The Distinct Conformational Dynamics of K-Ras and H-Ras A59G
The Distinct Conformational Dynamics of K-Ras and H-Ras A59G
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DOI：
10.1371/journal.pcbi.1000922
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发表时间：
2010-09-01
影响因子：
4.3
通讯作者：
McCammon, J. Andrew
中科院分区：
文献类型：
--
作者：
Lukman, Suryani;Grant, Barry J.;McCammon, J. Andrew
Ras蛋白通过在GTP和GDP结合构象之间切换来调节对细胞增殖和分化至关重要的信号级联。不同的Ras同工型具有独特的生理功能，其中个体同工型与不同的癌症和发育疾病相关。鉴于异构体和突变体之间的小结构差异，目前尚不清楚这些功能差异和异常特性是如何产生的。在这里，我们调查是否异构体和突变体之间的细微差异与可检测的动力学差异。广泛的分子动力学模拟表明，野生型K-Ras和突变型H-Ras A59 G本质上比野生型H-Ras更动态。关键的开关1和开关2区域沿着环3、螺旋3和环7有助于这种增强的柔性。从A59 G的结构中去除结合GTP的γ-磷酸导致在20-ns无偏模拟中自发的GTP到GDP构象转变。开关1和2区域表现出增强的灵活性和相关的运动相比，非过渡野生型H-Ras在类似的时间框架。野生型H-Ras的环3和螺旋5之间的相关运动在突变体A59 G中不存在，反映了环3区域的增强的动力学。与早期的研究结果一起，这些结果表明突变体的GTP和GDP状态之间存在较低的能量屏障。分子动力学模拟结合主成分分析可用Ras晶体结构可以用来区分配体和序列为基础的动态扰动与潜在的功能影响。此外，与不同的Ras亚型和突变体相关的特定构象的鉴定为尝试选择性干扰这些物种的异常功能的努力提供了有用的信息。
Ras proteins regulate signaling cascades crucial for cell proliferation and differentiation by switching between GTP- and GDP-bound conformations. Distinct Ras isoforms have unique physiological functions with individual isoforms associated with different cancers and developmental diseases. Given the small structural differences among isoforms and mutants, it is currently unclear how these functional differences and aberrant properties arise. Here we investigate whether the subtle differences among isoforms and mutants are associated with detectable dynamical differences. Extensive molecular dynamics simulations reveal that wild-type K-Ras and mutant H-Ras A59G are intrinsically more dynamic than wild-type H-Ras. The crucial switch 1 and switch 2 regions along with loop 3, helix 3, and loop 7 contribute to this enhanced flexibility. Removing the gamma-phosphate of the bound GTP from the structure of A59G led to a spontaneous GTP-to-GDP conformational transition in a 20-ns unbiased simulation. The switch 1 and 2 regions exhibit enhanced flexibility and correlated motion when compared to non-transitioning wild-type H-Ras over a similar timeframe. Correlated motions between loop 3 and helix 5 of wild-type H-Ras are absent in the mutant A59G reflecting the enhanced dynamics of the loop 3 region. Taken together with earlier findings, these results suggest the existence of a lower energetic barrier between GTP and GDP states of the mutant. Molecular dynamics simulations combined with principal component analysis of available Ras crystallographic structures can be used to discriminate ligand-and sequence-based dynamic perturbations with potential functional implications. Furthermore, the identification of specific conformations associated with distinct Ras isoforms and mutants provides useful information for efforts that attempt to selectively interfere with the aberrant functions of these species.