Automated building of carbohydrate molecules using X-ray crystallography data

使用 X 射线晶体学数据自动构建碳水化合物分子

• 批准号: BB/K008153/1
• 负责人: Keith Wilson
• 金额: $ 20.27万
• 依托单位: University of York
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK008153%2F1
• 关键词: Automated; building; carbohydrate; molecules; using

Carbohydrate molecules are an essential part of the living world, making up the sugars in our food, the fibres in clothes and the cell walls of green plants. The interaction of carbohydrates with other biological molecules, and in particular proteins, is an important part of many biological processes. Understanding this interaction is important for understanding how cells work and interact with one another, as well as being important to diverse bio-technologies such as the breaking down of fibrous landfill waste and the development of biological washing powders. Many proteins secreted by higher organisms have carbohydrates built directly into their structure and those incorporated into the cell membrane contribute to cell-cell recognition.X-ray crystallography - essentially an extremely powerful microscope - allows us to see the atoms in the 3D structures of biological macromolecules such as proteins. This knowledge is vital to an understanding of such molecules carry out their tasks. Protein-sugar complexes and glycoproteins can be studied using crystallography, but while the protein can often be seen fairly clearly in the resulting 3D structure, the sugar is often blurry because carbohydrates are often rather flexible. Interpreting the magnified image in terms of atoms and bonds can be a time consuming project, and the results somewhat subjective.The aim of this project is to provide an automated method for performing this interpretation. While automation is of value in that it frees up researcher time to concentrate on the scientific problems, a more important benefit is that it allows many possible interpretations of the magnified electron density image to be explored. In difficult cases this larger starting set of models is more likely to contain the correct answer that a single model built by a crystallographer. The different models can then be ranked to choose the best one.The structure of the protein is easily built by known methods, leaving a 'blob' of unaccounted for electron density into which the sugar must be placed. An initial set of possible structures for the sugar will be determined using existing web-based software and the Protein Data Bank (PDB). Dr. Cowtan at York University has previously written computer software which successfully identifyies the sugar rings in nucleic acids (including DNA which carries the genetic information) from their electron density alone. The 'fingerprint' technique involves the identification of shapes which are always present when the sugar is present. This approach will be modified to identify sugar rings in the carbohydrates. Each possible ring shape will be tested against the X-ray result, and neighbouring rings will be linked together. This will give a large pool of possible structures which can be ranked by automatic scoring methods based on the 3D X-ray maps and the plausibility of the chemistry.The resulting methods will be applied to two problems. The building of (1) carbohydrate molecules (such as enzyme substrates) crystallised in complex with proteins and (2) the sugars which are an integral part of glycoproteins. The software will be implemented in the ubiquitous 'Coot' graphical model building software, and will thus be made available to whole user community, both academic and commercial.The result will be a more reliable and more objective interpretation of sugars in 3D structures of macromolecules from living organisms, which in turn will enable greater understanding of the roles of these sugars in essential biological processes.

碳水化合物分子是生物世界的重要组成部分，构成了我们食物中的糖、衣服中的纤维和绿色植物的细胞壁。碳水化合物与其他生物分子，特别是蛋白质的相互作用是许多生物过程的重要组成部分。了解这种相互作用对于理解细胞如何工作和相互作用非常重要，同时对各种生物技术也很重要，例如纤维填埋场废物的分解和生物洗衣粉的开发。高等生物分泌的许多蛋白质的结构中都直接含有碳水化合物，而那些被纳入细胞膜的碳水化合物有助于细胞间的识别。x射线晶体学——本质上是一种极其强大的显微镜——使我们能够看到生物大分子（如蛋白质）的三维结构中的原子。这些知识对于理解这些分子执行它们的任务是至关重要的。蛋白质-糖复合物和糖蛋白可以用晶体学来研究，但是虽然蛋白质通常可以在三维结构中清晰地看到，但糖通常是模糊的，因为碳水化合物通常是相当灵活的。用原子和键来解释放大后的图像可能是一项耗时的工程，而且结果有些主观。该项目的目的是提供一种自动化的方法来执行这种解释。虽然自动化的价值在于它解放了研究人员的时间来专注于科学问题，但更重要的好处是它允许对放大的电子密度图像进行许多可能的解释。在困难的情况下，这个更大的初始模型集比晶体学家建立的单个模型更有可能包含正确的答案。然后可以对不同的模型进行排名，以选择最好的模型。这种蛋白质的结构很容易用已知的方法构建，只留下一团未知的电子密度，糖必须被放入其中。将使用现有的基于网络的软件和蛋白质数据库（PDB）确定糖的初始可能结构。约克大学的考坦博士之前已经编写了计算机软件，该软件仅从核酸（包括携带遗传信息的DNA）的电子密度就能成功识别出核酸中的糖环。“指纹”技术涉及到识别糖存在时总是存在的形状。这种方法将被改进以识别碳水化合物中的糖环。每个可能的圆环形状将根据x射线结果进行测试，相邻的圆环将连接在一起。这将提供大量可能的结构，这些结构可以通过基于3D x射线图和化学合理性的自动评分方法进行排名。所得方法将应用于两个问题。(1)碳水化合物分子（如酶底物）与蛋白质结晶体的构建；(2)糖是糖蛋白的组成部分。该软件将在无处不在的“Coot”图形模型构建软件中实现，因此将提供给整个用户社区，包括学术和商业。结果将是一个更可靠和更客观的解释糖在生物大分子的三维结构，这反过来将使这些糖在基本的生物过程中的作用的更好的理解。

项目成果

Validation of carbohydrate structures: not just nomenclature

碳水化合物结构的验证：不仅仅是命名

• 发表时间: 2014
• 期刊: International Union of Crystallography, world meeing.
• 作者: Jon Agirre

Structural Basis of Glycogen Biosynthesis Regulation in Bacteria

• DOI: 10.1016/j.str.2016.06.023
• 发表时间: 2016-09-06
• 期刊: STRUCTURE
• 影响因子: 5.7
• 作者: Cifuente, Javier O.;Comino, Natalia;Guerin, Marcelo E.
• 通讯作者: Guerin, Marcelo E.

Strategies for carbohydrate model building, refinement and validation.

• DOI: 10.1107/s2059798316016910
• 发表时间: 2017-02-01
• 期刊: Acta crystallographica. Section D, Structural biology
• 作者: Agirre J

Glycoblocks: a schematic three-dimensional representation for glycans and their interactions.

• DOI: 10.1107/s2059798316013553
• 发表时间: 2017-02-01
• 期刊: Acta crystallographica. Section D, Structural biology
• 作者: McNicholas S;Agirre J
• 通讯作者: Agirre J

Carbohydrate-Aromatic Interactions in Proteins.

• DOI: 10.1021/jacs.5b08424
• 发表时间: 2015-12-09
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: Hudson KL;Bartlett GJ;Diehl RC;Agirre J;Gallagher T;Kiessling LL;Woolfson DN
• 通讯作者: Woolfson DN