Axelsen P H, Haydock C, Prendergast F G
Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota 55905.
Biophys J. 1988 Aug;54(2):249-58. doi: 10.1016/S0006-3495(88)82954-0.
Molecular dynamics simulations of Ribonuclease-T1 (RNAse-T1) were performed using x-ray crystal coordinates for the enzyme and various simulation strategies. From each of the simulations, a predicted fluorescence anisotropy decay for the single-tryptophan residue was derived and compared with experimental values for the limiting anisotropy of this protein. Simulations conducted in vacuo demonstrated large displacements among some of the residues adjacent to the tryptophan side chain. As a consequence, the ring system rotates relatively unhindered through an angle far in excess of that implied by experimental data. In contrast, the explicit simulation of solvent within a stochastic boundary led to excellent agreement between simulation and experiment. In the case of RNAse-T1, the experimentally-determined limiting anisotropy is useful as a criterion of simulation accuracy in the vicinity of the tryptophan side chain.
使用该酶的X射线晶体坐标和各种模拟策略对核糖核酸酶-T1（RNAse-T1）进行了分子动力学模拟。从每个模拟中，得出了单个色氨酸残基的预测荧光各向异性衰减，并将其与该蛋白质极限各向异性的实验值进行了比较。在真空中进行的模拟表明，色氨酸侧链附近的一些残基之间存在较大位移。因此，环系统相对不受阻碍地旋转，旋转角度远远超过实验数据所暗示的角度。相比之下，在随机边界内对溶剂进行的显式模拟导致模拟结果与实验结果高度吻合。就RNAse-T1而言，实验确定的极限各向异性可作为色氨酸侧链附近模拟准确性的标准。
