RUI: Combining Experiments and Simulations to Optimize Biomolecular Ionic Liquids for Protein Stabilization

RUI：结合实验和模拟来优化生物分子离子液体以稳定蛋白质

• 批准号: 1904797
• 负责人: Timothy Vaden
• 金额: $ 30万
• 依托单位: Rowan University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-15 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1904797&HistoricalAwards=false
• 关键词: RUI; Combining; Experiments; Simulations; Optimize

Non-Technical AbstractIonic liquids (ILs) are liquid salts that could be used as selective protein-stabilization biomaterials if they can be designed with the right molecular properties. This project will study ILs based on biological molecules and their effects on a specific protein system. The system is the azurin-nitrite reductase complex involved in soil bacterial denitrification. Denitrification is the process of converting nitrate into atmospheric nitrogen, and usually requires a complex protein system in soil bacteria. If the azurin-nitrite reductase system can be selectively stabilized with IL-based biomaterials it can be used for removing nitrate contamination from polluted environments. The biological molecule-based ILs could be designed with the right competing molecular interactions for protein stabilization if these interactions are understood. This project will use experiments to quantify the effects of ILs on the azurin and nitrite reductase protein structures, stabilities, and functionalities. Molecular dynamics simulations will attempt to reproduce the experimental results and thereby uncover the fundamental interactions between ILs and proteins that are needed for protein stabilization. The project will use this insight to design new ILs and IL-inspired biomaterials in an iterative manner. The project will train undergraduate students on a cross-disciplinary project involving biochemistry, physical chemistry, and computational simulations. The results will be useful for designing future IL-based biomaterials.Technical AbstractIonic liquids (ILs) have potential applications in which the right cation-anion combination can selectively stabilize proteins for industrial and biotechnological applications. Novel biomolecule-based ILs could be used as versatile biocompatible materials for protein engineering. This RUI project will combine biophysical spectroscopic experiments with computer simulations to study ILs with cationic tetramethylguanidinium (TMG) and different biomolecular anions (e.g., amino acids) and their effects on protein structures, stabilities, and activities. The competing interactions in TMG-biomolecule ILs (protein-TMG, anion-protein, and TMG-biomolecule) can be tuned to destabilize some proteins and stabilize others. The target protein system is the azurin-nitrite reductase (azurin/NiR) complex involved in denitrification, which could be stabilized for engineered environmental bioremediation. The project will quantify the effects of novel TMG-biomolecule ILs interacting with target proteins to better model and design IL-based biomaterials. The project will prepare different TMG-based ILs, add ILs to the proteins (expressed and purified in the lab) in aqueous solution, quantify the effects of the ILs on protein structures and stabilities using optical spectroscopy and mass spectrometry techniques, assay enzyme activities in ILs, and use molecular dynamics (MD) simulations to interpret experimental results and develop models to predict new ILs for future study. The new ILs and new insights will potentially advance the current understanding of ILs and IL-based biomaterials for biotechnology applications, including enzyme modulation, drug delivery, antibiotic enhancement, biomass processing, and biomaterials self-assembly. The proposal contains a plan for maximizing the STEM educational impact of the research project beyond the technical results. This plan will benefit Rowan University undergraduate students as well as South Jersey high school students.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.

非技术摘要离子液体(ILS)是一种液体盐，如果能够设计成具有合适的分子性质，就可以用作选择性蛋白质稳定生物材料。这个项目将研究基于生物分子的ILS及其对特定蛋白质系统的影响。该系统是参与土壤细菌反硝化的天青-亚硝酸盐还原酶复合体。反硝化作用是将硝酸盐转化为大气氮的过程，通常需要土壤细菌中复杂的蛋白质系统。如果天青-亚硝酸盐还原酶体系能够被基于IL的生物材料选择性地稳定下来，它就可以用于去除污染环境中的硝酸盐污染。基于生物分子的ILS可以被设计成具有正确的竞争分子相互作用来稳定蛋白质，如果这些相互作用被理解的话。这个项目将利用实验来量化ILS对天青素和亚硝酸盐还原酶蛋白质结构、稳定性和功能的影响。分子动力学模拟将试图重现实验结果，从而揭示ILS和蛋白质之间的基本相互作用，这是蛋白质稳定所需的。该项目将利用这一洞察力以迭代的方式设计新的ILS和受ILL启发的生物材料。该项目将对本科生进行涉及生物化学、物理化学和计算模拟的跨学科项目培训。离子液体(ILs)具有潜在的应用前景，在工业和生物技术应用中，合适的阳离子-阴离子组合可以选择性地稳定蛋白质。基于新型生物分子的离子液体可作为生物相容性材料用于蛋白质工程。这个RUI项目将结合生物物理光谱实验和计算机模拟来研究含有阳离子四甲基胍(TMG)和不同生物分子阴离子(例如氨基酸)的ILS及其对蛋白质结构、稳定性和活性的影响。TMG-生物分子ILS(蛋白质-TMG、阴离子-蛋白质和TMG-生物分子)中的竞争相互作用可以被调节来使一些蛋白质不稳定，而使另一些蛋白质稳定。目的蛋白系统是参与反硝化作用的天青-亚硝酸盐还原酶(azurin/NIR)复合体，可稳定用于工程化环境生物修复。该项目将量化新型TMG-生物分子ILS与目标蛋白相互作用的效果，以更好地模拟和设计基于IL的生物材料。该项目将制备不同的基于TMG的ILS，将ILS添加到水溶液中的蛋白质(在实验室表达和纯化)，使用光学光谱和质谱学技术量化ILS对蛋白质结构和稳定性的影响，分析ILS中的酶活性，并使用分子动力学(MD)模拟来解释实验结果并开发模型来预测未来研究的新ILS。新的ILS和新的见解可能会促进目前对ILS和基于ILS的生物材料在生物技术应用方面的理解，包括酶调节、药物输送、抗生素增强、生物质加工和生物材料自组装。该提案包含一项计划，旨在最大限度地扩大研究项目对STEM教育的影响，使之超越技术成果。该计划将使罗文大学本科生和南泽西高中生受益。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

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• DOI: 10.1016/j.molliq.2022.120097
• 发表时间: 2022-11
• 期刊: Journal of Molecular Liquids
• 影响因子: 6
• 作者: Nicholas J. Paradis;Austin K. Clark;Hunter Gogoj;Phillip M. Lakernick;T. Vaden;Chun Wu

To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations

• DOI: 10.1155/2020/5314187
• 发表时间: 2020-04-01
• 期刊: PPAR RESEARCH
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• 作者: Sullivan，Holli-Joi;Wang，Xiaoyan;Wu，Chun
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To probe the activation mechanism of the Delta opioid receptor by an agonist ADL5859 started from inactive conformation using molecular dynamic simulations

• DOI: 10.1080/07391102.2022.2107074
• 发表时间: 2022-08
• 期刊: Journal of Biomolecular Structure and Dynamics
• 影响因子: 4.4
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QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase

QM/MM MD 模拟揭示了亚硝酸铜还原酶还原亚硝酸盐的异步 PCET 机制

• DOI: 10.1039/d0cp03053h
• 发表时间: 2020-09-28
• 期刊: PHYSICAL CHEMISTRY CHEMICAL PHYSICS
• 影响因子: 3.3
• 作者: Cheng, Ronny;Wu, Chun;Wang, Binju
• 通讯作者: Wang, Binju

Activation Mechanism of Corticotrophin Releasing Factor Receptor Type 1 Elucidated Using Molecular Dynamics Simulations

利用分子动力学模拟阐明促肾上腺皮质激素释放因子受体 1 型的激活机制

• DOI: 10.1021/acschemneuro.1c00126
• 发表时间: 2021
• 期刊: ACS Chemical Neuroscience
• 影响因子: 5
• 作者: Uba, Abdullahi Ibrahim;Scorese, Nicolas;Dean, Emily;Liu, Haiguang;Wu, Chun
• 通讯作者: Wu, Chun