Large-scale simulations of ribosomal decoding

核糖体解码的大规模模拟

• 批准号: 7086803
• 负责人: Karissa Y Sanbonmatsu
• 金额: $ 26.7万
• 依托单位: LOS ALAMOS NAT SECTY-LOS ALAMOS NAT LAB
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-07-01 至 2010-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7086803
• 关键词: aminoglycoside antibiotics; biochemistry; computer simulation; conformation; hydrogen bond; molecular dynamics; mutant; nucleic acid sequence; ribosomes; transfer RNA

DESCRIPTION (provided by applicant): The ribosome implements the genetic code by translating information residing in nucleic acid into protein, a process which lies at the heart of all organisms. Within the translational cycle, the decoding step distinguishes the ribosome from other molecular machines. During this step, the ribosome must discriminate between correct and incorrect transfer RNAs, accepting only those whose amino acid corresponds to the messenger RNA codon, as prescribed by the genetic code. Recent x-ray structural data has unveiled the local and global conformational changes involved in correct transfer RNA recognition by the ribosome; however, the order of events and cause-effect relation between local and global changes is not clear. We will use large-scale all-atom molecular dynamics simulations, validated by biochemical and x-ray data, to study the relation between local decoding interactions and large-scale conformational changes of the small ribosomal subunit. In particular, (1) We will use large-scale computer simulations to investigate the relative importance of codon-anticodon-ribosome hydrogen bonds at the decoding center on the open-to-closed conformational change of the small ribosomal subunit. Predictions based on these simulations will be tested biochemically. (2) We will use replica exchange molecular dynamics to investigate the flipping out of the decoding bases, A1492-A1493, from small subunit helix 44 in the presence of cognate tRNA, near-cognate tRNA, aminoglycoside antibiotics and resistance mutants. We will again compare with antibiotic-oligo binding. (3) We will investigate the order of events during tRNA recognition, in atomic detail, by testing whether the above base-flipping induces the open-to-closed conformational change of the small ribosomal subunit, with and without, decoding antibiotics. As alternative strategies, We will (1) improve sampling by using a mesoscale model, which couples small scale simulations of the decoding center, to information obtained from large scale simulations, (2) Perform all-atom normal mode calculations to study the effect of decoding base flipping and antibiotics on the overall motion of the ribosome, and (3) Attempt to modify force field potentials, by slightly modifying the delta gamma and epsilon torsional parameter coefficients. Our simulations will serve as a template for other researchers to perform million atom simulations. We will directly address the issues of time scale limitations, kinetic trapping and force field accuracy, with enhanced sampling simulation techniques and iteration between experimental data and simulation.

描述(申请人提供)：核糖体通过将存在于核酸中的信息翻译成蛋白质来实现遗传密码，这一过程位于所有生物体的心脏。在翻译周期中，解码步骤将核糖体与其他分子机器区分开来。在这一步骤中，核糖体必须区分正确和不正确的转移RNA，只接受其氨基酸对应于信使RNA密码子的那些，按照遗传密码的规定。最近的X射线结构数据揭示了核糖体正确识别转移RNA所涉及的局部和全局构象变化；然而，局部和全局变化之间的事件顺序和因果关系尚不清楚。我们将使用大规模的全原子分子动力学模拟，并经过生化和X射线数据的验证，来研究局部解码相互作用与核糖体小亚基的大尺度构象变化的关系。具体地说，(1)我们将使用大规模的计算机模拟来研究解码中心的密码子-反密码子-核糖体氢键对核糖体小亚基由开到闭的构象变化的相对重要性。基于这些模拟的预测将得到生化测试。(2)我们将利用复制交换分子动力学研究在同源tRNA、近同源tRNA、氨基糖苷类抗生素和耐药突变体存在的情况下，A1492-A1493从小亚单位螺旋44翻转出来的情况。我们将再次与抗生素-寡聚结合进行比较。(3)我们将通过测试上述碱基翻转是否诱导小核糖体亚基在解码抗生素和不使用抗生素的情况下由开到闭的构象变化，详细地研究tRNA识别过程中的事件顺序。作为替代策略，我们将(1)通过使用中尺度模型来改进采样，该模型将解码中心的小规模模拟耦合到从大规模模拟中获得的信息，(2)执行全原子简正模计算，以研究解码碱基翻转和抗生素对核糖体整体运动的影响，以及(3)尝试通过略微修改增量伽马和epsilon扭转参数系数来修改力场势能。我们的模拟将作为其他研究人员执行百万原子模拟的模板。我们将通过改进的采样模拟技术以及实验数据和模拟之间的迭代，直接解决时间尺度限制、动力学陷阱和力场精度问题。