采样长时间尺度蛋白质运动:OSRW模拟活性位点循环在formyl-CoA:oxalate CoA转移酶中的 conformational自由能量
Sangbae Lee1, Mengen Chen, Wei Yang
1Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
Journal of the American Chemical Society
|May 8, 2010
概括
坐标空间随机步行 (OSRW) 模拟显示,formyl-CoA:oxalate CoA转移酶 (FRC) 中的循环构造在能量上是相似的. 突变性研究表明,OSRW可以预测改变的循环动态和减少的酶效率.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 酶学 是一种酶学.
背景情况:
- 酶活性位点的 conformational 变化对于催化功能至关重要.
- 在formyl-CoA:oxalate CoA转移酶 (FRC) 中的四甘油循环在其催化循环期间经历了显著的结构变化.
- 射线晶体学提供静态快照,需要计算方法来研究动态过程.
研究的目的:
- 通过使用直角空间随机步行 (OSRW) 模拟,在FRC中计算"开放"和"闭合"循环构造的相对自由能量.
- 为了确定野生类型FRC中这些构造之间的相互转换的能量障碍.
- 通过模拟FRC变体 (G258A,G259A,G260A,G261A) 来研究四甘氨酸循环内的特定甘氨酸残留物的能量贡献.
主要方法:
- 使用直角空间随机步行 (OSRW) 模拟来建模结构变化和估计自由能量景观.
- 对于野生类型的FRC和现场定向突变 (G258A,G259A,G260A,G261A) 进行了自由能量计算.
- 模拟结果与实验动力学数据 (k ((cat) /K ((M)) 和X射线晶体学结构观测相关.
主要成果:
- OSRW模拟表明,野生类型FRC中的"开放"和"闭合"循环构造具有类似的自由能量.
- 在野生类型的FRC中,循环相互转换的计算能量障碍与实验性酶周转率保持一致.
- 对于具有减少催化效率的FRC变体,OSRW模拟确定了额外的低能环形状,包括G260AFRC的一种匹配的实验结构.
结论:
- OSRW模拟是探索构造空间和量化功能重要酶循环的自由能量的一个强大的工具.
- 该方法准确地模拟了突变对循环动态和酶效率的影响.
- 模拟提供了与循环形状变化相关的侧链运动的见解,使得研究长时间范围的动态成为可能.
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