The equilibrium unfolding pathway of a (β/α)8 barrel

Journal of Molecular Biology

Volumn 324, Issue 5, 2002, Pages 1031-1040

  Silverman, Joshua A ^a,b   Harbury, Pehr B ^a  

^a STANFORD UNIVERSITY   (United States)

^b MAXYGEN INC   (United States)

Author keywords

MPAX; Native state exchange; Protein folding; Triosephosphate isomerase; barrel

Indexed keywords

ALPHA BARREL PROTEIN; BETA BARREL PROTEIN; PROTEIN; TRIOSEPHOSPHATE ISOMERASE; UNCLASSIFIED DRUG; CYSTEINE; PROTON;

AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; CARBOXY TERMINAL SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; ALKYLATION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; METABOLISM; PROTEIN DENATURATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS; YEAST;

ALKYLATION; CYSTEINE; MODELS, MOLECULAR; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTONS; THERMODYNAMICS; TRIOSE-PHOSPHATE ISOMERASE; YEASTS;

EID: 0037073476     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01100-2     Document Type: Article

References (32)

1. Deng, Y. & Smith, D. L. (1998). Identification of unfolding domains in large proteins by their unfolding rates. Biochemistry, 37, 6256-6262.
2. Eder, J. & Kirschner, K. (1992). Stable substructures of eightfold beta alpha-barrel proteins: fragment complementation of phosphoribosylanthranilate isomerase. Biochemistry, 31, 3617-3625.
3. Hocker, B., Beismann-Driemeyer, S., Hettwer, S., Lustig, A. & Sterner, R. (2001). Dissection of a (beta-alpha)8-barrel enzyme into two folded halves. Nature Struct. Biol. 8, 32-36.
4. Jasanoff, A., Davis, B. & Fersht, A. R. (1994). Detection of an intermediate in the folding of the (beta alpha)8-barrel N-(5′- phosphoribosyl)anthranilate isomerase from Escherichia coli. Biochemistry, 33, 6350-6355.
5. Noland, B. W., Dangott, L. J. & Baldwin, T. O. (1999). Folding, stability, and physical properties of the alpha subunit of bacterial luciferase. Biochemistry, 38, 16136-16145.
6. Zitzewitz, J. A. & Matthews, C. R. (1999). Molecular dissection of the folding mechanism of the alpha subunit of tryptophan synthase: an amino-terminal autonomous folding unit controls several rate-limiting steps in the folding of a single domain protein. Biochemistry, 38, 10205-10214.
7. Englander, S. W. (2000). Protein folding intermediates and pathways studied by hydrogen exchange. Annu. Rev. Biophys. Biomol. Struct. 29, 213-238.
8. Raschke, T. M. & Marqusee, S. (1998). Hydrogen exchange studies of protein structure. Curr. Opin. Biotechnol. 9, 80-86.
9. Chamberlain, A. K. & Marqusee, S. (2000). Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms. Advan. Protein Chem. 53, 283-328.
10. Bai, Y., Sosnick, T. R., Mayne, L. & Englander, S. W. (1995). Protein folding intermediates: native-state hydrogen exchange. Science, 269, 192-197.
11. Myers, J. K., Pace, C. N. & 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.
12. Smith, D. L. (1998). Local structure and dynamics in proteins characterized by hydrogen exchange and mass spectrometry. Biochemistry (Moscow), 63, 285-293.
13. Feng, Z., Butler, M. C., Alam, S. L. & Loh, S. N. (2001). On the nature of conformational openings: native and unfolded-state hydrogen and thioldisulfide exchange studies of ferric aquomyoglobin. J. Mol. Biol. 314, 153-166.
14. Ha, J. H. & Loh, S. N. (1998). Changes in side-chain packing during apomyoglobin folding characterized by pulsed thiol-disulfide exchange. Nature Struct. Biol. 5, 730-737.
15. Hvidt, A. & Nielsen, S. O. (1966). Hydrogen exchange in proteins. Advan. Protein Chem. 21, 287-386.
16. Silverman, J. A. & Harbury, P. B. (2002). Rapid mapping of protein structure, interactions and ligand binding by misincorporation proton-alkyl exchange. J. Biol. Chem. 277, 30968-30975.
17. O'Neil, K. T. & DeGrado, W. F. (1990). A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science, 250, 646-651.
18. Myers, J. K., Pace, C. N. & Scholtz, J. M. (1997). A direct comparison of helix propensity in proteins and peptides. Proc. Natl. Acad. Sci. USA, 94, 2833-2837.
19. Myers, J. K., Pace, C. N. & Scholtz, J. M. (1997). Helix propensities are identical in proteins and peptides. Biochemistry, 36, 10923-10929.
20. Huyghues-Despointes, B. M., Langhorst, U., Steyaert, J., Pace, C. N. & Scholtz, J. M. (1999). Hydrogen-exchange stabilities of RNase T1 and variants with buried and solvent-exposed Ala → Gly mutations in the helix. Biochemistry, 38, 16481-16490.
21. Schliebs, W., Thanki, N., Jaenicke, R. & Wierenga, R. K. (1997). A double mutation at the tip of the dimer interface loop of triosephosphate isomerase generates active monomers with reduced stability. Biochemistry, 36, 9655-9662.
22. Morgan, C. J., Wilkins, D. K., Smith, L. J., Kawata, Y. & Dobson, C. M. (2000). A compact monomeric intermediate identified by NMR in the denaturation of dimeric triose phosphate isomerase. J. Mol. Biol. 300, 11-16.
23. Capaldi, A. P., Kleanthous, C. & Radford, S. E. (2002). Im7 folding mechanism: misfolding on a path to the native state. Nature Struct. Biol. 9, 209-216.
24. Rothwarf, D. M. & Scheraga, H. A. (1996). Role of non-native aromatic and hydrophobia interactions in the folding of hen egg white lysozyme. Biochemistry, 35, 13797-13807.
25. Balbach, J., Steegborn, C., Schindler, T. & Schmid, F. X. (1999). A protein folding intermediate of ribonuclease T1 characterized at high resolution by 1D and 2D real-time NMR spectroscopy. J. Mol. Biol. 285, 829-842.
26. Neira, J. L. & Fersht, A. R. (1999). Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments. J. Mol. Biol. 285, 1309-1333.
27. Eliezer, D., Chung, J., Dyson, H. J. & Wright, P. E. (2000). Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin. Biochemistry, 39, 2894-2901.
28. Forge, V., Hoshino, M., Kuwata, K., Arai, M., Kuwajima, K., Batt, C. A. & Goto, Y. (2000). Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix. J. Mol. Biol. 296, 1039-1051.
29. Troullier, A., Reinstadler, D., Dupont, Y., Naumann, D. & Forge, V. (2000). Transient non-native secondary structures during the refolding of alpha-lactalbumin detected by infrared spectroscopy. Nature Struct. Biol. 7, 78-86.
30. Zitzewitz, J. A., Gualfetti, P. J., Perkons, I. A., Wasta, S. A. & Matthews, C. R. (1999). Identifying the structural boundaries of independent folding domains in the alpha subunit of tryptophan synthase, a beta/ alpha barrel protein. Protein Sci. 8, 1200-1209.
31. Kunkel, T. A., Bebenek, K. & McClary, J. (1991). Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol. 204, 125-139.
32. Kraulis, P. J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.