High-definition NMR structure of PED/PEA-15 death effector domain reveals details of key polar side chain interactions

Biochemical and Biophysical Research Communications

Volumn 424, Issue 1, 2012, Pages 141-146

  Twomey, Edward C ^a   Wei, Yufeng ^a,b  

^a SETON HALL UNIVERSITY   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

Author keywords

Polar interactions; Protein structure; Protein protein interactions; Structure determination; Structure validation

Indexed keywords

PHOSPHOPROTEIN; PHOSPHOPROTEIN ENRICHED IN DIABETES; SOLVENT; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; DEATH EFFECTOR DOMAIN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RESIDUAL DIPOLAR COUPLING;

HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHOSPHOPROTEINS; PROTEIN STRUCTURE, TERTIARY;

EID: 84864103948     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2012.06.091     Document Type: Article

References (31)

1. Park H.H., Lo Y.-C., Lin S.-C., Wang L., Yang J.K., Wu H. The death domain superfamily in intracellular signaling of apoptosis and inflammation. Annual Review of Immunology 2007, 25:561-586.
2. Yang J.K., Wang L., Zheng L., Wan F., Ahmed M., Lenardo M.J., Wu H. Crystal structure of MC159 reveals molecular mechanism of DISC assembly and FLIP inhibition. Molecular Cell 2005, 20:939-949.
3. Li F.-Y., Jeffrey P.D., Yu J.W., Shi Y. Crystal structure of a viral FLIP. Journal of Biological Chemistry 2006, 281:2960-2968.
4. Fiory F., Formisano P., Perruolo G., Beguinot F. Frontiers: PED/PEA-15, a multifunctional protein controlling cell survival and glucose metabolism. American Journal of Physiology - Endocrinology and Metabolism 2009, 297:E592-E601.
5. Carrington P.E., Sandu C., Wei Y., Hill J.M., Morisawa G., Huang T., Gavathiotis E., Wei Y., Werner M.H. The structure of FADD and its mode of interaction with Procaspase-8. Molecular Cell 2006, 22:599-610.
6. Valmiki M., Ramos J. Death effector domain-containing proteins. Cellular and Molecular Life Sciences 2009, 66:814-830.
7. Hill J.M., Vaidyanathan H., Ramos J.W., Ginsberg M.H., Werner M.H. Recognition of ERK MAP kinase by PEA-15 reveals a common docking site within the death domain and death effector domain. EMBO Journal 2002, 21:6494-6504.
8. Bax A., Grishaev A. Weak alignment NMR: a hawk-eyed view of biomolecular structure. Current Opinion in Structural Biology 2005, 15:563-570.
9. Linge J.P., Williams M.A., Spronk C.A.E.M., Bonvin A.M.J.J., Nilges M. Refinement of protein structures in explicit solvent. Proteins: Structure, Function, and Genetics 2003, 50:496-506.
10. Hansen M.R., Hanson P., Pardi A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods in Enzymology 2000, 220-240.
11. Hansen M.R., Mueller L., Pardi A. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nature Structural Biology 1998, 5:1065-1074.
12. Rückert M., Otting G. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. Journal of the American Chemical Society 2000, 122:7793-7797.
13. Lerche M.H., Meissner A., Poulsen F.M., Sorensen O.W. Pulse sequences for measurement of one-bond N-15-H-1 coupling constants in the protein backbone. Journal of Magnetic Resonance 1999, 140:259-263.
14. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. Journal of Biomolecular NMR 1995, 6:277-293.
15. Johnson B.A., Blevins R.A. NMR view: a computer program for the visualization and analysis of NMR data. Journal of Biomolecular NMR 1994, 4:603-614.
16. Clore G.M., Gronenborn A.M., Bax A. A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. Journal of Magnetic Resonance 1998, 133:216-221.
17. Wei Y., Werner M. IDC: a comprehensive toolkit for the analysis of residual dipolar couplings for macromolecular structure determination. Journal of Biomolecular NMR 2006, 35:17-25.
18. Schwieters C.D., Kuszewski J.J., Tjandra N., Marius Clore G. The Xplor-NIH NMR molecular structure determination package. Journal of Magnetic Resonance 2003, 160:65-73.
19. Schwieters C.D., Kuszewski J.J., Marius Clore G. Using Xplor-NIH for NMR molecular structure determination. Progress in Nuclear Magnetic Resonance Spectroscopy 2006, 48:47-62.
20. Losonczi J.A., Andrec M., Fischer M.W.F., Prestegard J.H. Order matrix analysis of residual dipolar couplings using singular value decomposition. Journal of Magnetic Resonance 1999, 138:334-342.
21. Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R., Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR 1996, 8:477-486.
22. Vriend G. WHAT IF: a molecular modeling and drug design program. Journal of Molecular Graphics 1990, 8:52-56.
23. Spronk C.A.E.M., Nabuurs S.B., Bonvin A.M.J.J., Krieger E., Vuister G.W., Vriend G. The precision of NMR structure ensembles revisited. Journal of Biomolecular NMR 2003, 25:225-234.
24. Formstecher E., Ramos J.W., Fauquet M., Calderwood D.A., Hsieh J.-C., Canton B., Nguyen X.-T., Barnier J.-V., Camonis J., Ginsberg M.H., Chneiweiss H. PEA-15 mediates cytoplasmic sequestration of ERK MAP kinase. Developmental Cell 2001, 1:239-250.
25. Viparelli F., Cassese A., Doti N., Paturzo F., Marasco D., Dathan N.A., Monti S.M., Basile G., Ungaro P., Sabatella M., Miele C., Teperino R., Consiglio E., Pedone C., Beguinot F., Formisano P., Ruvo M. Targeting of PED/PEA-15 molecular interaction with phospholipase D1 enhances insulin sensitivity in skeletal muscle cells. Journal of Biological Chemistry 2008, 283:21769-21778.
26. Nabuurs S.B., Spronk C.A.E.M., Vuister G.W., Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Computational Biology 2006, 2:e9.
27. Prestegard J.H., Al-Hashimi H.M., Tolman J.R. NMR structures of biomolecules using field oriented media and residual dipolar couplings. Quarterly Reviews of Biophysics 2000, 33:371-424.
28. Jorgensen W.L., Tirado-Rives J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society 1988, 110:1657-1666.
29. Park H.H., Logette E., Raunser S., Cuenin S., Walz T., Tschopp J., Wu H. Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex. Cell 2007, 128:533-546.
30. Wang L., Yang J.K., Kabaleeswaran V., Rice A.J., Cruz A.C., Park A.Y., Yin Q., Damko E., Jang S.B., Raunser S., Robinson C.V., Siegel R.M., Walz T., Wu H. The Fas-FADD death domain complex structure reveals the basis of DISC assembly and disease mutations. Nature Structural & Molecular Biology 2010, 17:1324-1329.
31. Scott F.L., Stec B., Pop C., Dobaczewska M.K., Lee J.J., Monosov E., Robinson H., Salvesen G.S., Schwarzenbacher R., Riedl S.J. The Fas-FADD death domain complex structure unravels signalling by receptor clustering. Nature 2009, 457:1019-1022.