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首页> 外文期刊>Acta crystallographica. Section D, Structural biology. >Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins
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Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins

机译：使用迭代片段组装和进步促进逐步和序列截断晶体结构测定的远亲相关的蛋白质

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摘要

Molecular replacement (MR) often requires templates with high homology to solve the phase problem in X-ray crystallography. I-TASSER-MR has been developed to test whether the success rate for structure determination of distant-homology proteins could be improved by a combination of iterative fragmental structure-assembly simulations with progressive sequence truncation designed to trim regions with high variation. The pipeline was tested on two independent protein sets consisting of 61 proteins from CASP8 and 100 high-resolution proteins from the PDB. After excluding homologous templates, I-TASSER generated full-length models with an average TM-score of 0.773, which is 12% higher than the best threading templates. Using these as search models, I-TASSER-MR found correct MR solutions for 95 of 161 targets as judged by having a TFZ of >8 or with the final structure closer to the native than the initial search models. The success rate was 16% higher than when using the best threading templates. I-TASSER-MR was also applied to 14 protein targets from structure genomics centers. Seven of these were successfully solved by I-TASSER-MR. These results confirm that advanced structure assembly and progressive structural editing can significantly improve the success rate of MR for targets with distant homology to proteins of known structure.
机译：分子替换(MR)通常需要模板具有高同源性解决阶段在x射线结晶学的问题。开发测试成功率distant-homology结构的决心蛋白质的结合可以改善迭代碎屑structure-assembly模拟与渐进序列截断旨在削减地区高变异。管道测试在两个独立的蛋白质集61蛋白质从CASP8和100组成从PDB高分辨率的蛋白质。不含同源模板I-TASSER平均生成完整的模型TM-score 0.773,高于12%最好的线程模板。模型,I-TASSER-MR先生找到了正确的解决方案161年95年目标根据TFZ> 8或最终的结构接近本机比初始搜索模型。当使用成功率高于16%最好的线程模板。应用于14蛋白质的目标结构基因组学中心。成功地通过I-TASSER-MR解决。确认组装和高级结构编辑可以显著进步的结构改善目标的成功率遥远的同源蛋白质的结构。

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