Urzhumtsev Alexandre, Afonine Pavel V, Van Benschoten Andrew H, Fraser James S, Adams Paul D
Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1668-83. doi: 10.1107/S1399004715011426. Epub 2015 Jul 28.
The translation-libration-screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
克鲁克香克、肖梅克和特鲁布拉德首次提出的平移-摆动-螺旋模型描述了原子基团的协同运动。使用TLS模型可以提高计算衍射数据与实验衍射数据之间的吻合度。由于T、L和S矩阵描述了原子振动和摆动的组合，TLS模型还可能有助于揭示涉及相关运动的分子机制。然而，在将精修结果转化为分子运动或结构系综方面存在困难，这阻碍了TLS模型在机理研究中的应用。为了将矩阵转化为构成分子运动，矩阵元素必须满足若干条件。在不考虑这些条件的情况下将T、L和S矩阵元素作为独立参数进行精修，可能会得到不代表协同分子运动的矩阵。本文描述了一个数学框架和计算工具，用于分析TLS矩阵，从而要么明确分解为对潜在运动的描述，要么报告不满足的条件。然后，可以将有效潜在运动的描述输出为结构系综。所有方法都作为PHENIX项目的一部分来实现。
