蛋白质环的晶体学建模及其不均一性与Rappertk
Crystallographic modelling of protein loops and their heterogeneity with Rappertk
摘要：
背景蛋白质的全原子晶体学精修是一个费力的手动驱动程序，因此，替代和多构象异构体的解释没有进行常规研究。结果我们描述了有效的循环采样程序在Rappertk和证明，蛋白质中的单循环可以自动和准确地建模，很少的位置限制。用复合CNS/Rappertk方案构建的环始终具有比仅用CNS的环更好的Rfree。这种方法被扩展到一个更现实的情况下，往往有很大的位置不确定性，随着小的缺陷，在二级结构框架的循环。集成和收集方法被用来估计环区域的结构异质性。结论除了对Rappertk进行全原子蛋白质精制任务的基准测试外，这项工作还展示了它在环建模的两个方面的实用性-构建单个构象异构体和估计环可能表现出的结构异质性。
英文摘要：
Background. All-atom crystallographic refinement of proteins is a laborious manually driven procedure, as a result of which, alternative and multiconformer interpretations are not routinely investigated. Results. We describe efficient loop sampling procedures in Rappertk and demonstrate that single loops in proteins can be automatically and accurately modelled with few positional restraints. Loops constructed with a composite CNS/Rappertk protocol consistently have better Rfree than those with CNS alone. This approach is extended to a more realistic scenario where there are often large positional uncertainties in loops along with small imperfections in the secondary structural framework. Both ensemble and collection methods are used to estimate the structural heterogeneity of loop regions. Conclusion. Apart from benchmarking Rappertk for the all-atom protein refinement task, this work also demonstrates its utility in both aspects of loop modelling - building a single conformer and estimating structural heterogeneity the loops can exhibit.
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