Pressure-Based Mapping of Protein Free Energy Landscapes

标题：基于压力的蛋白质自由能图谱蛋白质是我们身体和所有其他生物体中的分子，植物、细菌、鱼类和动物，它们完成了维持和繁殖生命的大部分工作。它们是连接在一起的被称为氨基酸的小化学物质链。氨基酸的数量和顺序决定了蛋白质的形状或结构以及它的功能。蛋白质折叠成紧凑的形状，但为了完成消化食物或产生让鸟类和昆虫飞行的力量等工作，它们必须改变它们的形状。这项研究旨在了解氨基酸序列如何定义蛋白质的折叠，以及它们如何改变形状以发挥作用。了解蛋白质序列如何控制它们的形状和功能，将对设计用于生物技术的新蛋白质有很大帮助。例如，可以为绿色化学生物反应器设计更好、更活跃、更稳定的蛋白质，使日常生活中使用的化学物质不会对环境造成损害。蛋白质是纳米机器和纳米材料，将在电子、计算、生物传感和纳米制造中得到广泛应用。所有这些技术进步都将基于对蛋白质序列、稳定性和功能之间关系的理解。这项研究所基于的强大的国际合作将为学生提供科学努力的世界观，并帮助他们建立国际网络，帮助他们追求自己的职业生涯。将参与研究的研究生和本科生将沉浸在一个综合的跨学科环境中，结合多种实验和计算方法。这项研究产生的大量核磁共振数据集与美国国家科学基金会赞助的RPI计算机专业本科教育项目--数据分析本科数学项目(DATUM)--共享。将为生物技术中心举办的本科生研究项目提供支持。这项研究还将涉及由生物技术中心为特洛伊地区高中(少数民族人口较多)运营的RPI高中实习计划。本项目的目标是通过实验绘制选定模型蛋白质的折叠自由能景观图，并确定它们的折叠协作性、起始和路径的序列和结构决定因素。这将通过利用压力微扰与特定部位的核磁共振、荧光、SAXS和其他生物物理方法相结合的优势来实现。本提案的基本前提是，压力由于其独特的作用机制，可以为蛋白质折叠提供独一无二的见解。在主要目标的框架内，将解决三个具体问题：序列如何编码蛋白质折叠的协作性。蛋白质的协同作用如何与它们的体积热膨胀联系在一起。压力展开状态下的残余自然相互作用如何影响折叠机制。该项目将解决蛋白质折叠和构象动力学方面的中心悬而未决的问题，首先通过显著和系统地增加详细的蛋白质折叠能量景观的实验数据库。其次，它将提供实验场景，描述序列如何定义折叠路线和协作性。最后，它将揭示序列是如何具体控制折叠景观上激发态的访问的。该项目由生物科学局分子和细胞生物科学部的分子生物物理组和数学和物理科学局物理司的生命系统物理学项目共同资助。

Title: Pressure Based Mapping of Protein Free Energy LandscapesProteins are the molecules in our bodies and in all other living organisms, plants, bacteria, fish, animals, that do most of the work to maintain and reproduce life. They are chains of small chemicals, called amino acids that are linked together. The number and order of the amino acids defines the shape or structure of the protein and also its function. Proteins fold up into compact shapes, but to do their jobs like digesting food or generating the force that makes birds and insects fly, they have to change their shape. This research is aimed at understanding how the sequence of amino acids defines the folding of proteins and how they change their shapes to function. Understanding how protein sequences control their shape and function will be of great use in designing new proteins for applications in biotechnology. For example, better, more active and more stable proteins can be designed for green chemistry bioreactors to make the chemicals used in daily life without harming the environment. Proteins are nano-machines and nanomaterials that will find numerous applications in electronics, computing, biosensing and nano-fabrication. All of these technological advances will be based on the understanding of the relationship between protein sequence, stability and function. The strong international collaboration on which this research is based will provide the students with a world-view of the scientific endeavor, and help them establish international networks that will aid them as they pursue their careers. The graduate and undergraduate students who will participate in the research will be immersed in a comprehensive interdisciplinary environment, incorporating multiple experimental and computational approaches. The large NMR data sets generated by the research are shared with the NSF sponsored undergraduate educational program in the undergraduate computer science major at RPI, the Data Analytics Through-out Undergraduate Mathematics program (DATUM). Support will be provided for the undergraduate research program run by the Center for Biotechnology. The research will also involve the RPI high school internship program run by the Center for Biotechnology for Troy area high schools (with a large minority population). The objective of this project is to map experimentally the folding free energy landscapes for selected model proteins, and to identify the sequence and structural determinants of their folding cooperativity, initiation and pathways. This will be accomplished by exploiting the advantages of pressure perturbation coupled with site specific NMR, fluorescence, SAXS and other biophysical approaches. The underlying premise of the present proposal is that pressure, due to its unique mechanism of action, can provide exclusive insights into protein folding. Within the framework of the main objective, three specific questions will be addressed: How does sequence code for protein folding cooperativity. How are protein cooperative interactions linked to their volumetric thermal expansion. How do residual native interactions in pressure unfolded states affect folding mechanisms. This project will address central outstanding issues in protein folding and conformational dynamics, first by significantly and systematically increasing the experimental database of detailed protein folding energy landscapes. Secondly, it will provide experimental scenarios describing how sequence defines folding routes and cooperativity. Finally, it will reveal how sequence specifically controls access to excited states on folding landscapes. This project is jointly funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Physics of Living Systems Program in the Division of Physics in the Directorate of Mathematical and Physical Sciences.