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Modelling Carbohydrate Solution Structure Using a Novel Combined Experimental-Computational Strategy

使用新颖的实验-计算组合策略对碳水化合物溶液结构进行建模

基本信息

批准号：
EP/J019623/1
负责人：
Paul Lode Albert Popelier
金额：
$ 87.61万
依托单位：
University of Manchester
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2012
资助国家：
英国
起止时间：
2012 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=EP%2FJ019623%2F1
关键词：
Modelling Carbohydrate Solution Structure Using

项目摘要

Our ability to make new discoveries in biochemistry and to develop new pharmaceuticals, advanced materials, energy sources and foodstuffs is increasingly dependent on our understanding of how biomolecules work at the molecular level. This in turn depends on our understanding of the structure of these biomolecules, and how their structures control their functions. This has been the guiding principle that has resulted in many of the advances in medicine, biology, chemistry and materials science of the last few decades. These advances have owed much to the structural information that has been obtained for proteins and nucleic acids by X-ray crystallography and NMR spectroscopy, and which has revolutionised our view of how life works. Unfortunately, these techniques are far more difficult to apply to the main class of biomolecules, carbohydrates. As a result, even though carbohydrates constitute around 99% of the biomass of our planet and perform an almost limitless number of roles in living systems, from algae to plants to humans, we don't really understand how they work in the same way that we do for proteins and DNA. The lack of definitive data means there is still considerable debate as to how we even define structure in carbohydrate polymers. In order to best capitalise on the great potential of carbohydrates in both science and industry we will have to understand to a much greater level of detail the molecular principles that govern their assembly, organisation and interactions with other molecules. This will require new approaches to studying carbohydrate structure.In order to meet this urgent requirement we will develop a combined computer modelling and spectroscopic lab-based approach to characterising the structures of carbohydrates, from simple sugars to key carbohydrate polymers known to be involved in regulating biological functions. Three components to the project will combine to generate a uniquely incisive new tool for glycobiology. First, high level quantum chemistry calculations will provide highly detailed spectra that are sensitive to all aspects of carbohydrate conformation, so allowing us to identify subtle structural differences. Secondly, as recent work shows that hydration plays an important role in controlling carbohydrate conformation, we will use molecular dynamics simulations to identify which structures are formed by each carbohydrate in the solvated environments in which they are found naturally and how they interact with the water molecules around them. Thirdly, we will measure highly detailed Raman spectra to provide the gold standard benchmarks required to prove that our calculations and modelling are correct. This will also provide us with a rigorous standard against which to validate the novel computer modelling. Although this development of new computational tools will be focused on the structures and behaviour of carbohydrates, the end product will also be widely applicable to all other biomolecules, particularly proteins and nucleic acids. The challenges we will overcome are those faced by researchers attempting to model how other molecules behave, e.g. how stable is the structure? how do its components interact? how do interactions with solvent water or other molecules affect its shape? Because our novel computational tools are generic they will be able to provide new insights into many other areas of research, such as protein-ligand interactions and DNA-drug molecule binding.

我们在生物化学方面取得新发现、开发新药、先进材料、能源和食品的能力越来越依赖于我们对生物分子在分子水平上如何工作的理解。这反过来又取决于我们对这些生物分子结构的理解，以及它们的结构如何控制它们的功能。在过去的几十年里，这一指导原则导致了医学、生物学、化学和材料科学的许多进步。这些进步很大程度上要归功于通过x射线晶体学和核磁共振光谱学获得的蛋白质和核酸的结构信息，这些信息彻底改变了我们对生命如何运作的看法。不幸的是，这些技术很难应用于主要的生物分子——碳水化合物。因此，尽管碳水化合物占地球生物量的99%左右，并且在从藻类到植物再到人类的生命系统中发挥着几乎无限的作用，但我们并不真正了解它们是如何以与蛋白质和DNA相同的方式起作用的。由于缺乏明确的数据，对于我们如何定义碳水化合物聚合物的结构仍存在相当大的争议。为了最大限度地利用碳水化合物在科学和工业上的巨大潜力，我们必须更详细地了解控制碳水化合物组装、组织和与其他分子相互作用的分子原理。这就需要研究碳水化合物结构的新方法。为了满足这一迫切需求，我们将开发一种结合计算机建模和光谱实验室的方法来表征碳水化合物的结构，从单糖到已知参与调节生物功能的关键碳水化合物聚合物。该项目的三个组成部分将结合起来，为糖生物学产生一个独特而敏锐的新工具。首先，高水平的量子化学计算将提供非常详细的光谱，对碳水化合物构象的各个方面都很敏感，因此使我们能够识别细微的结构差异。其次，由于最近的研究表明水合作用在控制碳水化合物构象中起着重要作用，我们将使用分子动力学模拟来确定每种碳水化合物在溶剂化环境中形成的结构，以及它们如何与周围的水分子相互作用。第三，我们将测量非常详细的拉曼光谱，以提供证明我们的计算和建模正确所需的黄金标准基准。这也将为我们提供一个严格的标准来验证新的计算机模型。虽然这种新的计算工具的发展将集中在碳水化合物的结构和行为上，但最终产品也将广泛适用于所有其他生物分子，特别是蛋白质和核酸。我们将克服的挑战是那些试图模拟其他分子行为的研究人员所面临的挑战，例如，结构有多稳定？它的组件是如何相互作用的？与溶剂水或其他分子的相互作用如何影响其形状？由于我们的新型计算工具是通用的，它们将能够为许多其他研究领域提供新的见解，例如蛋白质-配体相互作用和dna -药物分子结合。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Encyclopaedia of Analytical Chemistry

分析化学百科全书

DOI：
发表时间：
期刊：
影响因子：
0
作者：
Blanch EW
通讯作者：
Blanch EW

Realistic sampling of amino acid geometries for a multipolar polarizable force field.

DOI：
10.1002/jcc.24006
发表时间：
2015-09-15
期刊：
Journal of computational chemistry
影响因子：
3
作者：
Hughes TJ;Cardamone S;Popelier PL
通讯作者：
Popelier PL

Prediction of conformationally dependent atomic multipole moments in carbohydrates.

DOI：
10.1002/jcc.24215
发表时间：
2015-12-15
期刊：
JOURNAL OF COMPUTATIONAL CHEMISTRY
影响因子：
3
作者：
Cardamone, Salvatore;Popelier, Paul L. A.
通讯作者：
Popelier, Paul L. A.

Synthesis of a heparin-related GlcN-IdoA sulfation-site variable disaccharide library and analysis by Raman and ROA spectroscopy.

DOI：
10.1016/j.carres.2014.06.026
发表时间：
2014-12-05
期刊：
CARBOHYDRATE RESEARCH
影响因子：
3.1
作者：
Miller, Gavin J.;Hansen, Steen U.;Barath, Marek;Johannessen, Christian;Blanch, Ewan W.;Jayson, Gordon C.;Gardiner, John M.
通讯作者：
Gardiner, John M.

Polarizable multipolar electrostatics for cholesterol