CAREER: Computational Modeling of Protein Evolvability

虽然人们认识到蛋白质的分子进化是物种进化的组成部分，但蛋白质进化的物理机制和促进进化的蛋白质的物理性质还没有得到很好的理解。该项目的目标是通过开发和应用新的理论模型来解决这些问题，这些模型可以快速准确地捕获与酶功能进化相关的基本物理和化学。该方法将具体涉及对突变对天然蛋白质折叠稳定性的影响以及突变对催化效率的影响进行建模。将这些理论工具和其他理论工具应用于信息模型系统，将为发现与分子进化相关的物理化学特征奠定基础。这些功能的例子包括补偿突变的物理机制以及蛋白质的稳定性和动力学在促进新的酶活性的转变中的作用。这个CAREER项目代表了一个综合的多学科教育和研究方法，专注于使用化学和物理定律来解释和预测生物学中的基本进化过程。该项目产生的分子进化的新方法和新的物理理解将对包括蛋白质工程和设计，定向进化和纳米技术在内的各种领域产生直接影响。除了研究的影响外，教育目标还将通过培训本科生和研究生从定量角度处理生物学问题来影响未来的科学家。这一目标将部分实现，通过一个新的本科生课程的化学生物学和一个新的研究生水平的生物物理化学课程的发展。此外，该项目还将涉及开发一个新的交互式软件包，为学生进一步确立将定量思维应用于生物问题的价值。该软件将通过让学生探索蛋白质的物理性质和蛋白质的生物功能之间的联系来实现这一点。开发的教育软件将产生广泛影响，因为它将免费向公众分发，因此将提供给国内和国际的大学。

While it is recognized that the molecular evolution of proteins is integral to the evolution of species, the physical mechanisms underlying protein evolution and the physical properties of proteins that facilitate evolution are not well understood. The objective of this CAREER project is to address these questions through the development and application of new theoretical models that rapidly and accurately capture the essential physics and chemistry relevant to the evolution of enzyme function. The approach will specifically involve modeling the effects of mutations on the stability of a native protein fold as well as the effects of mutation on catalytic efficiency. The application of these and other theoretical tools to informative model systems will form the basis for discovering physical-chemical features associated with molecular evolution. Examples of these features include the physical mechanisms underlying compensatory mutations as well as the role of protein stability and dynamics in facilitating transitions to new enzymatic activities.This CAREER project represents an integrated and multidisciplinary educational and research approach, focused on using the laws of chemistry and physics to explain and predict fundamental evolutionary processes in biology. The new methods and new physical understanding of molecular evolution resulting from this project will have direct implications for a variety of fields including protein engineering and design, directed evolution, and nanotechnology. In addition to the impact of the research, the educational goals will impact future scientists by training undergraduate and graduate students to approach biological questions from a quantitative perspective. This objective will be partially realized through the development of a new undergraduate course in chemical biology and a new graduate level course in biophysical chemistry. In addition, this project will involve the development of a new interactive software package that will further establish, for students, the value of applying quantitative thinking to biological questions. The software will do this by allowing students to explore the connection between the physical properties of proteins and the biological function of proteins. The developed educational software will have a broad impact as it will be distributed freely to the public and will therefore be available to universities nationally and internationally.