CheShift-2 resolves a local inconsistency between two X-ray crystal structures
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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 13C α chemical shifts. We report the application of CheShift-2 to a local inconsistency between two X-ray crystal structures (PDB IDs 1IKN and 1NFI) 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 13C α chemical shifts 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.
KeywordsChemical shift NFκB IκB Structure validation
This work was supported by grants GM71862 (HJD), DP5OD009180 (JSF), GM14312 (HAS) from the National Institutes of Health and PIP-112-2011-0100030 (JAV) from IMASL-CONICET, Argentina.
- Adams PD, Afonine PV, Bunkoczi 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 (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D 66:213–221Google Scholar
- Arnautova YA, Vila JA, Martin OA, Scheraga HA (2009) What can we learn by computing 13Calpha chemical shifts for X-ray protein models? Acta Crystallogr D 65:697–703Google Scholar
- Ernst MK, Dunn LL, Rice NR (1995) The PEST-like sequence of IkBα is responsible for inhibition of DNA binding but not for cytoplasmic retention of c-Rel or RelA homodimers. Mol Cell Biol 15:872–882Google Scholar
- Nabuurs SB, Spronk CAEM, Vuister GW, Vriend G (2006) Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2:71–79Google Scholar