Green Center for Systems Biology, Lyda Hill Department of Bioinformatics, Department of Biophysics, Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas.
Green Center for Systems Biology, Lyda Hill Department of Bioinformatics, Department of Biophysics, Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas.
Biophys J. 2023 Oct 3;122(19):3882-3893. doi: 10.1016/j.bpj.2023.08.010. Epub 2023 Aug 19.
Allostery, the transfer of information between distant parts of a macromolecule, is a fundamental feature of protein function and regulation. However, allosteric mechanisms are usually not explained by protein structure, requiring information on correlated fluctuations uniquely accessible to molecular simulation. Existing work to extract allosteric pathways from molecular dynamics simulations has focused on thermodynamic correlations. Here, we show how kinetic correlations encode complementary information essential to explain observed variations in allosteric regulation. We applied kinetic and thermodynamic correlation analysis on atomistic simulations of H, K, and NRas isoforms in the apo, GTP, and GDP-bound states of Ras protein, with and without complexing to its downstream effector, Raf. We show that switch I and switch II are the primary components of thermodynamic and kinetic allosteric networks, consistent with the key roles of these two motifs. These networks connect the switches to an allosteric loop recently discovered from a crystal structure of HRas. This allosteric loop is inactive in KRas, but is coupled to the hydrolysis arm switch II in NRas and HRas. We find that the mechanism in the latter two isoforms are thermodynamic and kinetic, respectively. Binding of Raf-RBD further activates thermodynamic allostery in HRas and KRas but has limited effect on NRas. These results indicate that kinetic and thermodynamic correlations are both needed to explain protein function and allostery. These two distinct channels of allosteric regulation, and their combinatorial variability, may explain how subtle mutational differences can lead to diverse regulatory profiles among enzymatic proteins.
变构作用是一种基本的蛋白质功能和调节机制，它可以在大分子的远程部分之间传递信息。然而，变构机制通常不能用蛋白质结构来解释，这就需要分子模拟中特有的关于相关波动的信息。从分子动力学模拟中提取变构途径的现有工作主要集中在热力学相关性上。在这里，我们展示了如何从原子模拟中提取变构途径，这些模拟是关于 H、K 和 NRas 同工型在 Ras 蛋白的 apo、GTP 和 GDP 结合状态下，以及与其下游效应物 Raf 结合时的变构调节的。我们表明，开关 I 和开关 II 是热力学和动力学变构网络的主要组成部分，这与这两个基序的关键作用一致。这些网络将开关与最近从 HRas 晶体结构中发现的变构环连接起来。该变构环在 KRas 中不活跃，但在 NRas 和 HRas 中与水解臂开关 II 相连。我们发现后两种同工型的机制分别是热力学和动力学的。Raf-RBD 的结合进一步激活了 HRas 和 KRas 的热力学变构作用，但对 NRas 的影响有限。这些结果表明，解释蛋白质功能和变构作用都需要热力学和动力学相关性。这两种不同的变构调节通道及其组合的可变性，可能解释了为什么微小的突变差异会导致酶蛋白之间存在不同的调节模式。
