Długosz Maciej, Antosiewicz Jan M
Center of New Technologies, University of Warsaw , Żwirki i Wigury 93, Warsaw 02-089, Poland.
Department of Biophysics, Faculty of Physics, University of Warsaw , Żwirki i Wigury 93, Warsaw 02-089, Poland.
J Chem Theory Comput. 2014 Jun 10;10(6):2583-90. doi: 10.1021/ct500124r.
We have investigated effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules. For that, we have performed rigid-body Brownian dynamics simulations of aqueous solutions of hen egg-white lysozyme (HEWL), at concentrations ranging from 1.25 mg/mL to 250 mg/mL and evaluated the lysozyme's self-diffusion. In the long time limit (above 1 μs), the protein's translational diffusion is isotropic, regardless the solution concentration. However, on the time scale of the order of up to hundreds of nanoseconds, the anisotropic translational diffusion is observed, with the transition time from the anisotropic to isotropic translational diffusion depending on the lysozyme concentration. The magnitude of the translational diffusion anisotropy in this transient regime is also concentration-dependent and steric interactions enhance the anisotropy. Moreover, steric interactions cause the anisotropy to be a nonmonotonic function of time. When the hydrodynamic anisotropy of the protein is neglected in Brownian dynamics simulations and its diffusion tensor is replaced with average translational and rotational diffusion coefficients, the lysozyme's translational dynamics in the long-time limit is similar to that in the case of the corresponding hydrodynamically anisotropic object. However, such a similarity is not observed below 1 μs and in this time regime the translational dynamics of lysozyme molecules modeled with isotropic diffusion coefficients substantially deviates from that derived from Brownian dynamics simulations of their hydrodynamically anisotropic counterparts.
我们研究了排除体积相互作用对流体动力学各向异性分子平移扩散的影响。为此，我们对蛋清溶菌酶（HEWL）水溶液进行了刚体布朗动力学模拟，浓度范围为1.25 mg/mL至250 mg/mL，并评估了溶菌酶的自扩散。在长时间极限（超过1 μs）下，蛋白质的平移扩散是各向同性的，与溶液浓度无关。然而，在高达数百纳秒的时间尺度上，观察到了各向异性的平移扩散，从各向异性到各向同性平移扩散的转变时间取决于溶菌酶浓度。在这个瞬态区域中，平移扩散各向异性的大小也与浓度有关，空间相互作用增强了各向异性。此外，空间相互作用导致各向异性成为时间的非单调函数。当在布朗动力学模拟中忽略蛋白质的流体动力学各向异性，并将其扩散张量替换为平均平移和旋转扩散系数时，溶菌酶在长时间极限下的平移动力学与相应的流体动力学各向异性物体的情况相似。然而，在1 μs以下未观察到这种相似性，在此时间范围内，用各向同性扩散系数建模的溶菌酶分子的平移动力学与从其流体动力学各向异性对应物的布朗动力学模拟得出的结果有很大偏差。
