Kinetic traps in the folding/unfolding of procaspase-1 CARD domain

Protein Science

Volumn 13, Issue 8, 2004, Pages 2196-2206

  Chen, Yun Ru ^a,b   Clark, A Clay ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

helical Greek key; Caspase recruitment domain; Double jump; Equilibrium folding; Interrupted refolding; Kinetic trap

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; PROCASPASE 1; PROCASPASE 1 CARD DOMAIN PROTEIN; PROCASPASE 3; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; ENZYME KINETICS; GEL PERMEATION CHROMATOGRAPHY; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STABILITY; REACTION TIME;

AMINO ACID SEQUENCE; ANIMALS; CASPASE 1; CASPASES; CHROMATOGRAPHY, GEL; ENZYME PRECURSORS; HUMANS; KINETICS; MOLECULAR SEQUENCE DATA; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 3342901587     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03521504     Document Type: Article

References (54)

1. Alonso, D.O. and Dill, K.A. 1991. Solvent denaturation and stabilization of globular proteins. Biochemistry 30: 5974-5985.
2. Baldwin, R.L. 1996. On-pathway versus off-pathway folding intermediates. Fold. Des. 1: R1-R8.
3. Bhuyan, A.K. and Udgaonkar, J.B. 1999. Observation of multistate kinetics during the slow folding and unfolding of barstar. Biochemistry 38: 9159-9168.
4. Brandts, J.F., Halvorson, H.R., and Brennan, M. 1975. Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 14: 4953-4963.
5. Capaldi, A.P., Shastry, M.C., Kleanthous, C., Roder, H., and Radford, S.E. 2001. Ultrarapid mixing experiments reveal that Im7 folds via an on-pathway intermediate. Nat. Struct. Biol. 8: 68-72.
6. Capaldi, A.P., Kleanthous, C., and Radford, S.E. 2002. Im7 folding mechanism: Misfolding on a path to the native state. Nat. Struct. Biol. 9: 209-216.
7. Chang, J.Y., Li, L., and Lai, P.H. 2001. A major kinetic trap for the oxidative folding of human epidermal growth factor. J. Biol. Chem. 276: 4845-4852.
8. Chen, Y.R. and Clark, A.C. 2003. Equilibrium and kinetic folding of a α-helical Greek key protein domain: Caspase recruitment domain (CARD) of RICK. Biochemistry 42: 6310-6320.
9. Chou, J.J., Matsuo, H., Duan, H., and Wagner, G. 1998. Solution structure of the RAIDD CARD and model for CARD/CARD interaction in caspase-2 and caspase-9 recruitment. Cell 94: 171-180.
10. Creighton, T.E. 1994. The energetic ups and downs of protein folding. Nat. Struct. Biol. 1: 135-138.
11. Day, C.L., Dupont, C., Lackmann, M., Vaux, D.L., and Hinds, M.G. 1999. Solution structure and mutagenesis of the caspase recruitment domain (CARD) from Apaf-1. Cell Death Differ. 6: 1125-1132.
12. Druilhe, A., Srinivasula, S.M., Razmara, M., Ahmad, M., and Alnemri, E.S. 2001. Regulation of IL-1β generation by pseudo-ICE and ICEBERG, two dominant negative caspase recruitment domain proteins. Cell Death Differ. 8: 649-657.
13. Eberstadt, M., Huang, B., Chen, Z., Meadows, R.P., Ng, S.C., Zheng, L., Lenardo, M.J., and Fesik, S.W. 1998. NMR structure and mutagenesis of the FADD (Mortl) death-effector domain. Nature 392: 941-945.
14. Edelhoch, H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6: 1948-1954.
15. Fairbrother, W.J., Gordon, N.C., Humke, E.W., O'Rourke, K.M., Starovasnik, M.A., Yin, J.P., and Dixit, V.M. 2001. The PYRIN domain: A member of the death domain-fold superfamily. Protein Sci. 10: 1911-1918.
16. Gromiha, M.M. and Selvaraj, S. 2001. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction. J. Mol. Biol. 310: 27-32.
17. Gunasekaran, K., Eyles, S.J., Hagler, A.T., and Gierasch, L.M. 2001. Keeping it in the family: Folding studies of related proteins. Curr. Opin. Struct. Biol. 11: 83-93.
18. Hazes, B. and Hol, W.G. 1992. Comparison of the hemocyanin β-barrel with other Greek key β-barrels: Possible importance of the "β-zipper" in protein structure and folding. Proteins 12: 278-298.
19. Hill, R.B., Raleigh, D.P., Lombardi, A., and DeGrado, W.F. 2000. De novo design of helical bundles as models for understanding protein folding and function. Acc. Chem. Res. 33: 745-754.
20. Hofmann, K. 1999. The modular nature of apoptotic signaling proteins. Cell. Mol. Life Sci. 55: 1113-1128.
21. Hoyer, W., Ramm, K., and Pluckthun, A. 2002. A kinetic trap is an intrinsic feature in the folding pathway of single-chain Fv fragments. Biophys. Chem. 96: 273-284.
22. Hua, Q.X., Jia, W., Frank, B.H., Phillips, N.F., and Weiss, M.A. 2002. A protein caught in a kinetic trap: Structures and stabilities of insulin disulfide isomers. Biochemistry 41: 14700-14715.
23. Humke, E.W., Shriver, S.K., Starovasnik, M.A., Fairbrother, W.J., and Dixit, V.M. 2000. ICEBERG: A novel inhibitor of interleukin-1β generation. Cell 103: 99-111.
24. Jeong, E.J., Bang, S., Lee, T.H., Park, Y.I., Sim, W.S., and Kim, K.S. 1999. The solution structure of FADD death domain. Structural basis of death domain interactions of Fas and FADD. J. Biol. Chem. 274: 16337-16342.
25. Kiefhaber, T. 1995. Kinetic traps in lysozyme folding. Proc. Natl. Acad. Sci. 92: 9029-9033.
26. Kiefhaber, T., Quaas, R., Hahn, U., and Schmid, F.X. 1990. Folding of ribonuclease T1. 1. Existence of multiple unfolded states created by proline isomerization. Biochemistry 29: 3053-3061.
27. Lee, S.H., Stehlik, C., and Reed, J.C. 2001. Cop, a caspase recruitment domain-containing protein and inhibitor of caspase-1 activation processing. J. Biol. Chem. 276: 34495-34500.
28. Lim, V.I. 1978. Polypeptide chain folding through a highly helical intermediate as a general principle of globular protein structure formation. FEBS Lett. 89: 10-14.
29. Mirny, L. and Shakhnovich, E. 2001. Evolutionary conservation of the folding nucleus. J. Mol. Biol. 308: 123-129.
30. Myers, J.K., Pace, C.N., and Scholtz, J.M. 1995. Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4: 2138-2148.
31. Nall, B.T., Garel, J.R., and Baldwin, R.L. 1978. Test of the extended two-state model for the kinetic intermediates observed in the folding transition of ribonuclease A. J. Mol. Biol. 118: 317-330.
32. 2+-binding protein. Biochem. J. 243: 611-615.
33. Pace, C.N., Shirley, B., and Thompson, J. 1989. Measuring the conformational stability of a protein. In Protein structure, a practical approach (ed. T.E. Creighton), pp. 311-330. IRL Press, New York.
34. Pappenberger, G., Aygun, H., Engels, J.W., Reimer, U., Fischer, G., and Kiefhaber, T. 2001. Nonprolyl cis peptide bonds in unfolded proteins cause complex folding kinetics. Nat. Struct. Biol. 8: 452-458.
35. Plaxco, K.W., Simons, K.T., and Baker, D. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277: 985-994.
36. Plaxco, K.W., Simons, K.T., Ruczinski, I., and Baker, D. 2000. Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics. Biochemistry 39: 11177-11183.
37. Qin, H., Srinivasula, S.M., Wu, G., Fernandes-Alnemri, T., Alnemri, E.S., and Shi, Y. 1999. Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1. Nature 399: 549-557.
38. Reader, J.S., Van Nuland, N.A., Thompson, G.S., Ferguson, S.J., Dobson, C.M., and Radford, S.E. 2001. A partially folded intermediate species of the β-sheet protein apo-pseudoazurin is trapped during proline-limited folding. Protein Sci. 10: 1216-1224.
39. Richardson, J.S. 1977. β-sheet topology and the relatedness of proteins. Nature 268: 495-500.
40. Royer, C.A., Mann, C.J., and Matthews, C.R. 1993. Resolution of the fluorescence equilibrium unfolding profile of trp aporepressor using single tryptophan mutants. Protein Sci. 2: 1844-1852.
41. Rumbley, J.N., Hoang, L., and Englander, S.W. 2002. Recombinant equine cytochrome c in Escherichia coli: High-level expression, characterization, and folding and assembly mutants. Biochemistry 41: 13894-13901.
42. Santoro, M.M. and Bolen, D.W. 1988. Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethane-sulfonyl α-chymotrypsin using different denaturants. Biochemistry 27: 8063-8068.
43. Schellman, J.A. 1978. Solvent denaturation. Biopolymers 17: 1305-1322.
44. Schiffmann, D.A., White, J.H., Cooper, A., Nutley, M.A., Harding, S.E., Jumel, K., Solari, R., Ray, K.P., and Gay, N.J. 1999. Formation and biochemical characterization of tube/pelle death domain complexes: Critical regulators of postreceptor signaling by the Drosophila toll receptor. Biochemistry 38: 11722-11733.
45. Schmid, F.X. 1986. Fast-folding and slow-folding forms of unfolded proteins. Methods Enzymol. 131: 70-82.
46. Shi, Y. 2002. Mechanisms of caspase activation and inhibition during apoptosis. Mol. Cell 9: 459-470.
47. Shiozaki, E.N., Chai, J., and Shi, Y. 2002. Oligomerization and activation of caspase-9, induced by Apaf-1 CARD. Proc. Natl. Acad. Sci. 99:4197-4202.
48. Thome, M., Hofmann, K., Burns, K., Martinon, F., Bodmer, J.L., Mattmann, C., and Tschopp, J. 1998. Identification of CARDIAK, a RIP-like kinase that associates with caspase-1. Curr. Biol. 8: 885-888.
49. Vaughn, D.E., Rodriguez, J., Lazebnik, Y., and Joshua-Tor, L. 1999. Crystal structure of Apaf-1 caspase recruitment domain: An α-helical Greek key fold for apoptotic signaling. J. Mol. Biol. 293: 439-447.
50. Weber, C.H. and Vincenz, C. 2001. The death domain superfamily: A tale of two interfaces? Trends Biochem. Sci. 26: 475-481.
51. Weissman, J.S. and Kim, P.S. 1991. Reexamination of the folding of BPTI: Predominance of native intermediates. Science 253: 1386-1393.
52. Xiao, T., Towb, P., Wasserman, S.A., and Sprang, S.R. 1999. Three-dimensional structure of a complex between the death domains of Pelle and Tube. Cell 99: 545-555.
53. Zhou, P., Chou, J., Olea, R.S., Yuan, J., and Wagner, G. 1999. Solution structure of Apaf-1 CARD and its interaction with caspase-9 CARD: A structural basis for specific adaptor/caspase interaction. Proc. Natl. Acad. Sci. 96: 11265-11270.
54. Ziegler, M.M., Goldberg, M.E., Chaffotte, A.F., and Baldwin, T.O. 1993. Refolding of luciferase subunits from urea and assembly of the active heterodimer. Evidence for folding intermediates that precede and follow the dimerization step on the pathway to the active form of the enzyme. J. Biol. Chem. 268: 10760-10765.