Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
Phys Chem Chem Phys. 2019 Aug 21;21(33):18149-18160. doi: 10.1039/c9cp02504a.
Conformational entropies are of great interest when studying the binding of small ligands to proteins or the interaction of proteins. Unfortunately, there are no experimental methods available to measure conformational entropies of all groups in a protein. Instead, they are normally estimated from molecular dynamics (MD) simulations, although such methods show problems with convergence and correlation of motions, and depend on the accuracy of the underlying potential-energy function. Crystallographic atomic displacement parameters (also known as B-factors) are available in all crystal structures and contain information about the atomic fluctuations, which can be converted to entropies. We have studied whether B-factors can be employed to extract conformational entropies for proteins by comparing such entropies to those measured by NMR relaxation experiments or obtained from MD simulations in solution or in the crystal. Unfortunately, our results show that B-factor entropies are unreliable, because they include the movement and rotation of the entire protein, they exclude correlation of the movements and they include contributions other than the fluctuations, e.g. static disorder, as well as errors in the model and the scattering factors. We have tried to reduce the first problem by employing translation-libration-screw refinement, the second by employing a description of the correlated movement from MD simulations, and the third by studying only the change in entropy when a pair of ligands binds to the same protein, thoroughly re-refining the structures in exactly the same way and using the same set of alternative conformations. However, the experimental B-factors seem to be incompatible with fluctuations from MD simulations and the precision is too poor to give any reliable entropies.
当研究小分子配体与蛋白质的结合或蛋白质相互作用时，构象熵非常重要。不幸的是，目前没有实验方法可用于测量蛋白质中所有基团的构象熵。相反，它们通常是根据分子动力学 (MD) 模拟来估计的，尽管这些方法在运动的收敛性和相关性方面存在问题，并且依赖于潜在势能函数的准确性。晶体学原子位移参数（也称为 B 因子）在所有晶体结构中都可用，并且包含有关原子波动的信息，这些信息可以转换为熵。我们研究了 B 因子是否可以通过将这些熵与通过 NMR 弛豫实验测量的熵或从溶液或晶体中的 MD 模拟获得的熵进行比较，来提取蛋白质的构象熵。不幸的是，我们的结果表明，B 因子熵是不可靠的，因为它们包括整个蛋白质的运动和旋转，它们排除了运动的相关性，并且包括除波动之外的其他贡献，例如静态无序，以及模型和散射因子中的错误。我们试图通过采用平移-摆动-螺旋精修来减少第一个问题，通过采用 MD 模拟中相关运动的描述来减少第二个问题，通过仅研究当一对配体结合到相同蛋白质时熵的变化来减少第三个问题，彻底重新精修结构，以完全相同的方式并使用相同的替代构象集。然而，实验 B 因子似乎与 MD 模拟中的波动不兼容，并且精度太差，无法给出任何可靠的熵。
