CAREER: The Functional Evolution of Sequence-specific DNA-binding Proteins

现代生物学的一个新教训是，生物体不能被理解为其组成分子的总和，而是涉及复杂的信息网络，这些网络表现为集成系统。第二个新出现的教训是，生物分子成分本身并不是恒定的，而是在进化过程中结构和功能的变化。该项目的研究重点是生物分子网络的重要组成部分的功能进化，即通过与双链DNA上的某些核苷酸碱基结合来调节基因表达的蛋白质。在一个功能多样的微生物DNA结合蛋白家族中，对数据库的分析表明了一种“进化密码”，即蛋白质对靶DNA中单个碱基的偏好似乎是通过蛋白质中简单的单个氨基酸变化而进化的。该项目涉及测试这个简单的代码的限制，通过并行应用定点诱变，结合亲和力测量，结合位点选择，和结构生物学不同的Cro蛋白。这些研究还包括评估更复杂和微妙的因素对功能进化的贡献，例如蛋白质结构的进化变化。该项目的教育部分强调本科生研究的机会，将其作为培养新一代科学家的关键因素，并将计算机实验室设施纳入研究生教学，以促进课堂学习和独立研究之间的过渡。更广泛的影响包括通过加强和使用计算机实验室设施，为研究和教育发展基础设施，增加本科生和来自代表性不足群体的学生的研究经验的机会。

An emerging lesson of modern biology is that living organisms cannot be understood as the sum of their component molecules but involve complex informational networks that behave as integrated systems. A second emerging lesson is that the biomolecular components themselves are not constant but change in structure and function during evolution. This project's research focuses on the functional evolution of important components of biomolecular networks, namely proteins that regulate gene expression by binding to certain patterns of nucleotide bases on double-stranded DNA. In a functionally diverse family of microbial DNA-binding proteins called Cro, analysis of databases suggested an "evolutionary code", whereby the preferences of the protein for single bases in target DNA appeared to evolve through simple, single amino-acid changes in the protein. The project involves testing the limits of this simple code by parallel application of site-directed mutagenesis, binding affinity measurements, binding site selection, and structural biology to diverse Cro proteins. These studies also include assessment of the contribution of more complex and subtle factors to functional evolution, such as evolutionary changes in protein structure. The educational portion of the project emphasizes opportunities for undergraduate research as a critical element in the development of a new generation of scientists, and incorporation of computer lab facilities in graduate-level teaching to facilitate a transition between classroom study and independent research. Broader impacts include development of the infrastructure for research and education through enhancement and use of computer lab facilities, increased opportunities for research experiences for undergraduates and students from underrepresented groups.