SusChEM: Carbohydrate Recognition in Type B Carbohydrate Binding Modules

植物细胞壁是由一种叫做纤维素的碳水化合物分子的固体聚合物构成的。微生物产生的酶能够将纤维素分解成单独的糖分子，然后这些糖分子可以用于化学过程中制造燃料。这些酶通常至少由两个区域组成：一个负责断裂化学键，另一个负责定位纤维素表面(碳水化合物结合模块或CBM)。CBM还帮助酶区分完美的结晶区和不完美的非结晶区，但蛋白质的结构如何能够做到这一点尚不清楚。了解这是如何发生的，将使开发用于生物燃料生产和许多其他应用的新生物技术成为可能。这项研究将培训研究生和本科生开发现实的蛋白质-碳水化合物模型和高级热力学计算。该项目还将被整合到一个推广计划中，旨在促进未被充分代表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。NSF-EPSCoR和化学部的生命过程化学计划正在资助肯塔基大学的Christina Payne博士，以确定CBM中碳水化合物识别的机制，以及这些蛋白质能够比可溶性低聚物更紧密地结合非晶体纤维素的方式。分子动力学模拟和增强的采样自由能方法将被用来评估三种纤维素特异性的B型CBM内和跨三个家族的低聚碳水化合物识别的分子水平来源。与非晶态纤维素结合的CBM将被模拟为结合在不溶于水的底物上，炼金术自由能途径将被用来确定与非晶态纤维素结合的自由能。将使用分子动力学模拟在溶液中和代表性非晶态纤维素底物附近的串联CBM构造，以将单个模块的发现与串联构造行为联系起来。主成分分析和弹性网络建模将揭示残基关联和机械耦合对协同结合和亲和力的贡献。这项研究的结果将对CBMS复杂的固体和可溶性碳水化合物底物识别机制提供前所未有的洞察力，其结果将为提高生物质转化技术带来巨大的希望。

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.