CAREER: Programming proteins by deep sequencing and design

蛋白质是细胞生命所必需的一系列基本活动的核心。同样的多功能性使得蛋白质在医学上具有巨大的潜力，如单克隆抗体，如利妥昔单抗，可以靶向并摧毁非霍奇金淋巴瘤，在工业上，如酶，可以将纤维素生物质分解为简单的碳水化合物。然而，天然蛋白质并不总是工业或医疗应用的最佳选择，而且目前改善蛋白质的方法既昂贵又费力。我们需要的是一种新的方法，从大量的突变组合中寻找能够改善功能的少数突变。该职业奖的主要研究目标是设计和测试一种大规模并行、快速的DNA深度测序方法，以定量分析数十万种蛋白质变体的序列-功能关系。这种方法能够快速确定那些少数有益的突变。PI建议开发、应用和整合这种方法与计算设计，以重编程特异性的天然和设计的蛋白质。这些优化的蛋白质将使微生物能够将纤维素生物质转化为下一代燃料和增值化学品。这个职业奖的教育外展旨在通过创造更多积极参与研究的机会，提高女性在科学和工程专业的留用率。为了实现这一目标，PI将通过以下方式整合他的教育和研究目标：(i)利用现有的密歇根州立大学项目，将高中生和本科生安置在PI实验室的研究项目中；（ii）为高中学生讲授生化工程基础的一系列讲习班；（iii）在密歇根州立大学为本科生开设一门新的合成生物学实验室/讲座课程；（iv）组建首支密歇根州立大学的国际基因工程机器（iGEM）竞赛团队，在该竞赛中，本科生进行自主研究项目，并在全国会议上展示成果。我们将积极招募女性参与这些项目。该职业奖由生物基础设施部（DBI）通过生物研究仪器开发（IDBR）项目和化学、生物工程、环境和运输系统部（CBET）共同资助。

1254238 WhiteheadProteins are central to a diverse set of fundamental activities necessary for cellular life. This same versatility leads to tremendous potential for proteins as designable agents in medicine such as monoclonal antibodies like Rituximab that can target and destroy non-Hodgkin lymphomas, and in industry such as enzymes that can deconstruct cellulosic biomass to simple carbohydrates. Yet natural proteins are not always optimal for industrial or medicinal applications, and current methods of improving proteins can be expensive and laborious. What is needed are new ways to search through the vast combinations of mutations to find the few that impart improvements to function. The primary research objective of this CAREER award is to design and test a massively parallel, rapid DNA deep sequencing method in order to quantitate sequence-function relationships for hundreds of thousands of protein variants. This method enables the rapid determination of those few beneficial mutations. The PI proposes to develop, apply, and integrate this method with computational design to reprogram specificity in natural and designed proteins. These optimized proteins will enable microbes to convert cellulosic biomass to next-generation fuels and value-added chemicals. The educational outreach of this CAREER award aims to increase the retention of women in science and engineering majors by creating additional opportunities for active participation in research. Towards this goal, the PI will integrate his educational and research objectives by: (i) utilizing existing MSU programs to place high school and undergraduate students in research projects in the PI's laboratory; (ii) teaching a series of workshops on biochemical engineering fundamentals for high school students; (iii) developing a new synthetic biology lab/lecture course at MSU for undergraduate students; and (iv) forming the first MSU team for the international genetically engineered machines (iGEM) competition, in which undergraduates perform self-guided research projects and present results at a national meeting. Women will be aggressively recruited to participate in each of these programs.This CAREER award is co-funded by the Division of Biological Infrastructure (DBI) through the Instrument Development for Biological Research (IDBR) program, and by the Division of Chemical, Bioengineering, Environmental, and Transport Systems (CBET).