RNA-ligand interactions: simulation and experiment

RNA-配体相互作用：模拟和实验

• 批准号: 8737909
• 负责人: Thomas E. Cheatham
• 金额: $ 52.48万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-30 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8737909
• 关键词: 2-Aminopurine; Adopted; Antibiotics; Area; Back; Benchmarking; Binding; Biological; Biological Models; Biology; Catalysis; Cells; Collaborations; Comparative Study; Computer Simulation; Computing Methodologies; DNA; Data; Databases; Development; Disease; Electrostatics; Elements; Enzymes; Error Sources; Escherichia coli; Fluorescence; Gene Expression; Genetic Transcription; Goals; Guanosine Triphosphate Phosphohydrolases; In Vitro; Individual; Ions; Knowledge; Laboratories; Ligand Binding; Ligands; Measurement; Measures; Metabolism; Methods; Modeling; Modification; Molecular; Monitor; Nucleic Acids; Nucleotides; Outcome; Play; Property; Protein Binding; Protein Biosynthesis; Proteins; Protocols documentation; RNA; RNA Folding; RNA-Protein Interaction; Recruitment Activity; Regulatory Pathway; Relaxation; Reporting; Ribosomes; Role; Sampling; Simulate; Site; Solutions; Structure; System; Testing; Time; Torsion; Work; base; biophysical techniques; flexibility; improved; molecular dynamics; mutant; next generation; novel; prototype; receptor; research study; sensor; simulation; small hairpin RNA; small molecule; stem; theories; tool; varkud satellite ribozyme

DESCRIPTION (provided by applicant): This project represents collaboration between established computational and experimental labs to combine biophysical methods to produce, assess, and validate the next generation of biomolecular simulation methods to study RNA molecules. In the past decade our knowledge of the widely varied functional roles of RNA molecules has exploded; RNA molecules can be regulatory or catalytic, can act as sensors, can both up- and down- regulate gene expression, and have great potential as targets for control by exogenous ligands in all phyla. The structures of RNA are modular and contain a mix of structural elements including short duplex regions, hairpin loops, internal bulges, four-way junctions, and receptor sites. These structural elements, along with their conformational changes and dynamics, are the keys to RNA function. However, these functionally important structural, dynamic, and energetic properties cannot yet be reliably predicted or fully experimentally understood. To characterize RNA structures, their structural transitions, and their local and global dynamics, a synergy of simulation and experiment is necessary. The goal of this project is to use theoretical and experimental biophysical methods to more fully develop biomolecular simulation tools to accurately describe RNA molecules, especially how they interact with small molecules, ions, and proteins, using experimental data as a benchmark to assess, validate and improve the models. Aim 1 is built around the Varkud satellite ribozyme Stem loop V RNA (SL5). This small RNA hairpin has a flexible loop that undergoes a conformational change when it binds to ions, and acts as a model system to test electrostatics, sampling, structural accuracy, and the ability of the simulations to model the subtle influences of ions on the structure and dynamics. New molecular dynamics simulations based on the latest AMBER nucleic acid force fields (ff99+parmbsc0) will assess the force field parameters and apply novel biased enhanced sampling methods to more richly sample the configurational space of the RNA loop. At the same time, NMR will further refine the solution structure, and 13C NMR relaxation experiments will measure dynamics of SL5 in the presence of different ions. Aim 2 expands the RNA model systems to the GTPase center (GAC) of the ribosome, to model ion binding, electrostatics, and antibiotic binding. NMR is used for structure and dynamics determination, 2-aminopurine fluorescence reports on folding of the GAC, and MD begins with crystal structures of the 58 nucleotide GAC. These two aims are synergistic: primary NMR data are back- calculated from the MD simulations to assess the accuracy and precision of the computational methods through direct comparison to the measured NMR data. Aim 3 takes the outcome of the comparative study to identify deficiencies and implement improvements. Force field modifications and conformational sampling will be facilitated through Hamiltonian replica exchange molecular dynamics and finally applied to the tertiary folding of the GAC RNA.

描述（由申请人提供）：该项目代表了已建立的计算和实验实验室之间的合作，以联合收割机生物物理方法来产生，评估和验证下一代生物分子模拟方法来研究RNA分子。 在过去的十年中，我们对RNA分子广泛多样的功能作用的认识已经爆炸; RNA分子可以是调节性的或催化性的，可以充当传感器，可以上调和下调基因表达，并且在所有门中具有作为外源配体控制的靶点的巨大潜力。RNA的结构是模块化的，并且包含结构元件的混合，包括短双链体区域、发夹环、内部凸起、四向连接和受体位点。这些结构元件，沿着它们的构象变化和动力学，是RNA功能的关键。然而，这些功能上重要的结构，动态和能量特性还不能可靠地预测或完全实验理解。为了表征RNA结构，它们的结构转换，以及它们的局部和全局动力学，模拟和实验的协同作用是必要的。该项目的目标是使用理论和实验生物物理方法，更全面地开发生物分子模拟工具，以准确描述RNA分子，特别是它们如何与小分子，离子和蛋白质相互作用，使用实验数据作为基准来评估，验证和改进模型。 Aim 1是围绕Varkud卫星核酶Stem loop V RNA（SL 5）构建的。这种小RNA发夹有一个灵活的环，当它与离子结合时会发生构象变化，并作为一个模型系统来测试静电，采样，结构准确性以及模拟离子对结构和动力学的微妙影响的能力。基于最新AMBER核酸力场（ff 99 + parmbsc 0）的新分子动力学模拟将评估力场参数，并应用新的偏置增强采样方法来更丰富地采样RNA环的构型空间。同时，NMR将进一步细化溶液结构，13 C NMR弛豫实验将测量SL 5在不同离子存在下的动力学。目的2将RNA模型系统扩展到核糖体的GTdR中心（GAC），以模拟离子结合、静电和抗生素结合。NMR用于结构和动力学测定，2-氨基嘌呤荧光报告GAC的折叠，MD从58个核苷酸GAC的晶体结构开始。这两个目标是协同的：从MD模拟反算原始NMR数据，以通过与测量的NMR数据的直接比较来评估计算方法的准确度和精确度。目标3采用比较研究的结果，以确定不足之处并实施改进。力场的修改和构象采样将促进通过哈密尔顿副本交换分子动力学，并最终应用到GAC RNA的三级折叠。

项目成果

Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.

• DOI: 10.1016/j.jmb.2016.09.015
• 发表时间: 2016-11-06
• 期刊: JOURNAL OF MOLECULAR BIOLOGY
• 影响因子: 5.6
• 作者: Welty, Robb;Hall, Kathleen B.
• 通讯作者: Hall, Kathleen B.

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent.

• DOI: 10.1021/ja5032776
• 发表时间: 2014-10-08
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Hai Nguyen;Maier, James;Huang, He;Perrone, Victoria;Simmerling, Carlos
• 通讯作者: Simmerling, Carlos

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

Varkud卫星RNA的茎环V在存在单价离子的情况下表现出Mg（2+）结构的特征。

• DOI: 10.1021/acs.jpcb.5b05190
• 发表时间: 2015-09-24
• 期刊: The journal of physical chemistry. B
• 作者: Bergonzo C;Hall KB;Cheatham TE 3rd
• 通讯作者: Cheatham TE 3rd

Formation of Tertiary Interactions during rRNA GTPase Center Folding.

rRNA GTPase 中心折叠过程中三级相互作用的形成。

• DOI: 10.1016/j.jmb.2015.07.013
• 发表时间: 2015
• 期刊: Journal of molecular biology
• 影响因子: 5.6
• 作者: Rau,MichaelJ;Welty,Robb;TomStump,W;Hall,KathleenB
• 通讯作者: Hall,KathleenB