Theoretical and MD Simulation Studies of U1A-RNA Binding and Specificity

U1A-RNA 结合和特异性的理论和 MD 模拟研究

• 批准号: 7014174
• 负责人: DAVID Lewis BEVERIDGE
• 金额: $ 24.2万
• 依托单位: WESLEYAN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-01-01 至 2008-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7014174
• 关键词: RNA binding protein; biophysics; chemical structure function; computer simulation; conformation; fluorescence polarization; gene mutation; intermolecular interaction; mathematical model; model design /development; molecular assembly /self assembly; molecular dynamics; molecular energy level; nuclear magnetic resonance spectroscopy; solutions; thermodynamics; time resolved data

DESCRIPTION (provided by applicant): The objective of the proposed project is to elucidate the mechanism of U1A protein stem loop RNA binding based on computational models of dynamical structures obtained from molecular dynamics (MD) simulation and corresponding continuum electrostatics and free energy calculations using several methods as a cross check on results. U1A is a prototype of a large class of RNA binding proteins which utilize a characteristic structural motif comprised of an sandwich fold that forms a four-stranded antiparallel -sheet supported by two -helices known as the RNA recognition motif (RRM) or RNA binding domain (RBD). The U1A RNA complexation process appears to be multistep affair in which the outstanding problems are the mechanism of structural adaptation (induced fit or conformational capture), local U1A - RNA contacts vs. cooperative effects in the binding event, solvent release and magnitude of the entropy involved, and the contribution of various chemical forces to binding affinity. Structural adaptation effects will be studied by comparison of the calculated dynamical structures for U1A and RNA free in solution with those of the complexed state. The cooperative networks of protein residues involved in RNA binding will be investigated based on calculated cross correlations of atomic fluctuations from the MD, which reveal through space domain correlations. The link between dynamical structure and functional energetics will be established using an additive free energy component calculation of free energy, enthalpy and entropy resolved into contributions from various amino acids, ribonucleotide bases and into electrostatic, van der Waals repulsions and dispersion terms due to solute and solvation. The proposed research will focus initially on U1A RNA and a set of protein mutants and RNA base replacements in regions critical to observed affinity and specificity and in a later phase be extended to a series of related complexes for which initial structural determination and observed binding affinities and specificities indicate to be critical for a full understanding of RRM/RBD RNA complex formation. The proposed research is closely correlated with concurrent experiment based bio-organic and biophysical chemistry, time resolved fluorescence anisotropy and NMR structure determination on U1A RNA and related systems currently in progress in the Chemistry Department and Molecular Biophysics Training Program at Wesleyan University.

描述（由申请人提供）：拟议项目的目的是基于分子动力学（MD）模拟和相应的连续静电和自由能计算获得的动态结构计算模型，使用多种方法对结果进行交叉检查，阐明U1A蛋白茎环RNA结合的机制。 U1A 是一大类 RNA 结合蛋白的原型，其利用由夹心折叠组成的特征结构基序，形成由两个螺旋支撑的四链反平行片，称为 RNA 识别基序 (RRM) 或 RNA 结合域 (RBD)。 U1A RNA 络合过程似乎是多步骤的，其中突出的问题是结构适应机制（诱导配合或构象捕获）、局部 U1A - RNA 接触与结合事件中的协同效应、溶剂释放和所涉及的熵的大小，以及各种化学力对结合亲和力的贡献。将通过比较溶液中 U1A 和 RNA 的计算动态结构与复合状态的动态结构来研究结构适应效应。参与 RNA 结合的蛋白质残基的协作网络将基于计算出的 MD 原子涨落互相关性进行研究，该互相关性通过空间域相关性揭示。动态结构和功能能量学之间的联系将通过自由能、熵和熵的附加自由能分量计算来建立，这些自由能分量计算可分解为各种氨基酸、核糖核苷酸碱基的贡献以及由于溶质和溶剂化而产生的静电、范德华排斥和色散项。拟议的研究最初将重点关注对观察到的亲和力和特异性至关重要的区域中的 U1A RNA 和一组蛋白质突变体和 RNA 碱基替换，并在后期扩展到一系列相关复合物，这些复合物的初始结构确定和观察到的结合亲和力和特异性表明对于全面了解 RRM/RBD RNA 复合物的形成至关重要。拟议的研究与卫斯理大学化学系和分子生物物理学培训项目目前正在进行的基于生物有机和生物物理化学、时间分辨荧光各向异性和 U1A RNA 的 NMR 结构测定以及相关系统的并行实验密切相关。