COMPUTATIONAL STUDIES OF RNA RECOGNITION AND CATALYSIS

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目及 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 RNA被其他生物分子如蛋白质、辅因子和其他生物分子准确识别。 RNA分子对许多细胞功能至关重要。采用各种 计算化学工具，如分子动力学模拟，量子化学模拟， 计算和混合量子力学/分子力学方法，我们的 研究主要涉及三个领域，信使RNA -转移RNA（mRNA-tRNA） 识别，蛋白质翻译的关键步骤，蛋白质-RNA相互作用， 人类免疫缺陷病毒（HIV）和催化RNA分子的pKa计算。 在第一个领域，自然发生的，转录后修饰的碱基的作用， 在影响tRNA-mRNA识别的研究。在人类tRNALys，3，我们已经发现 在位置37处需要修改的基部以维护规范楼梯- 反密码子碱基中的阶梯构象（34-36）。从头算研究采用 正在进行M05-2X功能的自然键轨道分析，以确定 潜在的稳定力量和作用的修改基地在第37位， 在所有的tRNA中保持阶梯状构象。氢气优化 在M05-2X/6-31+G（d，p）理论水平上的位置， 四核苷酸和三核苷酸（二聚体是~1400个基函数），根据我们的研究， 本地计算机可能需要超过45天/计算。更快的计算 要在这一项目上取得进展，需要资源。的所述第二区域中 研究，我们正在研究水和静电在RNA肽中的作用， 识别.在晚期阶段，Rev-RRE识别介导了 部分和未剪接的HIV mRNA。来自体外选择研究， Frankel和同事们发现，一种称为RSG-1.2的合成肽 以比天然Rev肽更大的亲和力和特异性结合RRE。我们有 模拟Rev和RSG-1.2肽与RRE RNA复合， 水使用琥珀，并发现了水结构之间的相关性， 肽-RNA复合物和结合亲和力。更多的模拟来证实早些时候 需要调查结果。系统大约有35，000个原子，可以收集数据 更有效地使用并行AMBER码。最后，与Darrin合作， 约克，我们正在计算催化RNA分子，即核酶的pKa。的 热力学积分方法需要平衡的起动系统。电流 系统在显式溶剂（TIP 4Pew）中进行，包括150 mM NaCl缓冲液 溶液超过中和的RNA，大约有75，000个原子。这些系统 需要多个模拟退火循环来平衡离子气氛 然后RNA必须随后在缓冲液存在下平衡 在TI计算可以执行之前。这一分配要求采取 并行计算设施的优势，同时也探索最佳的Teragrid 未来的分配请求。

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.