Exploring the Impact of Backbone Flexibility on Folding Mechanisms of Protein Mimetics: Integrating Experiment and Simulation

探索主链柔韧性对蛋白质模拟物折叠机制的影响：实验与模拟相结合

• 批准号: 1807301
• 负责人: William Horne
• 金额: $ 52.5万
• 依托单位: University of Pittsburgh
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1807301&HistoricalAwards=false
• 关键词: Exploring; Impact; Backbone; Flexibility; Folding

With this award, the Chemistry of Life Processes Program in the Division of Chemistry is funding Dr. Seth Horne and Dr. Lillian Chong from the University of Pittsburgh to characterize folding mechanisms in artificial, protein-like molecules. Proteins, the intricate molecular machines that perform the majority of functions necessary to sustain life, are made up of combinations of molecular building blocks known as amino acids, arrayed in long chains. Nature provides twenty different amino acid molecules, and variations in the sequence in which they are chained together leads proteins to adopt diverse three-dimensional folded shapes. These folded shapes, in turn, dictate protein function. In recent years, researchers have shown that a variety of artificial protein backbones, where some of the natural amino acids are replaced by different molecules of approximately the same size, can fold to adopt complex protein-like shapes. Artificial backbones have fundamental value in helping understand how proteins work and also offer practical benefits over their natural counterparts. Small proteins currently find widespread use as agents for the diagnosis and treatment of disease; however, an important limitation to such application is rapid degradation by enzymes that are abundant in the bloodstream. Changing the backbone while keeping side chains intact can create a molecule that mimics the folded shape and biological function of a prototype natural protein but is less prone to degradation in the body. A crucial component in the design of artificial backbones with predictable shapes is understanding how they fold. This project seeks to elucidate the molecular mechanism by which artificial backbones fold through closely-coupled experiments and computational modeling. This work includes the development of a new force field---the mathematical model describing interactions among the natural and artificial amino acids---for the modeling component of the research. The force field will be disseminated as open source through the widely-used AMBER molecular dynamics simulation package. This interdisciplinary, collaborative project is providing a valuable training ground for graduate and undergraduate students participating in the research, and is supporting diverse educational and outreach activities, including a summer undergraduate creative science writing workshop, guest lectures on issues related to scientific research and science communication, and a three-week workshop on Python coding at a local high school. The creative science writing workshop is being designed and offered by the Chemistry, English, and the History and Philosophy of Science Departments at the University of Pittsburgh, and provides students with joint science and writing mentorship, culminating in submission of one or more capstone pieces for publication in news outlets with broad readership.A key recent advance that pushed the frontier of structural complexity possible in protein mimetics is the finding that backbone connectivity can be substantially altered without compromising the fold specified by a natural side-chain sequence. Compared to the growing body of structural information on such "heterogeneous-backbone" protein mimics, virtually nothing is known about how backbone alteration impacts dynamics or folding pathways. Addressing this gap in knowledge has the potential to reveal new insights into the folding behavior in artificial backbones, aid in the design of more effective protein mimics, and provide insights into fundamental issues related to natural protein folding. This project is determining how protein backbone connectivity influences chain dynamics and folding mechanisms. The research is guided by the central hypothesis that a combination of experimental biophysical analysis and atomistic computer simulations can reveal the complex interplay among backbone composition, folded structure, chain dynamics, solvation, and folding pathways. The project includes the design and parameterization of a modified AMBER force field for simulating folding and molecular recognition events involving artificial protein-like backbones, and the development of novel protocols for simulating protein folding processes using the weighted ensemble enhanced sampling strategy. The force field is being disseminated as part of the AMBER molecular dynamics package. The new simulation strategies are being used to model the thermodynamic, structural, and kinetics experiments performed on corresponding protein mimetics synthesized in the PI's lab. This unique combination of experimental and computational research is providing insights into the molecular origins of stability differences between natural proteins and artificial counterparts, folding behavior in artificial-backbone protein mimetics, and the fundamental role of backbone preorganization in protein folding. The project is providing research training opportunities for high school, undergraduate, and graduate students in state-of-the-art protein design and modeling. An undergraduate Creative Science Summer Program at the University of Pittsburgh is being expanded, enabling students to develop valuable writing skills in the sciences, to communicate the critical roles that science plays in society.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该奖项将资助匹兹堡大学的Seth Horne博士和Lillian Chong博士研究人造类蛋白质分子的折叠机制。蛋白质是复杂的分子机器，执行维持生命所需的大部分功能，由被称为氨基酸的分子构建块组合组成，以长链排列。自然界提供了20种不同的氨基酸分子，它们连接在一起的序列的变化导致蛋白质采用不同的三维折叠形状。这些折叠的形状反过来决定了蛋白质的功能。近年来，研究人员表明，各种人造蛋白质骨架可以折叠成复杂的蛋白质形状，其中一些天然氨基酸被大小大致相同的不同分子取代。人工骨骼在帮助了解蛋白质如何工作方面具有基本价值，并提供了比自然同行更多的实际好处。小蛋白目前被广泛用作疾病诊断和治疗的试剂；然而，这种应用的一个重要限制是血液中丰富的酶的快速降解。在保持侧链不变的情况下改变骨架可以创造出一种分子，它模仿天然蛋白质原型的折叠形状和生物功能，但在体内不太容易降解。在设计形状可预测的人造脊椎时，一个关键的组成部分是了解它们是如何折叠的。该项目试图通过紧密耦合的实验和计算模型来阐明人工脊椎折叠的分子机制。这项工作包括开发一种新的力场-描述天然和人造氨基酸之间相互作用的数学模型--用于研究的建模部分。力场将通过广泛使用的Amber分子动力学模拟包作为开源进行传播。这个跨学科的合作项目为参与研究的研究生和本科生提供了一个宝贵的培训场所，并正在支持各种教育和推广活动，包括夏季本科生创造性科学写作研讨会、关于科学研究和科学交流相关问题的客座讲座，以及在当地一所高中举行的为期三周的Python编码研讨会。创造性的科学写作研讨会由匹兹堡大学的化学、英语以及科学史和科学哲学系设计和提供，为学生提供联合的科学和写作指导，最终提交一篇或多篇顶尖文章，在拥有广泛读者的新闻媒体上发表。最近的一项关键进展推动了蛋白质模拟学结构复杂性的可能前沿，即发现骨架连接可以在不影响天然侧链序列指定的折叠的情况下得到显著改变。与越来越多的关于这种“异质-骨架”蛋白质模拟物的结构信息相比，关于骨架变化如何影响动力学或折叠途径，几乎什么都不知道。解决这一知识差距有可能揭示人工骨骼中折叠行为的新见解，有助于设计更有效的蛋白质模拟物，并为与天然蛋白质折叠相关的基本问题提供见解。该项目正在确定蛋白质骨架连接如何影响链动力学和折叠机制。这项研究是在一个中心假设的指导下进行的，即实验生物物理分析和原子计算机模拟相结合可以揭示骨架组成、折叠结构、链动力学、溶剂化和折叠路径之间的复杂相互作用。该项目包括改进的琥珀力场的设计和参数化，用于模拟涉及人造蛋白质样骨架的折叠和分子识别事件，以及开发使用加权集成增强抽样策略模拟蛋白质折叠过程的新协议。该力场正在作为琥珀分子动力学包的一部分进行传播。新的模拟策略正被用于模拟在PI的实验室合成的相应蛋白质模拟物上进行的热力学、结构和动力学实验。这种独特的实验和计算研究相结合的方法，为了解天然蛋白质和人工蛋白质之间稳定性差异的分子根源，人工骨架蛋白质模拟中的折叠行为，以及骨架预组织在蛋白质折叠中的基础作用提供了见解。该项目为高中生、本科生和研究生提供最先进的蛋白质设计和建模方面的研究培训机会。匹兹堡大学的本科生创意科学暑期项目正在扩大，使学生能够发展有价值的科学写作技能，交流科学在社会中扮演的关键角色。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations

• DOI: 10.1063/5.0041278
• 发表时间: 2021-03-21
• 期刊: JOURNAL OF CHEMICAL PHYSICS
• 影响因子: 4.4
• 作者: DeGrave, Alex J.;Bogetti, Anthony T.;Chong, Lillian T.
• 通讯作者: Chong, Lillian T.

A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics

• DOI: 10.1063/5.0019054
• 发表时间: 2020-08-14
• 期刊: JOURNAL OF CHEMICAL PHYSICS
• 影响因子: 4.4
• 作者: Bogetti, Anthony T.;Piston, Hannah E.;Chong, Lillian T.
• 通讯作者: Chong, Lillian T.