论文标题
距离的相互作用：MB中的采摘迁移
Interaction at a Distance: Xenon Migration in Mb
论文作者
论文摘要
通过内部腔的配体的运输，例如NO或O $ _2 $，对于球状蛋白的功能至关重要，包括血红蛋白，肌红蛋白（MB），Neuroglobin，Neuroglobin，Truncated Hemoglobim或thuncated Hemogobobins或细胞蛋白。对于MB，通过X射线晶体学实验，通过实验观察到几个内部空腔（XE1至XE4）。在功能水平上，它们与配体储存和内部配体扩散有关。配体扩散和相对稳定能的障碍物在初始和最终袋中连接过渡的障碍可能会有所不同，具体取决于其余口袋的占用状态。在当前的工作中，从偏见（伞采样）和无偏分子动力学模拟中考虑了这一点。发现特定配体迁移途径的能量学可能取决于遵循过渡的方向（向前或反向）以及其他空腔的占用状态。 Furthermore, the barrier for a particular transition can depend in a non-additive fashion on the occupation of either cavity A or B or simultaneous occupation of both cavities, A and B. Multiple repeats for the Xe1$\rightarrow$Xe2 transition reveals that the activation barrier is a distribution of barrier heights rather than one single value which is confirmed by a distribution of transition times for the same transition from unbiased simulations.该过渡的动态跨相关图表明，相邻残基或通过空间之间发生相关运动。残基PHE138的特征是XE1和XE2之间的门，对于Xe1 $ \ rightarrow $ XE2过渡。还发现，内部空腔的体积沿扩散途径有所不同，该途径指向配体和蛋白质之间的动态通信。这些发现是在蛋白质变构的背景下讨论的。
The transport of ligands, such as NO or O$_2$, through internal cavities is essential for the function of globular proteins, including hemoglobin, myoglobin (Mb), neuroglobin, truncated hemoglobins, or cytoglobin. For Mb, several internal cavities (Xe1 through Xe4) were observed experimentally through X-ray crystallography experiments. At a functional level, they were linked to ligand storage and internal ligand diffusion. Barriers for ligand diffusion and relative stabilization energies for the ligand in the initial and final pocket linking a transition may differ depending on the occupation state of the remaining pockets. This is considered in the present work from biased (umbrella sampling) and unbiased molecular dynamics simulations. It is found that the energetics of a particular ligand migration pathway may depend on the direction in which the transition is followed (forward or reverse) and the occupation state of other cavities. Furthermore, the barrier for a particular transition can depend in a non-additive fashion on the occupation of either cavity A or B or simultaneous occupation of both cavities, A and B. Multiple repeats for the Xe1$\rightarrow$Xe2 transition reveals that the activation barrier is a distribution of barrier heights rather than one single value which is confirmed by a distribution of transition times for the same transition from unbiased simulations. Dynamic cross correlation maps for this transition demonstrate that correlated motions occur between adjacent residues or through space. Residue Phe138 is characterized as a gate between Xe1 and Xe2 for the Xe1$\rightarrow$Xe2 transition. It is also found that the volumes of the internal cavities vary along the diffusion pathway which points towards dynamic communication between the ligand and the protein. The findings are discussed in the context of protein allostery.
