CheShift-2 resolves a local inconsistency between two X-ray crystal structures.
CheShift-2 resolves a local inconsistency between two X-ray crystal structures.
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DOI：
10.1007/s10858-012-9663-0
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发表时间：
2012-10
影响因子：
2.7
通讯作者：
Dyson HJ
中科院分区：
文献类型：
--
作者：
Vila JA;Sue SC;Fraser JS;Scheraga HA;Dyson HJ
由于化学位移在溶液中提供了关于蛋白质结构的重要且相对容易获取的信息，基于13Cα化学位移的量子力学数据库，开发了用于结构查询的网络服务器CHESHIFT-2。CheShift-2的原因是核因子κB的p65/p50异二聚体与其抑制剂IκBα之间的复合体的两个X射线晶体结构(PDB ID 1IKN和INFI)局部不一致。包括不一致区域的核磁共振分配的可用性为CheShift-2服务器的独立验证提供了机会。服务器的应用表明，IψBκC末端附近的Gly270-Pro281序列的13Cα化学位移与1IKN结构中模拟的骨架结构明确一致，而与1NFI结构不一致。以前的NOE测量表明，色氨酸环在该区域N-末端附近的位置与这两种结构中的任何一种结构都不一致。随后根据1IKN沉积结构因子的电子密度重新计算了该区域的局部结构，证实了1IKN对局部主干结构的模拟效果最好，但Trp258的旋转异构体与1NFI结构一致，包括Trp258的环NεH和Gln278的主链羰基之间存在氢键。所有这些措施之间的共识表明，CheShift-2服务器在主干化学位移可用但局部可塑性可能使X射线结构数据模糊不清的情况下运行良好。
Since chemical shifts provide important and relatively accessible information about protein structure in solution, a Web server, CheShift-2, was developed for structure interrogation, based on a quantum mechanics database of 13Cα chemical shifts. CheShift-2 to a local inconsistency between two X-ray crystal structures (PDB IDs 1IKN and INFI) of the complex between the p65/p50 heterodimer of NFκB and its inhibitor IκBα. The availability of NMR resonance assignments that included the region of the inconsistency provided an opportunity for independent validation of the CheShift-2 server. Application of the server showed that the 13Cψ chemical shift measured for the Gly270-Pro281 sequence close to the C-terminus of IκBα were unequivocally consistent with the backbone structure modeled in the 1IKN structure, and were inconsistent with the 1NFI structure. Previous NOE measurements had demonstrated that the position of a tryptophan ring in the region immediately N-terminal in this region was not consistent with either structure. Subsequent recalculation of the local structure in this region, based on the electron density of the deposited structure factors for 1IKN, confirmed that the local backbone structure was best modeled by 1IKN, but that the rotamer of Trp258 is consistent with the 1NFI structure, including the presence of a hydrogen bond between the ring NεH of Trp258 and the backbone carbonyl group of Gln278. The consensus between all of these measures suggests that the CheShift-2 server operates well under circumstances in which backbone chemical shifts are available but where local plasticity may render X-ray structural data ambiguous.
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影响因子：
5.8
作者：
Martin, Osvaldo A.;Vila, Jorge A.;Scheraga, Harold A.
通讯作者：
Scheraga, Harold A.
影响因子：
4.3
作者：
Nabuurs, Sander B.;Spronk, Chris A. E. M.;Vriend, Gert
通讯作者：
Vriend, Gert
影响因子：
64.5
作者：
Huxford, T;Huang, DB;Ghosh, G
通讯作者：
Ghosh, G
DOI：
10.1107/s0907444909012086
发表时间：
2009-07-01
影响因子：
2.2
作者：
Arnautova, Yelena A.;Vila, Jorge A.;Scheraga, Harold A.
通讯作者：
Scheraga, Harold A.
DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH