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A-Site Residues Move Independently from P-Site Residues in all-Atom Molecular Dynamics Simulations of the 70S Bacterial Ribosome

机译:在70S细菌核糖体的全原子分子动力学模拟中,A部位残基独立于P部位残基移动

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摘要

The ribosome is a large macromolecular machine, and correlated motion between residues is necessary for coordinating function across multiple protein and RNA chains. We ran two all-atom, explicit solvent molecular dynamics simulations of the bacterial ribosome and calculated correlated motion between residue pairs by using mutual information. Because of the short timescales of our simulation (ns), we expect that dynamics are largely local fluctuations around the crystal structure. We hypothesize that residues that show coupled dynamics are functionally related, even on longer timescales. We validate our model by showing that crystallographic B-factors correlate well with the entropy calculated as part of our mutual information calculations. We reveal that A-site residues move relatively independently from P-site residues, effectively insulating A-site functions from P-site functions during translation.
机译:核糖体是大型的大分子机器,残基之间的相关运动对于协调跨越多个蛋白质和RNA链的功能是必需的。我们运行了细菌核糖体的两个全原子,显式溶剂分子动力学模拟,并通过使用互信息计算了残基对之间的相关运动。由于仿真的时间尺度较短(ns),因此我们期望动力学主要是晶体结构周围的局部波动。我们假设显示耦合动力学的残基在功能上相关,即使在更长的时间范围内。我们通过证明晶体学B因子与作为互信息计算一部分而计算出的熵很好地相关来验证我们的模型。我们揭示了A位残基相对于P位残基相对独立地移动,从而在翻译过程中有效地将A位功能与P位功能隔离开来。

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