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首页> 外文期刊>Acta crystallographica. Section D, Structural biology >Improving sampling of crystallographic disorder in ensemble refinement
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Improving sampling of crystallographic disorder in ensemble refinement

机译：提高采样的晶体障碍套refinement

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Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single-model structures. However, suboptimal sampling of the molecular-dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models. Here, two improvements to the ensemble refinement method implemented within Phenix are presented: DEN restraints, which guide the local sampling of conformations and allow a more robust exploration of local conformational landscapes, and ECHT disorder models, which allow the selection of more physically meaningful and effective disorder models for parameterizing the continuous disorder components within a crystal. These improvements lead to more consistent and physically interpretable simulations of macromolecules in crystals, and allow structural heterogeneity and disorder to be systematically explored on different scales. The new approach is demonstrated on several case studies and the SARS-CoV-2 main protease, and demonstrates how the choice of disorder model affects the type of disorder that is sampled by the restrained molecular-dynamics simulation.
机译：整体优化,分子的应用动力学结晶细化,显式模型固有的障碍大分子的结构。已被证明产生更准确结构比传统的单模结构。分子动力学模拟和造型晶体障碍的效用有限的方法,会导致非物质的和紧张的模型。整体优化方法中实现凤凰介绍:窝限制,指南当地的抽样的构象和允许更健壮的探索当地的构象风景,和真正的障碍模型,它允许的更多的选择和物理意义有效的参数化的障碍模型连续障碍组件在一个晶体。这些改进和导致更多的一致身体可判断的模拟大分子晶体,并允许结构系统的异构性和混乱探讨在不同的尺度上。在几个案例研究和演示的那样SARS-CoV-2主要蛋白酶,演示了如何疾病模式的选择影响的类型障碍所采样的克制分子动力学模拟。

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