Rationalising glycomics with GPU-accelerated equilibrium simulations: a novel route to 3D-structure biological function and molecular design

碳水化合物、氨基酸、核酸和脂质构成了生命的基本组成部分。虽然碳水化合物是第一个从生物体中提取出来并加以表征的物质，但我们对蛋白质和核酸生物学功能的理解远远超前，这在一定程度上要归功于20世纪50年代用x射线探测结晶生物物质结构的卓越进展。通过研究氨基酸和核酸所采用的几何形状，沃森、克里克、鲍林、菲利普斯等人提出了一个理论，即生物功能是微观形状的一种表现，这推动了生物化学的一场革命：人们认识到蛋白质由一串折叠成特定功能形状的氨基酸组成，就像微型机器一样工作。它还导致了dna双螺旋结构的发现，它携带着我们的遗传信息，是分子生物学和遗传学的前身。不幸的是，类似的革命并没有发生在我们对碳水化合物的理解和利用上，例如，尽管肝素碳水化合物已经在外科手术中常规使用了近一个世纪，但其作用机制直到最近才开始被理解。问题是碳水化合物不易结晶，而且研究其微观形状的其他技术还没有发展起来。因此，碳水化合物组成和功能之间的关系是脆弱的。因此，碳水化合物代表了生物化学的一个主要未开发的前沿领域，由于它们在工业上的基础重要性（例如，食品、纸张、木材、药品、生物材料），理解这种关系的任何突破肯定会导致生物技术的另一场革命。这项研究通过开发研究碳水化合物微观形状的新技术，推动了碳水化合物组成和功能之间的重要联系。我们不是使用x射线，而是使用精确而广泛的计算机模拟、提炼纯碳水化合物的先进方法和基于磁共振的分子显微镜（类似于医院里的核磁共振扫描仪）来实现这一目标。到目前为止，我们的研究主要集中在解开围绕被称为糖胺聚糖（GAGs）的大型聚合碳水化合物分子的一些谜团，这种分子填满细胞之间的空间，将它们连接在一起，赋予器官、关节和皮肤力量，同时允许我们的身体生长和变化。在显微镜下，碳水化合物分子是由化学环组成的，它们连接在一起形成聚合链。我们发现，为了准确地描述这些分子的形状，我们需要了解这些环之间的连接关节周围发生了什么，以及这些环是如何动态弯曲的。碳水化合物的计算机模拟考虑了数千种与溶剂水的相互作用，迄今为止已经成功地研究了关节，但到目前为止，计算机硬件的限制还不允许研究环弯曲，因为它发生在数百倍长的时间尺度上。我们克服了这个问题，使用图形处理器（用于电脑游戏的硬件）来显著加快模拟速度，并深入了解GAG硫酸肝素，这是一种类似于肝素的抗凝血剂，排列在血管中。它揭示了环弯曲是碳水化合物功能的核心，环弯曲的缺失导致区域变硬，从而与体内其他分子相互作用。我们现在计划进一步研究和测试这一假设，并确定这种环弯曲行为是否对其他gag的功能至关重要，例如在软骨和皮肤中发现的那些，它在其他人类和植物碳水化合物中是否重要，以及它是否可以用于理解如何设计基于碳水化合物的新型药物和生物材料。

Carbohydrates, amino acids, nucleic acids and lipids constitute the fundamental building blocks of life. Although carbohydrates were the first of these to be extracted from living organisms and characterised, our understanding of protein and nucleic acid biological function is far advanced, which is, in part, due to the excellent progress made in the 1950s on probing the structure of crystallised biological matter with x-rays. By investigating the geometries adopted by amino acids and nucleic acids, Watson, Crick, Pauling, Phillips and others theorised that biological function is a manifestation of microscopic shape, which drove a revolution in Biochemistry: the realisation that proteins comprise a string of amino acids folded into specific functional shapes and work as micro-machines. It also led to discovery of the DNA-double helix, which carries our genetic information and is the progenitor of Molecular Biology and Genetics. Unfortunately, a similar revolution has not occurred in our understanding and harnessing of carbohydrates, for example, although the heparin carbohydrate has been routinely used in surgical procedures for almost a century, the mechanism of action has only recently begun to be understood. The problem is that carbohydrates do not crystallise readily and other techniques to investigate their microscopic shape have not been developed. Consequently, the relationship between carbohydrate composition and function is tenuous. Carbohydrates, therefore, represent a major unexplored frontier in Biochemistry and due to their fundamental industrial importance (e.g., food, paper, wood, pharmaceuticals, biomaterials) any breakthrough in understanding this relationship would certainly lead to another revolution in biotechnology. This research is driving toward providing this important link between carbohydrate composition and function by developing new techniques for investigating their microscopic shape. Rather than using x-rays, we are using precise and extensive computer simulations, advanced methods for refining pure carbohydrates and a molecular microscope based on magnetic resonance (similar to MRI-scanners found in hospitals) to achieve this goal. To date our research has focused on unravelling some of the mysteries surrounding the large polymeric carbohydrate molecules called glycosaminoglycans (GAGs), which fill the space between cells, bonding them together, conferring strength to organs, joints and skin, while allowing our bodies to grow and change. Microscopically, carbohydrate molecules are composed of chemical rings, joined together to form polymeric chains. We found that to accurately describe the shape of these molecules we need to understand both what is happening around the connection joints between these rings and also how the rings flex dynamically. Computer simulations of carbohydrates, which take into account thousands of interactions with solvent water, have so far managed to investigate the joints, but up until now limitations in computer hardware has not permitted an investigation into ring flexing because it happens on timescales that are hundreds of times longer. We overcame this problem using graphics processors (hardware used for computer gaming) to dramatically speed-up simulations and provide insight into the GAG heparan sulphate, an anticoagulant similar to heparin that lines blood vessels. It has revealed that ring flexing is central to carbohydrate function and that absence of ring flexing leads to regions that are stiffened, which consequently interact with other molecules in the body. We now plan to research and test this hypothesis further and determine whether this ring flexing behaviour is central to the function of other GAGs, such as those found in cartilage and skin, whether it is important in other human and plant carbohydrates and whether it can be used for understanding how to design novel pharmaceuticals and biomaterials based on carbohydrates.