The objective of this study is to observe the echo feature curves, vibrational dephasing, and heat capacity of a protein–hormone system taking thyroid hormone receptor-beta (THR-β) as an example. Constrained and unconstrained molecular dynamics simulations are performed by implementing the theory of velocity reassignments to probe the phase coherent state in terms of echo pulses. The constrained vibrations are incorporated by adjusting rigid bonds to all hydrogen atoms with an integrator parameter of 2 fs/step in order to reduce the degrees of freedom whereas 1 fs/step is used in the free vibrations of the atomic cluster. The nature of temperature auto-correlation functions changes so that echo feature curves also show a distinct nature in the cases of constrained and unconstrained vibrations. There is a large variation in kinetic temperature and internal potential energy in the echo time zone. The temperature rate of change of internal potential energy is the main contributor to the heat capacity of the native state protein–hormone system. The heat capacity of proteins estimated from this technique is in good agreement with the values from experiments. This study shows that triiodothyronine (T3) hormone makes some differences in heat capacity upon binding to the THR-β ligand binding domain (LBD). The physical properties of unliganded THR-β and T3-bound THR-β LBD in the cases of constrained and unconstrained dynamics are observed distinctly under the effect of anharmonicity on the phase coherent state of normal modes and the dephasing time lies in a range of 0.6–0.8 ps when the systems are perturbed suddenly.

中文翻译：

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三碘甲状腺原氨酸核受体蛋白受约束和不受约束动力学的回声移相和热容量

本研究的目的是以甲状腺激素受体-β（THR-β）为例，观察蛋白质-激素系统的回波特征曲线、振动移相和热容量。受约束和不受约束的分子动力学模拟是通过实施速度重新分配理论来探测回波脉冲方面的相位相干状态来执行的。约束振动通过调整与所有氢原子的刚性键结合，积分器参数为 2 fs/step 以降低自由度，而 1 fs/step 用于原子簇的自由振动。温度自相关函数的性质发生变化，因此回波特征曲线在受约束和不受约束的振动情况下也表现出不同的性质。回波时区的动能温度和内部势能变化很大。内部势能的温度变化率是天然状态蛋白质-激素系统热容量的主要贡献者。从该技术估计的蛋白质的热容量与实验值非常一致。该研究表明，三碘甲状腺原氨酸 (T3) 激素在与 THR-β 配体结合域 (LBD) 结合后会产生一些热容量差异。在非谐性对正常模式相位相干状态的影响下，可以清楚地观察到在约束和无约束动力学情况下未配位的 THR-β 和 T3 结合的 THR-β LBD 的物理性质，并且去相时间在 0.6 –0.8 ps 当系统突然扰动时。