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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution
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Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution

机译：超分子配合物在3.42-A晶体学分辨率下的各向异性热参数的标准模式细化

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摘要

Here we report a normal-mode-based protocol for modeling anisotropic thermal motions of proteins in x-ray crystallographic refinement. The foundation for this protocol is a recently developed elastic normal mode analysis that produces much more accurate eigenvectors without the tip effect. The effectiveness of the procedure is demonstrated on the refinement of a 3.42-A structure of formimino- transferase cyclodeaminase, a 0.5-MDa homooctameric enzyme. Using an order of magnitude fewer adjustable thermal parameters than the conventional isotropic refinement, this protocol resulted in a decrease of the values of R_(cryst) and R_(free) and improvements of the density map. Several poorly resolved regions in the original isotropically refined structure became clearer so that missing side chains were fitted easily and mistraced backbone was corrected. Moreover, the distribution of anisotropic thermal ellipsoids revealed functionally important structure flexibility. This normal-mode-based refinement is an effective way of describing anisotropic thermal motions in x-ray structures and is particularly attractive for the refinement of very large and flexible supramolecular complexes at moderate resolutions.
机译：在这里，我们报告了基于正常模式的协议，用于对X射线晶体学细化中蛋白质的各向异性热运动进行建模。该协议的基础是最近开发的弹性法线模式分析，该分析可产生更精确的特征向量而不会产生尖端效应。该方法的有效性在精制的三聚氰胺转移酶环脱氨酶（一种0.5-MDa同八聚酶）的3.42-A结构上得到了证明。该协议使用的可调节热参数比常规的各向同性改进少了一个数量级，因此该协议导致R_（cryst）和R_（free）的值减小，并改善了密度图。原始各向同性精炼结构中的几个分辨较差的区域变得更清晰，因此容易装配缺失的侧链并纠正了雾化的骨架。此外，各向异性热椭球的分布揭示了功能上重要的结构柔韧性。这种基于正常模式的细化是描述x射线结构中各向异性热运动的有效方法，对于以中等分辨率细化非常大且灵活的超分子复合物特别有吸引力。

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