Leu Bogdan M, Zhang Yong, Bu Lintao, Straub John E, Zhao Jiyong, Sturhahn Wolfgang, Alp E Ercan, Sage J Timothy
Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts, USA.
Biophys J. 2008 Dec 15;95(12):5874-89. doi: 10.1529/biophysj.108.138198. Epub 2008 Oct 3.
Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.
构象灵活性对于蛋白质的功能行为至关重要。我们使用扎卡伊引入的有效力常数——弹性，来量化这种灵活性。位点选择性实验和计算方法使我们能够确定血红素蛋白活性位点的弹性。利用核共振振动光谱法测定的血红素铁的振动态密度提供了铁环境弹性的直接实验测量值，我们将其与分子动力学模拟中原子均方位移的温度依赖性得出的值进行了定量比较。太赫兹频率范围内的振动简正模式主导着弹性。实验和计算方法均发现，细胞色素c的弹性高于肌红蛋白，我们将其归因于前者蛋白质中与肽的共价连接数量增加。对于肌红蛋白，铁环境的弹性大于先前使用中子散射确定的氢位点的平均弹性。实验结果表明，氧化后细胞色素c的弹性略有降低，尽管这种变化比先前对细菌细胞色素c的穆斯堡尔研究报告的要小，且模拟结果未重现这一变化。氧化态对细胞色素c计算出的压缩性也没有显著影响，尽管预计肌红蛋白的压缩性略大。
