CheShift-2 resolves a local inconsistency between two X-ray crystal structures

Journal of Biomolecular NMR

Volumn 54, Issue 2, 2012, Pages 193-198

  Vila, Jorge A ^a,b   Sue, Shih Che ^c,d   Fraser, James S ^e   Scheraga, Harold A ^a   Dyson, H Jane ^c  

^a Cornell University ^*  (United States)

^b UNIVERSIDAD NACIONAL DE SAN LUIS   (Argentina)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Chemical shift; I B; NF B; Structure validation

Indexed keywords

HETERODIMER; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TRYPTOPHAN;

ALGORITHM; ARTICLE; CHEMICAL SHIFT 2; CONTROLLED STUDY; CRYSTAL STRUCTURE; NUCLEAR MAGNETIC RESONANCE; PLASTICITY; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTON NUCLEAR MAGNETIC RESONANCE; VALIDATION PROCESS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; HYDROGEN BONDING; I-KAPPA B PROTEINS; INTERNET; MOLECULAR SEQUENCE DATA; NF-KAPPA B P50 SUBUNIT; PROTEIN CONFORMATION; QUANTUM THEORY; SOFTWARE; TRANSCRIPTION FACTOR RELA;

EID: 84868210931     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-012-9663-0     Document Type: Article

References (28)

1. 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 66:213-221
2. 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 65:697-703
3. Baeuerle PA (1998) IjB-NF-jB structures: At the interface of inflammation control. Cell 95:729-731 (Pubitemid 29014451)
4. Baeuerle PA, Baltimore D (1996) NF-jB: Ten years after. Cell 87:13-20
5. Baldwin AS (1996) The NF-jB and I-jB proteins: New discoveries and insights. Ann Rev Immunol 14:649-683
6. Bergqvist S, Ghosh G, Komives EA (2008) The IjBa/NF-jB complex has two hot spots, one at either end of the interface. Protein Sci 17:2051-2058
7. Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA (2009) Kinetic enhancement of NF-jB-DNA dissociation by IjBa. Proc Natl Acad Sci USA 106:19328-19333
8. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778-795
9. Chen FE, Huang DB, Chen YQ, Ghosh G (1998) Crystal structure of p50/p65 heterodimer of transcription factor NF-jB bound to DNA. Nature 391:410-413
10. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of coot. Acta Crystallogr D Biol Crystallogr 66:486-501
11. Ernst MK, Dunn LL, Rice NR (1995) The PEST-like sequence of IkBa is responsible for inhibition of DNA binding but not for cytoplasmic retention of c-Rel or RelA homodimers. Mol Cell Biol 15:872-882
12. Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462:669-673
13. Han B, Liu Y, Ginzinger SW, Wishart DS (2011) SHIFTX2: Significantly improved protein chemical shift prediction. J Biomol NMR 50:43-57
14. Hayden MS, Ghosh S (2004) Signaling to NF-jB. Genes Dev 18:2195-2224
15. Hayden MS, Ghosh S (2008) Shared principles in NF-jB signaling. Cell 132:344-362
16. Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665-1674 (Pubitemid 40229151)
17. Huxford T, Huang DB, Malek S, Ghosh G (1998) The crystal structure of the IjBa/NF-jB complex reveals mechanisms of NF-jB inactivation. Cell 95:759-770 (Pubitemid 29014456)
18. Jacobs MD, Harrison SC (1998) Structure of an IjBa/NF-jB complex. Cell 95:749-758
19. Joosten RP, Joosten K, Murshudov GN, Perrakis A (2012) PDB-REDO: Constructive validation, more than just looking for errors. Acta Crystallogr D Biol Crystallogr 68:484-496
20. Karin M, Cao Y, Greten FR, Li ZW (2002) NF-jB in cancer: From innocent bystander to major culprit. Nat Rev Cancer 2:301-310 (Pubitemid 37328783)
21. Kumar S, Gelinas C (1993) IjBa-mediated inhibition of v-Rel DNA binding requires direct interaction with the RXXRXRXXC Rel/ jB DNA-binding motif. Proc Natl Acad Sci USA 90:8962-8966 (Pubitemid 23306431)
22. Martin OA, Vila JA, Scheraga HA (2012) CheShift-2: Graphic validation of protein structures. Bioinformatics 28:1538-1539
23. Nabuurs SB, Spronk CAEM, Vuister GW, Vriend G (2006) Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2:71-79
24. Sen R, Baltimore D (1986) Inducibility of j immunoglobulin enhancer-binding protein NF-jB by a posttranslational mechanism. Cell 47:921-928 (Pubitemid 17005065)
25. Shen Y, Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289-302 (Pubitemid 47108511)
26. Sue SC, Dyson HJ (2009) Interaction of the IjBa C-terminal PEST sequence with NF-jB: Insights into the inhibition of NF-jB DNA binding by IjBa. J Mol Biol 388:824-838
27. Sue SC, Cervantes C, Komives EA, Dyson HJ (2008) Transfer of flexibility between ankyrin repeats in IjBa upon formation of the NF-jB complex. J Mol Biol 380:917-931
28. Vila JA, Scheraga HA (2009) Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. Acc Chem Res 42:1545-1553