MOLECULAR DYNAMICS SIMULATIONS ON CBH I WITH A CELLULOSE STRAND INSIDE THE CATA

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 纤维素乙醇是一种乐观的化石燃料替代品，它从可再生资源中高效生产将对确保美国未来的繁荣至关重要。目前，工业规模的生物质乙醇生产是利用酸催化的不溶纤维素的水解。这种方法不仅在可伸缩性方面受到限制，而且会带来许多环境问题。一种更环保的工艺--纤维素酶水解法--是一个诱人的目标。然而，酶催化途径的低转化率阻碍了这一过程的大规模应用。了解纤维素酶的催化机制是最终将是一个长期和雄心勃勃的蛋白质工程项目的先决条件。我们是第一个利用分子动力学模拟来研究完整的Cbh I酶(包括在单个模拟中的催化、连接和结合区域)在溶液中完整的结晶纤维纤维上的小组。这项初步工作是利用SDSC资源进行的，部分结果最近已被接受，将发表在《纤维素》杂志上。我们还想研究当一条纤维素链进入催化隧道时蛋白质的行为，希望它将揭示催化机制，并用于识别参与这一过程的重要氨基酸残基。这些知识将有助于突变实验，以生产更有活性的蛋白质。在此，我们申请30,000个SU的开发拨款，以使用CHARMM软件对计划中的模拟进行初始基准测试。这项初步研究将构成我们计划在不久的将来提交的MRAC提案的基础。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Cellulosic ethanol is an optimistic substitute for fossil fuels and its efficient production from renewable sources will be essential in securing the future prosperity of the United States. Currently industrial scale production of ethanol from biomass utilizes acid catalyzed hydrolysis of insoluble cellulose. This approach is both limited in scalability and presents a number of environmental issues. A more environmentally friendly process, hydrolysis by cellulase enzymes, is a enticing goal. However, the massive application of such a process is hindered by the low turnover rates of the enzyme's catalytic pathway. An understanding of the catalytic mechanism of cellulase is a prerequisite of what will ultimately be a long term and ambitious project in protein engineering. We have been the first group to utilize molecular dynamics simulations to study the complete CBH I enzyme (including the catalytic, linker and binding domains in a single simulation) on an intact crystalline cellulose microfibril in solution. This initial work was conducted using SDSC resources and part of the results have recently been accepted for publication in the journal Cellulose. We also want to study the behavior of the protein when a strand of cellulose is threaded into the catalytic tunnel in the hope that it will reveal the catalytic mechanism and be used to identify important amino acid residues involved in such a process. Such knowledge will be useful for mutagenesis experiments to produce more active proteins. Here we are requesting a Development Allocation of 30,000 SUs to carry out initial benchmarking and testing of the planned simulations using the CHARMM software. This initial study will form the basis of a MRAC proposal that we plan to submit in the near future.