Roh J H, Briber R M, Damjanovic A, Thirumalai D, Woodson S A, Sokolov A P
Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, USA.
Biophys J. 2009 Apr 8;96(7):2755-62. doi: 10.1016/j.bpj.2008.12.3895.
The influence of hydration on the nanosecond timescale dynamics of tRNA is investigated using neutron scattering spectroscopy. Unlike protein dynamics, the dynamics of tRNA is not affected by methyl group rotation. This allows for a simpler analysis of the influence of hydration on the conformational motions in RNA. We find that hydration affects the dynamics of tRNA significantly more than that of lysozyme. Both the characteristic length scale and the timescale of the conformational motions in tRNA depend strongly on hydration. Even the characteristic temperature of the so-called "dynamical transition" appears to be hydration-dependent in tRNA. The amplitude of the conformational motions in fully hydrated tRNA is almost twice as large as in hydrated lysozyme. We ascribe these differences to a more open and flexible structure of hydrated RNA, and to a larger fraction and different nature of hydrophilic sites. The latter leads to a higher density of water that makes the biomolecule more flexible. All-atom molecular-dynamics simulations are used to show that the extent of hydration is greater in tRNA than in lysozyme. We propose that water acts as a "lubricant" in facilitating enhanced motion in solvated RNA molecules.
利用中子散射光谱研究了水合作用对转运核糖核酸（tRNA）纳秒时间尺度动力学的影响。与蛋白质动力学不同，tRNA的动力学不受甲基旋转的影响。这使得对水合作用对RNA构象运动影响的分析更加简单。我们发现，水合作用对tRNA动力学的影响比溶菌酶显著得多。tRNA中构象运动的特征长度尺度和时间尺度都强烈依赖于水合作用。甚至所谓“动力学转变”的特征温度在tRNA中似乎也依赖于水合作用。完全水合的tRNA中构象运动的幅度几乎是水合溶菌酶中的两倍。我们将这些差异归因于水合RNA更开放灵活的结构，以及亲水位点的比例更高和性质不同。后者导致更高的水密度，使生物分子更具柔韧性。全原子分子动力学模拟用于表明tRNA中的水合程度比溶菌酶中的更大。我们提出，水在促进溶剂化RNA分子增强运动方面起到了“润滑剂”的作用。
