Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
J Am Chem Soc. 2011 Jun 8;133(22):8753-61. doi: 10.1021/ja202587a. Epub 2011 May 17.
The internal cavity matrix of globins plays a key role in their biological function. Previous studies have already highlighted the plasticity of this inner network, which can fluctuate with the proteins breathing motion, and the importance of a few key residues for the regulation of ligand diffusion within the protein. In this Article, we combine all-atom molecular dynamics and coarse-grain Brownian dynamics to establish a complete mechanical landscape for six different globins chain (myoglobin, neuroglobin, cytoglobin, truncated hemoglobin, and chains α and β of hemoglobin). We show that the rigidity profiles of these proteins can fluctuate along time, and how a limited set of residues present specific mechanical properties that are related to their position at the frontier between internal cavities. Eventually, we postulate the existence of conserved positions within the globin fold, which form a mechanical nucleus located at the center of the cavity network, and whose constituent residues are essential for controlling ligand migration in globins.
球蛋白的内腔基质在其生物功能中起着关键作用。先前的研究已经强调了这个内部网络的可变性，它可以随着蛋白质的呼吸运动而波动，以及几个关键残基对于调节蛋白质内部配体扩散的重要性。在本文中，我们结合全原子分子动力学和粗粒布朗动力学，为六个不同的球蛋白链（肌红蛋白、神经球蛋白、细胞球蛋白、截断血红蛋白以及血红蛋白的α和β链）建立了一个完整的力学景观。我们表明，这些蛋白质的刚性谱可以随时间波动，以及一组有限的残基如何具有与其在内部空腔边界位置相关的特定力学特性。最终，我们假设球蛋白折叠中存在保守位置，它们形成一个位于空腔网络中心的力学核心，其组成残基对于控制球蛋白中的配体迁移至关重要。
