Painter Jay, Merritt Ethan A
Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA.
Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):439-50. doi: 10.1107/S0907444906005270. Epub 2006 Mar 18.
A single protein crystal structure contains information about dynamic properties of the protein as well as providing a static view of one three-dimensional conformation. This additional information is to be found in the distribution of observed electron density about the mean position of each atom. It is general practice to account for this by refining a separate atomic displacement parameter (ADP) for each atomic center. However, these same displacements are often described well by simpler models based on TLS (translation/libration/screw) rigid-body motion of large groups of atoms, for example interdomain hinge motion. A procedure, TLSMD, has been developed that analyzes the distribution of ADPs in a previously refined protein crystal structure in order to generate optimal multi-group TLS descriptions of the constituent protein chains. TLSMD is applicable to crystal structures at any resolution. The models generated by TLSMD analysis can significantly improve the standard crystallographic residuals R and R(free) and can reveal intrinsic dynamic properties of the protein.
单个蛋白质晶体结构不仅包含蛋白质动态特性的信息，还提供了一种三维构象的静态视图。这些额外的信息可以在围绕每个原子平均位置的观测电子密度分布中找到。通常的做法是通过为每个原子中心细化一个单独的原子位移参数（ADP）来对此进行解释。然而，这些相同的位移通常可以用基于大组原子的TLS（平移/摆动/螺旋）刚体运动的更简单模型很好地描述，例如结构域间的铰链运动。已经开发出一种程序TLSMD，它分析先前精修的蛋白质晶体结构中ADP的分布，以便生成组成蛋白质链的最佳多组TLS描述。TLSMD适用于任何分辨率的晶体结构。通过TLSMD分析生成的模型可以显著改善标准晶体学残差R和R（自由），并能揭示蛋白质的内在动态特性。
