Singh Priya, Sarkar Subir K, Bandyopadhyay Pradipta
School of Physical Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India.
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India.
J Chem Phys. 2014 Jul 7;141(1):015103. doi: 10.1063/1.4885726.
We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energy--along with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peak in the temperature dependence of the computed specific heat. This is corroborated further by the structural signatures of folding in the distributions for radius of gyration and the number of native contacts as a function of temperature. The potentials of mean force are also calculated for these variables, both separately and jointly. A local free energy minimum, in addition to the global minimum, is found in a temperature range substantially below the folding temperature. The free energy at this second minimum is approximately 5 k(B)T higher than the value at the global minimum.
我们展示了对20个残基的微型蛋白质色氨酸笼（TC5b）在水中折叠/去折叠转变进行的高统计平衡研究结果。使用了ECEPP/3力场，并通过溶剂可及表面积方法处理与水的相互作用。采用王-朗道型模拟来计算状态密度以及在固定能量值下回转半径和天然接触数各种值的条件概率，并对其收敛性进行系统检查。所有感兴趣的热力学量均根据此信息计算得出。折叠-去折叠转变对应于计算出的比热对温度依赖性的一个峰值。回转半径分布和天然接触数随温度变化的折叠结构特征进一步证实了这一点。还分别和联合计算了这些变量的平均力势。在远低于折叠温度的温度范围内，除了全局最小值外，还发现了一个局部自由能最小值。这个第二最小值处的自由能比全局最小值处的值高约5k(B)T。
