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的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目及 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 纤维素乙醇是化石燃料的乐观替代品，其从可再生资源的有效生产将是确保美国未来繁荣的关键。目前，从生物质工业规模生产乙醇利用不溶性纤维素的酸催化水解。这种方法在可扩展性方面受到限制，并且存在许多环境问题。一个更环保的过程，纤维素酶水解，是一个诱人的目标。然而，这种方法的大规模应用受到酶催化途径的低周转率的阻碍。了解纤维素酶的催化机制是最终成为蛋白质工程长期且雄心勃勃的项目的先决条件。我们一直是第一组利用分子动力学模拟研究完整的CBH I酶（包括催化，接头和结合结构域在一个单一的模拟）在一个完整的结晶纤维素微纤维在溶液中。这项初步工作是使用SDSC资源进行的，部分结果最近已被接受发表在《纤维素》杂志上。我们还想研究当一条纤维素链被穿入催化隧道时蛋白质的行为，希望它能揭示催化机制，并用于识别参与这一过程的重要氨基酸残基。这些知识将有助于诱变实验，以产生更多的活性蛋白质。在这里，我们要求分配30，000个SU的开发，以便使用CHARMM软件对计划的模拟进行初始基准测试和测试。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.