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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Quantum-mechanics-derived ~(13)C~α chemical shift server (CheShift) for protein structure validation
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Quantum-mechanics-derived ~(13)C~α chemical shift server (CheShift) for protein structure validation

机译：量子力学衍生的〜（13）C〜α化学位移服务器（CheShift）用于蛋白质结构验证

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摘要

A server (CheShift) has been developed to predict ~(13)C~α chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the Φ, Ψ, ω,X~1 and X~2 torsional angles for all 20 naturally occurring amino acids. Their ~(13)C~α chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set. Analysis of the accuracy and sensitivity of the CheShift predictions, in terms of both the correlation coefficient Ft and the conformational-averaged rmsd between the observed and predicted ~(13)C~α chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 A or better resolution, for which sets of ~(13)C~α chemical shifts were available; (ii) 15 pairs of x-ray and NMR-derived sets of protein conformations; and (iii) a set of decoys for 3 proteins showing an rmsd with respect to the x-ray structure from which they were derived of up to 3 A. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that CheShift is the most sensitive server with which to detect subtle differences between protein models and, hence, to validate protein structures determined by either x-ray or NMR methods, if the observed ~(13)C~α chemical shifts are available. CheShift is available as a web server.
机译：已经开发了服务器（CheShift）来预测蛋白质结构的〜（13）C〜α化学位移。它基于对所有20种天然氨基酸的Φ，Ψ，ω，X〜1和X〜2扭转角的函数生成696,916个构象。他们的〜（13）C〜α化学位移是在理论的DFT级别上使用较小的基集进行计算的，并通过经验确定的线性回归公式进行外推，以重现在较大基集下获得的值。对CheShift预测的准确性和敏感性进行了分析，根据相关系数Ft和观察到和预测的〜（13）C〜α化学位移之间的构象平均rmsd，对3组构象进行了分析： i）36种x射线衍生的蛋白质结构在2.3 A或更高分辨率下解析，可获得〜（13）C〜α化学位移集合； （ii）15对X射线和NMR衍生的蛋白质构象集； （iii）一组针对3种蛋白质的诱饵，这些诱饵相对于其衍生自其X射线结构的均方根最大为3A。使用4种常用服务器（SHIFTS，SHIFTX，SPARTA和PROSHIFT对于这三组构象证明，如果观察到〜（13），则CheShift是检测蛋白质模型之间细微差异并因此验证通过X射线或NMR方法确定的蛋白质结构的最灵敏的服务器。 C〜α化学位移可用。 CheShift可作为Web服务器使用。

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    Jorge A. Vila; Yelena A. Arnautova; Osvaldo A. Martin; Harold A. Scheraga;

  • 作者单位

    Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca NY, 14853-1301 Universidad Nacional de San Luis, Institute de Matematica Aplicada de San Luis-Consejo Nacional de Investigaciones Cientificas y Tecnicas, Ejercito de Los Andes 950-5700 San Luis, Argentina;

    Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca NY, 14853-1301 Molsoft L.L.C., 3366 North Torrey Pines Court, Suite 300, La Jolla, CA,92037;

    Universidad Nacional de San Luis, Institute de Matematica Aplicada de San Luis-Consejo Nacional de Investigaciones Cientificas y Tecnicas, Ejercito de Los Andes 950-5700 San Luis, Argentina;

    Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca NY, 14853-1301;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
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  • 关键词

    chemical shifts prediction; DFT calculations; validation server;

    机译：化学位移预测;DFT计算;验证服务器;

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