What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed?
What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed?
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DOI：
10.1021/ct400398e
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发表时间：
2013-10-01
影响因子：
5.5
通讯作者：
Simonson, Thomas
中科院分区：
文献类型：
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作者：
Simonson, Thomas
具有固定蛋白质主链但具有移动的侧链的蒙特卡罗（MC）模拟对于酸/碱常数和蛋白质设计是常见的。为了表征这些模型中的波动，估计Frohlich-Kirkwood介电常数可以提供物理见解，并允许与更严格（完全灵活）和更简单（没有任何明确的蛋白质灵活性的泊松-玻尔兹曼）的模型进行比较。两个小蛋白质的MC模拟产生的蛋白质介电常数为12和14，约为MD结果（16和22）的70%。因此，完全显式MD和部分显式MC之间的一致性是公平的。
Monte Carlo (MC) simulations with a fixed protein backbone but mobile sidechains are common for acid/base constants and protein design. To characterize the fluctuations in these models, estimating the Frohlich-Kirkwood dielectric constant can give physical insight and allow comparison both with models that are more rigorous (fully flexible) and ones that are simpler (Poisson-Boltmann without any explicit protein flexibility). MC simulations of two small proteins yield protein dielectric constants of 12 and 14, about 70% of the result from MD (16 and 22). Thus, the consistency between the fully explicit MD and partly explicit MC is only fair.