Approaches to ab initio molecular replacement of a-helical transmembrane proteins.

α-螺旋跨膜蛋白的从头开始分子替换的方法。

• DOI: http://dx.10.1107/s2059798317016436
• 发表时间: 2017
• 期刊: Acta crystallographica. Section D, Structural biology
• 作者: Thomas JMH

Crystal structure of the nipah virus phosphoprotein tetramerization domain.

尼帕病毒磷蛋白四聚结构域的晶体结构。

• DOI: http://dx.10.1128/jvi.02294-13
• 发表时间: 2014
• 期刊: Journal of virology
• 作者: Bruhn JF

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

使用 QUARK 从头开始​​蛋白质模型探索 AMPLE 分子替换的速度和性能。

• DOI: http://dx.10.1107/s1399004714025784
• 发表时间: 2015
• 期刊: Acta crystallographica. Section D, Biological crystallography
• 作者: Keegan RM

Crystal structure of the type IV secretion system component CagX from Helicobacter pylori.

幽门螺杆菌 IV 型分泌系统成分 CagX 的晶体结构。

• DOI: http://dx.10.1107/s2053230x17001376
• 发表时间: 2017
• 期刊: Acta crystallographica. Section F, Structural biology communications
• 作者: Zhang J