Metal ion-mediated reduction in surface entropy improves diffraction quality of crystals of the IRAK-4 death domain

Journal of Biomolecular Techniques

Volumn 17, Issue 2, 2006, Pages 114-121

  Lasker, Michael V ^a,b   Kuruvilla, Santosh M ^a   Gajjar, Mark M ^a   Kapoor, Anubhav ^a   Nair, Satish K ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Death domain; Diffraction; Innate immunity; References; Surface entropy; X ray crystallography

Indexed keywords

ASPARTIC ACID; CHLORIDE; INTERLEUKIN 1 RECEPTOR ASSOCIATED KINASE; ION; IRAK4 PROTEIN, MOUSE; LYSINE; MANGANESE; MANGANESE CHLORIDE; MANGANESE DERIVATIVE; PHOSPHOTRANSFERASE;

ANIMAL; ARTICLE; CHEMISTRY; ENTROPY; ENZYME ACTIVE SITE; HUMAN; METHODOLOGY; MOUSE; MUTAGENESIS; POINT MUTATION; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ANIMALS; ASPARTIC ACID; CATALYTIC DOMAIN; CHLORIDES; CRYSTALLOGRAPHY, X-RAY; ENTROPY; HUMANS; INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASES; IONS; LYSINE; MANGANESE; MANGANESE COMPOUNDS; MICE; MUTAGENESIS; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); POINT MUTATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; X-RAY DIFFRACTION;

EID: 33747035087     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: None     Document Type: Article

References (35)

1. Flajnik MF, Du Pasquier L. Evolution of innate and adaptive immunity: Can we draw a line? Trends Immunol 2004;25:640-644.
2. Imler JL, Hoffmann JA. Toll and Toll-like proteins: An ancient family of receptors signaling infection. Rev Immunogenet 2000;2:294-304.
3. Janeway CA, Jr., Medzhitov R. Introduction: the role of innate immunity in the adaptive immune response. Semin Immunol 1998;10:349-350.
4. Imler JL, Hoffmann JA. Toll receptors in innate immunity. Trends Cell Biol 2001;11:304-311.
5. Akira S, Takeda K. Toll-like receptor signalling. Nat Rev Immunol 2004;4:499-511.
6. O'Neill LA, Fitzgerald KA, Bowie AG. The Toll-IL-1 receptor adaptor family grows to five members. Trends Immunol 2003;24:286-290.
7. Janssens S, Beyaert R. Functional diversity and regulation of different interleukin-1 receptor-associated kinase (IRAK) family members. Mol Cell 2003;11:293-302.
8. Wheeler TT, Hood KA. The mammalian innate immune system: potential targets for drug development. Curr Drug Targets Immune Endocr Metabol Disord 2005;5:237-247.
9. Lasker MV, Gajjar MM, Nair SK. Cutting edge: Molecular structure of the IL-1R-associated kinase-4 death domain and its implications for TLR signaling. J Immunol 2005;175:4175-4179.
10. Dauter Z, Dauter M. Entering a new phase: Using solvent halide ions in protein structure determination. Structure (Camb) 2001;9:R21-26.
11. Read RJ. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst 1986;140-149.
12. Matte A, Tari LW, Goldie H, Delbaere LT. Structure and mechanism of phosphoenolpyruvate carboxykinase. J Biol Chem 1997;272:8105-8108.
13. 2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions. Nat Struct Biol 1997;4:990-994.
14. Kanyo ZF, Scolnick LR, Ash DE, Christianson DW. Structure of a unique binuclear manganese cluster in arginase. Nature 1996;383:554-557.
15. Di Costanzo L, Sabio G, Mora A, Rodriguez PC, Ochoa AC, Centeno F, et al. Crystal structure of human arginase I at 1.29-Å resolution and exploration of inhibition in the immune response. Proc Natl Acad Sci USA 2005;102:13058-13063.
16. Trakhanov S, Quiocho FA. Influence of divalent cations in protein crystallization. Protein Sci 1995;4:1914-1919.
17. Newcomer ME, Jones TA, Aqvist J, Sundelin J, Eriksson U, Rask L, et al. The three-dimensional structure of retinol-binding protein. EMBO J 1984;3:1451-1454.
18. Newcomer ME, Liljas A, Eriksson U, Sundelin J, Rask L, Peterson PA. Crystallization of and preliminary X-ray data for an intracellular vitamin A-binding protein from rat liver. J Biol Chem 1981;256:8162-8163.
19. Newcomer ME, Liljas A, Sundelin J, Rask L, Peterson PA. Crystallization of and preliminary X-ray data for the plasma retinol-binding protein. J Biol Chem 1984;259:5230-5231.
20. Yao N, Trakhanov S, Quiocho FA. Refined 1.89-A structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins. Biochemistry 1994;33:4769-4779.
21. Chandonia JM, Brenner SE. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 2005;58:166-179.
22. Schwartz TU, Walczak R, Blobel G. Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit. Protein Sci 2004;13:2814-2818.
23. Schwartz T, Blobel G. Structural basis for the function of the beta subunit of the eukaryotic signal recognition particle receptor. Cell 2003;112:793-803.
24. Cohen SL, Ferre-D'Amare AR, Burley SK, Chait BT. Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci 1995;4:1088-1099.
25. Kim AR, Dobransky T, Rylett RJ, Shilton BH. Surface-entropy reduction used in the crystallization of human choline acetyltransferase. Acta Crystallogr D Biol Crystallogr 2005;61:1306-1310.
26. Derewenda U, Mateja A, Devedjiev Y, Routzahn KM, Evdokimov AG, Derewenda ZS, et al. The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague. Structure (Camb) 2004;12:301-306.
27. Garrard SM, Longenecker KL, Lewis ME, Sheffield PJ, Derewenda ZS. Expression, purification, and crystallization of the RGS-like domain from the Rho nucleotide exchange factor, PDZ-RhoGEF, using the surface entropy reduction approach. Protein Expr Purif 2001;21:412-416.
28. Longenecker KL, Garrard SM, Sheffield PJ, Derewenda ZS. Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Acta Crystallogr D Biol Crystallogr 2001;57:679-688.
29. Longenecker KL, Lewis ME, Chikumi H, Gutkind JS, Derewenda ZS. Structure of the RGS-like domain from PDZ-RhoGEF: linking heterotrimeric g protein-coupled signaling to Rho GTPases. Structure (Camb) 2001;9:559-569.
30. Rayment I. Reductive alkylation of lysine residues to alter crystallization properties of proteins. Methods Enzymol 1997;276:171-179.
31. Kobayashi M, Kubota M, Matsuura Y. Crystallization and improvement of crystal quality for x-ray diffraction of maltooligosyl trehalose synthase by reductive methylation of lysine residues. Acta Crystallogr D Biol Crystallogr 1999;55 (Pt 4):931-933.
32. Kurinov IV, Mao C, Irvin JD, Uckun FM. X-ray crystallographic analysis of pokeweed antiviral protein-II after reductive methylation of lysine residues. Biochem Biophys Res Commun 2000;275:549-552.
33. Saxena AK, Saul A, Garboczi DN. Crystallization and preliminary X-ray analysis of the Plasmodium vivax sexual stage 25 kDa protein Pvs25, a transmission-blocking vaccine candidate for malaria. Acta Crystallogr D Biol Crystallogr 2004;60:706-708.
34. Szyk A, Lu W, Xu C, Lubkowski J. Structure of the scorpion toxin BmBKTtx1 solved from single wavelength anomalous scattering of sulfur. J Struct Biol 2004;145:289-294.
35. Schubot FD, Waugh DS. A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB. Acta Crystallogr D Biol Crystallogr 2004;60:1981-1986.