SusChEM: Carbohydrate Recognition in Type B Carbohydrate Binding Modules

植物细胞壁由碳水化合物分子的固体聚合物纤维素构成。微生物产生能够将纤维素分解成单个糖分子的酶，然后可以在化学过程中用于制造燃料。酶通常由至少两个结构域组成：一个负责切割化学键，另一个负责定位纤维素表面（碳水化合物结合模块或CBM）。CBMs还帮助酶区分完美的结晶区域和不完美的非结晶区域，但蛋白质的结构如何能够进行这种区分仍然是未知的。了解这种情况是如何发生的，将有助于开发用于生物燃料生产的新生物技术以及许多其他应用。这项研究将训练研究生和本科生在现实的蛋白质碳水化合物模型的发展和先进的热力学计算。该项目还将被纳入一个推广计划，旨在促进代表性不足的研究人员对高性能计算的兴趣，并提供必要的工具来产生成功的结果。EPSCoR和化学部的生命过程化学项目正在资助来自肯塔基州大学的Christina Payne博士，以确定CBM中碳水化合物识别的机制以及这些蛋白质被识别的方式。能够比可溶性低聚物更紧密地结合非结晶纤维素。分子动力学模拟和增强的采样自由能方法将被用来评估低聚碳水化合物识别内和跨三个家庭的纤维素特异性，B型CBM的分子水平的起源。非结晶纤维素结合的CBM将被建模为与不溶性基质结合，并且炼金术自由能途径将用于确定与非结晶纤维素结合的自由能。将使用溶液中和接近代表性非结晶纤维素基质的串联CBM构建体的分子动力学模拟将来自各个模块的发现与串联构建体行为相关联。主成分分析和弹性网络建模将揭示残基相关性和机械耦合有助于合作结合和亲合力。这项研究的结果将提供一个前所未有的深入了解复杂的固体和可溶性碳水化合物底物的识别机制的CBM，其结果持有相当大的希望，为提高生物质转化技术。

Plant cell walls are constructed from a solid polymer of carbohydrate molecules called cellulose. Microbes produce enzymes capable of breaking down the cellulose into individual sugar molecules, which can then be used in chemical processes to make fuel. The enzymes often consist of at least two domains: one responsible for cleaving chemical bonds and one responsible for locating the cellulose surface (Carbohydrate Binding Modules or CBMs). CBMs also help the enzyme differentiate between perfect, crystalline regions and imperfect, non-crystalline regions, yet how the structure of the protein is capable of this distinction remains unknown. Understanding how this happens will enable development of new biotechnology for biofuels production as well as many other applications. This study will train graduate and undergraduate students in the development of realistic protein-carbohydrate models and in advanced thermodynamic calculations. This project will also be integrated into an outreach program intended to promote interest in high performance computing among underrepresented researchers and provide the necessary tools to generate successful results.NSF-EPSCoR and the Chemistry of Life Processes Program in the Chemistry Division are funding Dr. Christina Payne from the University of Kentucky to determine the mechanisms of carbohydrate recognition in CBMs and the means by which these proteins are capable of binding non-crystalline cellulose more tightly than soluble oligomers. Molecular dynamics simulations and enhanced sampling free energy methods will be used to evaluate the molecular-level origins of oligomeric carbohydrate recognition within and across three families of cellulose-specific, Type B CBMs. Non-crystalline cellulose-binding CBMs will be modeled bound to the insoluble substrate, and alchemical free energy pathways will be used to determine the free energy of binding to non-crystalline cellulose. Molecular dynamics simulations of a tandem CBM construct in solution and in proximity to representative non-crystalline cellulose substrate will be used to relate findings from the individual modules to the tandem construct behavior. Principle component analysis and elastic network modeling will uncover residue correlation and mechanical coupling contributing to cooperative binding and avidity. The outcome of this study will provide an unprecedented level of insight into the complex solid and soluble carbohydrate substrate recognition mechanisms of CBMs, the findings of which hold considerable promise for enhancing biomass conversion technology.