Coupling between hydration layer dynamics and unfolding kinetics of HP-36
Coupling between hydration layer dynamics and unfolding kinetics of HP-36
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DOI：
10.1063/1.2335451
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发表时间：
2006-08-28
影响因子：
4.4
通讯作者：
Bagchi, Biman
中科院分区：
文献类型：
--
作者：
Bandyopadhyay, Sanjoy;Chakraborty, Sudip;Bagchi, Biman
我们进行了原子分子动力学模拟的水溶液中的HP-36在300 K在其原生状态，以及在高温下，以探索解折叠动力学的蛋白质及其与周围的水的运动的相关性it. On增加温度的部分解折叠熔融球状态形成的最小的α螺旋（螺旋2）展开成线圈。据观察，展开是在残基Phe-18周围开始的，其在展开期间显示出急剧的位移。我们已经注意到，蛋白质的解折叠会影响蛋白质表面附近的水的密度。此外，水在蛋白质水化层中的动力学已被发现与展开过程的时间演化密切相关。我们已经引入并计算了位移时间相关函数，以监测水运动相对于蛋白质骨架在展开过程中的变化。我们发现，螺旋2的展开与它周围的水的流动性增加有关，与其他两个螺旋周围的水相比。我们还探讨了蛋白质的二级结构特异性和位点特异性溶剂化动力学的微观方面。计算结果表明，展开影响的溶剂化动力学的蛋白质分子在一个异质的方式取决于极性探针残基的位置。这似乎与最近的实验结果一致。(c)2006年，美国物理学会。
We have performed atomistic molecular dynamics simulations of aqueous solutions of HP-36 at 300 K in its native state, as well as at high temperatures to explore the unfolding dynamics of the protein and its correlation with the motion of water around it. On increasing the temperature a partially unfolded molten globule state is formed where the smallest alpha helix (helix 2) unfolds into a coil. It is observed that the unfolding is initiated around the residue Phe-18 which shows a sharp displacement during unfolding. We have noticed that the unfolding of the protein affects the density of water near the protein surface. Besides, the dynamics of water in the protein hydration layer has been found to be strongly correlated with the time evolution of the unfolding process. We have introduced and calculated a displacement time correlation function to monitor the change in water motion relative to the protein backbone during unfolding. We find that the unfolding of helix 2 is associated with an increase in mobility of water around it as compared to water around the other two helices. We have also explored the microscopic aspects of secondary structure specific and site specific solvation dynamics of the protein. The calculations reveal that unfolding influences the solvation dynamics of the protein molecule in a heterogeneous manner depending on the location of the polar probe residues. This seems to be in agreement with recent experimental findings. (c) 2006 American Institute of Physics.