COMPUTATIONAL STUDIES OF RNA RECOGNITION AND CATALYSIS

RNA 识别和催化的计算研究

• 批准号: 8171777
• 负责人: Maria Colleen Nagan
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8171777
• 关键词: Affect; Affinity; Amber; Anticodon; Area; Binding; Buffers; Catalysis; Catalytic RNA; Cell physiology; Code; Collaborations; Complex; Computer Retrieval of Information on Scientific Projects Database; Data; Electrostatics; Funding; Future; Grant; HIV; Human; Hybrids; Hydrogen; In Vitro; Institution; Ions; Lysine-Specific tRNA; Maintenance; Mechanics; Mediating; Messenger RNA; Methods; Molecular Conformation; Peptides; Phase; Positioning Attribute; Proteins; RNA; RNA-Protein Interaction; Research; Research Personnel; Resources; Role; Simulate; Solutions; Solvents; Source; Specificity; Structure; System; Thermodynamics; Transfer RNA; Translations; United States National Institutes of Health; Water; base; cofactor; computational chemistry; computer studies; computing resources; dimer; molecular dynamics; molecular mechanics; parallel computing; planetary Atmosphere; quantum; simulation; synthetic peptide; theories; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Accurate RNA recognition by other biomolecules such as proteins, cofactors and other RNA molecules are critical to many cellular functions. Employing a variety of computational chemistry tools such as molecular dynamics simulations, quantum calculations and hybrid quantum mechanical/molecular mechanics methods, our research examines three primary areas, messenger RNA - transfer RNA (mRNA-tRNA) recognition, a key step in the translation of proteins, protein-RNA interactions in human immunodeficiency virus (HIV) and pKa calculations in catalytic RNA molecules. In the first area, the role of naturally occurring, posttranscriptionally modified bases in affecting tRNA-mRNA recognition is examined. In human tRNALys,3, we have found that a modified base at position 37 are required for maintenance of a canonical stair- stepped conformation in the anticodon bases (34-36). Ab initio studies employing natural bond orbital analysis with the M05-2X functional are underway to determine the underlying stabilizing forces and the role of modified bases at the 37th position in retaining a stair-stepped conformation in all tRNAs. Optimization of hydrogen positions at the M05-2X/6-31+G(d,p) theory level needs to be carried out for tetranucleotides and trinucleotides (dimers are ~1400 basis functions), which on our local machines can take greater than 45 days/calculation. Faster computing resources are required to make progress on this project. In the second area of research, we are examining the role of water and electrostatics in RNA-peptide recognition. In late phase Rev-RRE recognition mediates nucleocytoplasmic export of partially and unspliced HIV mRNA. From in vitro selection studies performed by Frankel and coworkers, a synthetic peptide known as RSG-1.2 has been found to bind RRE with greater affinity and specificity than the native Rev peptide. We have simulated both Rev and RSG-1.2 peptides complexed with the RRE RNA in explicit water using AMBER and have found a correlation between water structure in the peptide-RNA complexes and binding affinity. More simulations to corroborate earlier findings are required. Systems are roughly 35,000 atoms and data could be collected more efficiently employing parallel AMBER code. Lastly, in collaboration with Darrin York, we are calculating pKas in catalytic RNA molecules known as ribozymes. The thermodynamic integration methods require equilibrated starting systems. Current systems are carried out in explicit solvent (TIP4Pew), include 150 mM NaCl buffer solution beyond the neutralized RNA and are about 75,000 atoms. These systems require a number of simulated annealing rounds to equilibrate the ion atmosphere and then the RNA must be subsequently equilibrated in the presence of the buffer before TI calculations can be performed. This allocation is requested to take advantage of parallel computing facilities while also exploring optimum Teragrid platforms for future allocation requests.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 其他生物分子（例如蛋白质，辅助因子和其他生物分子）的精确RNA识别 RNA分子对于许多细胞功能至关重要。采用各种各样的 计算化学工具，例如分子动力学模拟，量子 计算和杂交量子力学/分子力学方法，我们 研究检查了三个主要区域：Messenger RNA-转移RNA（mRNA -tRNA） 识别，这是蛋白质翻译的关键步骤，蛋白RNA相互作用 催化RNA分子中的人免疫缺陷病毒（HIV）和PKA计算。 在第一个区域，自然发生的，转录后修改后的作用 在影响tRNA-mRNA识别时。在《人类的trnalys》中，我们发现了 维护规范楼梯需要37位的修改基础 在反密码子碱基中踩踏构象（34-36）。从头算研究 使用M05-2X功能的天然键轨道分析正在进行中以确定 基础稳定力和在第37位位置的修改基础的作用 在所有trnas中保留楼梯稳定的构象。优化氢 需要执行M05-2X/6-31+G（D，P）理论水平的位置 四核苷酸和三核苷酸（二聚体〜1400个基函数），这在我们的 本地机器可能需要超过45天/计算。更快的计算 需要资源来取得该项目的进展。在第二区 研究，我们正在研究水和静电在RNA肽中的作用 认出。在后期，Rev-RRE识别介导的核细胞质出口 部分和未填充的艾滋病毒mRNA。来自体外选择研究 弗兰克尔和同事，一种称为RSG-1.2的合成肽 比天然REV肽具有更大的亲和力和特异性的RRE。我们有 模拟了与RRE RNA复合的REV和RSG-1.2肽 使用琥珀色的水，发现水结构之间的相关性 肽-RNA复合物和结合亲和力。更多的模拟以证实早期 需要调查结果。系统大约为35,000个原子，可以收集数据 更有效地采用平行琥珀色代码。最后，与达林合作 约克，我们正在计算称为核酶的催化RNA分子中的PKA。这 热力学整合方法需要平衡的启动系统。当前的 系统以显式溶剂（TIP4PEW）进行，包括150毫米NACL缓冲液 超出中和RNA的溶液，约为75,000个原子。这些系统 需要许多模拟退火回合以平衡离子气氛 然后必须在缓冲液存在下将RNA平衡 在进行TI计算之前。要求进行此分配 并行计算设施的优势，同时还探索最佳teragrid 未来分配请求的平台。