Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations
Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations
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DOI：
10.1073/pnas.0812752106
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发表时间：
2009-02-10
影响因子：
11.1
通讯作者：
Carter, Charles W., Jr.
中科院分区：
文献类型：
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作者：
Laowanapiban, Poramaet;Kapustina, Maryna;Carter, Charles W., Jr.
嗜热脂肪芽孢杆菌色氨酸-tRNA 合成酶 (TrpRS) 的两个新晶体结构提供了证据，证明闭合域间铰链角需要 AMP 与焦磷酸或色氨酸亚位点占据者之间存在共价键。它们也在非平衡分子动力学模拟中观察到的一组结构的实验误差范围内，显示部分活性位点组装。此外，通过使用完全配位的TrpRS单体的开放和过渡态(PreTS)构象的弹性网络模型计算出的最小作用途径中的最高能量结构介于该模拟结构和来自未配位的PreTS的非平衡分子动力学轨迹的部分分解结构之间。这些相互一致性为分子模拟得出的推论提供了意想不到的验证。
Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamics trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.