MacKerell A D, Nilsson L, Rigler R, Heinemann U, Saenger W
Department of Medical Biophysics, Karolinska Institutet, Stockholm, Sweden.
Proteins. 1989;6(1):20-31. doi: 10.1002/prot.340060103.
Molecular dynamics simulations were performed on free RNase T1 and the 2'GMP-RNase T1 complex in vacuum and with water in the active site along with crystallographically identified waters, allowing analysis of both active site and overall structural and dynamics changes due to the presence of 2'GMP. Differences in the active site include a closing in the presence of 2'GMP, which is accompanied by a decrease in mobility of active site residues. The functional relevance of the active site fluctuations is discussed. 2'GMP alters the motion of Tyr-45, suggesting a role for that residue in providing a hydrophobic environment for the protein-nucleic acid interactions responsible for the specificity of RNase T1. The presence of 2'GMP causes a structural change of the C-terminus of the alpha-helix, indicating the transmission of structural changes from the active site through the protein matrix. Overall fluctuations of both the free and 2'GMP enzyme forms are in good agreement with X-ray temperature factors. The motion of Trp-59 is influenced by 2'GMP, indicating differences in enzyme dynamics away from the active site, with the calculated changes following those previously seen in time-resolved fluorescence experiments.
在真空中以及活性位点存在水（包括晶体学鉴定的水）的情况下，对游离的核糖核酸酶T1和2'-鸟苷单磷酸-核糖核酸酶T1复合物进行了分子动力学模拟，从而能够分析由于2'-鸟苷单磷酸的存在而导致的活性位点以及整体结构和动力学变化。活性位点的差异包括在2'-鸟苷单磷酸存在时的闭合，这伴随着活性位点残基流动性的降低。讨论了活性位点波动的功能相关性。2'-鸟苷单磷酸改变了酪氨酸-45的运动，表明该残基在为负责核糖核酸酶T1特异性的蛋白质-核酸相互作用提供疏水环境中发挥作用。2'-鸟苷单磷酸的存在导致α-螺旋C末端的结构变化，表明结构变化从活性位点通过蛋白质基质进行传递。游离和2'-鸟苷单磷酸酶形式的整体波动与X射线温度因子高度一致。色氨酸-59的运动受2'-鸟苷单磷酸影响，表明酶在远离活性位点处的动力学存在差异，计算出的变化与之前在时间分辨荧光实验中观察到的一致。
