Sutcliffe M J
Biological NMR Centre, University of Leicester, United Kingdom.
Protein Sci. 1993 Jun;2(6):936-44. doi: 10.1002/pro.5560020607.
The usefulness of representing an ensemble of NMR-derived protein structures by a single structure has been investigated. Two stereochemical properties have been used to assess how a single structure relates to the ensemble from which it was derived, namely the distribution of phi psi torsion angles and the distribution of chi 1 torsion angles. The results show that the minimized average structure derived from the ensemble (a total of 11 ensembles from the Brookhaven Protein Data Bank were analyzed) does not always correspond well with this ensemble, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue. An alternative method that selects the member of the ensemble which is closest to the "average" of the ensemble has been investigated (a total of 23 ensembles from the Brookhaven Protein Data Bank were analyzed). Although this method selected a structure that on the whole corresponded more closely to the ensemble than did the minimized average structure, this is still not a totally reliable means of selecting a single structure to represent the ensemble. This suggests that it is advisable to study the ensemble as a whole. A study has also been made of the practice of selecting the "best" rather than the most representative member of the ensemble. This too suggests that the ensemble should be studied as a whole. A study of the conformational space occupied by the ensemble also suggests the need to consider the ensemble as a whole, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue.
研究了用单一结构表示核磁共振衍生的蛋白质结构集合的实用性。使用了两种立体化学性质来评估单一结构与其所衍生的集合之间的关系，即φ ψ扭转角的分布和χ1扭转角的分布。结果表明，从集合中导出的最小化平均结构（共分析了来自布鲁克海文蛋白质数据库的11个集合）并不总是与该集合很好地对应，特别是对于那些每个残基由较少实验衍生约束生成的集合。研究了另一种方法，即选择集合中最接近集合“平均值”的成员（共分析了来自布鲁克海文蛋白质数据库的23个集合）。尽管这种方法选择的结构总体上比最小化平均结构更接近集合，但这仍然不是选择单一结构来表示集合的完全可靠的方法。这表明最好对整个集合进行研究。还对选择集合中“最佳”而非最具代表性成员的做法进行了研究。这也表明应该对整个集合进行研究。对集合所占据的构象空间的研究也表明需要将集合作为一个整体来考虑，特别是对于那些每个残基由较少实验衍生约束生成的集合。
