THE TEMPERATURE DEPENDENCE OF DYNAMICS OF HYDRATED MYOGLOBIN

水合肌红蛋白动力学的温度依赖性

• 批准号: 3896424
• 负责人: R J LONCHARICH
• 金额: --
• 依托单位: CENTER FOR INFORMATION TECHNOLOGY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/3896424
• 关键词: chemical structure; computer simulation; electronic spectra; hemoprotein structure; molecular dynamics; myoglobin; neutron diffraction; temperature; thermodynamics

Eleven molecular dynamics simulations of 150 psec in length are carried out on the carboxy-myoglobin protein at 20, 60, 100, 180, 220, 240, 260, 280, 300, 320 and 340 K. The simulations attempt to mimic neutron scattering experiments very closely by including 349 waters around the protein. Theoretically determined elastic, quasielastic, and inelastic neutron scattering data are directly compated with experiment. The elastic scattering is decreased compared to experiment. Inelastic and quasielastic spectra show that the inelastic peak is shifted to lower frequency than the experimental value, while quasielastic behavior is in good agreement with experiment. In addition, we analyze simulation trajectories by comparing rms deviations from the starting structure, average atomic fluctuations, and a helical time series. The anisotropy and anharmonicity of the atomic position distributions are also determined, The anisotropy is small below 180 K and dramatically increases above this temperature. The anharmonicity is large at all temperatures. Overall simulation results indicate that the protein behaves with near harmonic vibration in well defined substates at temperatures below 180 K. Protein behavior becomes much more anharmonic with transitions between many conformational substates at higher temperatures.

进行了11个长度为150皮秒的分子动力学模拟 在20，60，100，180，220，240，260， 280、300、320和340 K。模拟试图模拟中子 散射实验非常密切，包括349沃茨周围的 蛋白理论上确定的弹性、准弹性和非弹性 中子散射数据直接与实验结果进行了比较。弹性 与实验相比，散射减小。非弹性和准弹性 谱表明，非弹性峰移动到较低的频率， 实验值，而准弹性行为是吻合得很好 做实验此外，我们分析模拟轨迹， 比较与起始结构的均方根偏差，平均原子 波动和螺旋时间序列。各向异性和非谐性 的原子位置分布也被确定， 在低于180 K时很小，在高于此温度时急剧增加。 非谐性在所有温度下都很大。总体模拟结果 表明蛋白质在阱中表现为近简谐振动， 在低于180 K的温度下定义的亚态。蛋白质行为变得 许多构象之间的过渡更加不协调 在更高的温度下分解。