Effects of Cellular Environment on Protein Structure and Folding Dynamics

在这个研究项目中，PI将研究细胞环境对蛋白质结构和折叠动力学的影响，并将在这一研究领域培养学生。蛋白质在细胞内执行各种生物特定功能，与许多其他大分子一起在拥挤的基质中运作。她将从她教授的物理学入门课程中招收少数族裔和女性本科生参加她的研究项目，以保持他们对科学的兴趣。休斯敦大学（UH）是一所指定的西班牙裔服务机构，拥有4万多名学生。PI是物理科学教学公平项目（物理STEP）的负责人，这是一个专业发展计划，用于继续教育。“物理STEP”的重点是每年为20名在职的非物理教师提供培训，这些教师被指派教授高中物理。这20名教师在大休斯顿地区的高需求学区共教授3000名高中生。年轻学生和教师学习物理的机会将大大提高我们下一代的科学素养。在与休斯敦大学教育学院的合作下，物理步骤为每位教师提供内容知识和教学方法，包括通过年度课程选择物理主题的“探究式”实验。PI计划招募高中学生加入她的研究项目，将他们与参加物理STEP的教师配对。此外，通过与STEP小学科学教师的协调，PI将通过参加职业日和在UH校园举办科学实地考察活动来接触四年级和五年级的学生。PI将利用她广泛的教师网络和经验来增强研究的广泛影响。从长远来看，这种方法可能有助于揭示细胞适应的分子机制和蛋白质网络对应激信号的调节。通过互联网传播开发的计算机程序将促进建模工具的免费使用，以研究细胞中的蛋白质折叠。本研究的目的是表征细胞环境对模型蛋白的结构和折叠动力学的影响。大多数关于蛋白质结构和折叠动力学的实验、理论和模拟都是在试管中的稀释溶液中进行的，这并不能代表细胞中拥挤的生物环境。细胞环境的竞争效应对蛋白质生物物理学的影响程度尚不清楚。迫切需要发展理论和计算方法，以提供对细胞中决定蛋白质结构和构象动力学的环境影响的定量理解。只有使用定量评估细胞内蛋白质生物物理学的工具，才能对蛋白质响应细胞信号提示的行为有一个基本的了解。该研究包括三个综合方向：首先，首席研究员（PI）将应用计算机模拟来量化化学变性剂和拥挤介质存在下的折叠动力学，并将这些结果与类似的体外实验联系起来。这将允许研究过渡状态结构和细胞样介质中蛋白质折叠过渡状态的可能运动，然后可以为进一步的体外实验设计提供信息。接下来，PI将在拥挤环境中开发能量景观剖面和蛋白质折叠动力学之间的定量描述，这对于更好地理解计算机模拟和体外实验数据背后的潜在物理原理至关重要。最后，PI将结合计算机模拟，改进理论的发展，以及与实验家的合作，以推进对细胞竞争效应（如大分子拥挤，静电和流体动力学相互作用）如何调整细胞中蛋白质的结构和折叠动力学的了解。这项研究意义重大，因为其结果将提供分子解释和预测，将蛋白质的残留细节与其在细胞中的折叠过程联系起来。该项目由生物科学理事会分子与细胞生物科学部的分子生物物理学和数学与物理科学理事会物理部的计算物理项目共同支持。

In this research project, the PI will study the effects of the cellular environment on the structure and folding dynamics of proteins and will train students in this area of research. Proteins perform a variety of biological specific functions inside cells, operating in a crowded matrix with many other macromolecules. The PI will recruit minority and female undergraduate students for her research program from introductory physics courses that she teaches to retain their interest in science. The University of Houston (UH) is a designated Hispanic-serving institute with over 40,000 students. The PI is a director of the Physics Science Teaching Equity Project (Physics STEP), a professional develop program for continuing education. The focus of Physics STEP is to provide training to 20 in-service non-physics teachers who are assigned to teach high-school physics each year. These 20 teachers teach a total of 3000 high-school students from high-need school districts at the greater Houston area. The opportunity for young students and teachers to learn physics would greatly improve the science literacy of our future generation. In collaboration with the College of Education at UH, the Physics STEP offers each teacher content knowledge and pedagogy, including "inquiry-based" experiments on selected physics topics through a yearly curriculum. The PI plans to recruit high-school students to join her research program by pairing them with teachers who participate in the Physics STEP. Additionally, through coordination with science teachers of elementary schools in STEP, the PI will reach out to fourth- and fifth-grade students by participating in a Career Day and by hosting science field trips at the UH campus. The PI will use her extensive teacher's network and experience to enhance the broader impacts of the research. In the long term, this methodology may help reveal molecular mechanisms of cellular adaptation and regulation of protein networks in response to stress cues. The dissemination of the developed computer program through the internet will promote modeling tools that are freely available to study protein-folding in cells. The objective of the research is to characterize the effects of the cellular environment on the structure and folding dynamics of model proteins. Most experiments, theories, and simulations on the structures and folding dynamics of proteins have been addressed in dilute solutions in test tubes, which are not representative of the congested biological environment in cells. The extent to which the competing effects of the cellular environment affect protein biophysics is poorly understood. There is an urgent need for the development of theories and computational methods to provide a quantitative understanding of the environmental effects that dictate protein structures and conformational dynamics in cells. Only with tools to quantitatively assess protein biophysics inside cells can a fundamental understanding of protein's behaviors in response to cellular signaling cues be achieved. The research includes three integrated directions: First, the principal investigator (PI) will apply computer simulations to quantify folding kinetics in the presence of chemical denaturants and crowded media and relate these results to similar in vitro experiments. This will allow the investigation of transition-state structures and possible movements of the transition states of protein folding in cell-like media, which can then inform the design of further in vitro experiments. Next, the PI will develop a quantitative description between energy landscape profiles and protein-folding kinetics in crowded environments, which is essential to better understand the underlying physical principles behind computer simulations and in vitro experimental data. Finally, the PI will combine computer simulations, development of improved theories, and collaboration with experimentalists to advance the knowledge of how competing cellular effects, such as macromolecular crowding, electrostatics, and hydrodynamic interactions, tune the structures and folding kinetics of proteins in cells. The research is significant because the outcome will offer molecular explanations and predictions that connect residual details of proteins to their folding processes in cells. This project is jointly supported by Molecular Biophysics in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Computational Physics Program in the Division of Physics in the Mathematical and Physical Sciences Directorate.