Ghosh Rikhia, Banerjee Saikat, Hazra Milan, Roy Susmita, Bagchi Biman
SSCU, Indian Institute of Science, Bangalore 560012, India.
J Chem Phys. 2014 Dec 14;141(22):22D531. doi: 10.1063/1.4902821.
Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (∼80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of ∼2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ⟨δMW(0)δMW(t)⟩ is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (∼50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work.
自柯克伍德时代以来，人们观察到蛋白质水溶液的介电常数在大小上与纯水（约80）存在偏差，且极化衰减较慢，这些一直是备受关注、充满争议和辩论的主题。大多数常见蛋白质具有较大的永久偶极矩（通常超过100德拜），这会影响甚至远处水分子的结构和动力学，进而影响溶液的集体极化涨落，而这反过来又会显著改变溶液的介电常数。因此，极化涨落的距离依赖性能够为生物水的本质提供重要见解。我们通过研究四种具有不同特性和不同大小的蛋白质的水溶液来探索这些方面，这四种蛋白质分别是鸡肌动蛋白头部亚结构域（HP - 36）、免疫球蛋白结合结构域蛋白G（GB1）、鸡蛋清溶菌酶（LYS）和肌红蛋白（MYO）。我们模拟了由单个蛋白质分子和20000 - 30000个水分子组成的相当大的系统（根据蛋白质大小而变化），浓度范围约为2 - 3 mM。我们发现，与纯水相比，该系统计算得到的介电常数在所有情况下都有显著增加。发现水的总偶极矩自时间关联函数⟨δMW(0)δMW(t)⟩对蛋白质的性质敏感。令人惊讶地是，发现蛋白质的偶极矩与水分子的总偶极矩仅存在弱耦合。蛋白质周围水分子的逐壳层分解显示，第一层的密度高于后续层。我们还计算了连续层的启发式有效介电常数，发现与蛋白质相邻的层的值要低得多（约50）。然而，随着层数增加，介电常数逐渐增大，最终在远离蛋白质4 - 5层处达到接近本体的值。我们还计算了逐壳层取向关联函数和四面体序参量，以了解水的局部动力学和结构重排。本文详细讨论了提供逐壳层局部介电常数计算简单方法的理论分析以及这些发现的意义。
