Trapping the on-pathway folding intermediate of Im7 at equilibrium

Journal of Molecular Biology

Volumn 341, Issue 1, 2004, Pages 215-226

  Spence, Graham R ^a   Capaldi, Andrew P ^a   Radford, Sheena E ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

, histidine tagged Im7; equilibrium intermediate; folding; Im7; immunity protein; Kxy, the equilibrium constant between x and y; kxy, the rate constant of folding unfolding from x to y; kinetic analysis; rational design

Indexed keywords

8 ANILINO 1 NAPHTHALENESULFONIC ACID; DOCKING PROTEIN; GLYCINE; HISTIDINE; MUTANT PROTEIN; TRYPTOPHAN;

AMINO ACID SEQUENCE; ARTICLE; CIRCULAR DICHROISM; EQUILIBRIUM CONSTANT; FLUORESCENCE; HYDROPHOBICITY; MUTATION; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN DETERMINATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN VARIANT; PROTON NUCLEAR MAGNETIC RESONANCE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; SURFACE PROPERTY; THERMODYNAMICS;

CLIDEMIA HIRTA;

EID: 4143080376     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.05.049     Document Type: Article

References (48)

1. Khan F., Chuang J.I., Gianni S., Fersht A.R. The kinetic pathway of folding of barnase. J. Mol. Biol. 333:2003;169-186
2. Ferguson N., Capaldi A.P., James R., Kleanthous C., Radford S.E. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. J. Mol. Biol. 286:1999;1597-1608
3. Sanchez I.E., Kiefhaber T. Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325:2003;367-376
4. Qi P.X., Sosnick T.R., Englander S.W. The burst phase in ribonuclease a folding and solvent dependence of the unfolded state. Nature Struct. Biol. 5:1998;882-884
5. Sosnick T.R., Shtilerman M.D., Mayne L., Englander S.W. Ultrafast signals in protein folding and the polypeptide contracted state. Proc. Natl Acad. Sci. USA. 94:1997;8545-8550
6. Silow M., Tan Y.J., Fersht A.R., Oliveberg M. Formation of short-lived protein aggregates directly from the coil in two-state folding. Biochemistry. 38:1999;13006-13012
7. Silow M., Oliveberg M. Transient aggregates in protein folding are easily mistaken for folding intermediates. Proc. Natl Acad. Sci. USA. 94:1997;6084-6086
8. Krantz B.A., Mayne L., Rumbley J., Englander S.W., Sosnick T.R. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J. Mol. Biol. 324:2002;359-371
9. Parker M.J., Marqusee S. A kinetic folding intermediate probed by native state hydrogen exchange. J. Mol. Biol. 305:2001;593-602
10. Shastry M.C., Roder H. Evidence for barrier-limited protein folding kinetics on the microsecond time scale. Nature Struct. Biol. 5:1998;385-392
11. Capaldi A.P., Shastry M.C.R., Kleanthous C., Roder H., Radford S.E. Ultrarapid mixing experiments reveal that Im7 folds via an on-pathway intermediate. Nature Struct. Biol. 8:2001;68-72
12. Capaldi A.P., Kleanthous C., Radford S.E. Im7 folding mechanism: misfolding on a path to the native state. Nature Struct. Biol. 9:2002;209-216
13. Takei J., Pei W., Vu D., Bai Y. Populating partially unfolded forms by hydrogen exchange-directed protein engineering. Biochemistry. 41:2002;12308-12312
14. Eliezer D., Chung J., Dyson H.J., Wright P.E. Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin. Biochemistry. 39:2000;2894-2901
15. Pandya M.J., Williams P.B., Dempsey C.E., Shewry P.R., Clarke A.R. Direct kinetic evidence for folding via a highly compact, misfolded state. J. Biol. Chem. 274:1999;26828-26837
16. Roder H., Colon W. Kinetic role of early intermediates in protein folding. Curr. Opin. Struct. Biol. 7:1997;15-28
17. Parker M.J., Dempsey C.E., Lorch M., Clarke A.R. Acquisition of native beta-strand topology during the rapid collapse phase of protein folding. Biochemistry. 36:1997;13396-13405
18. Krishna M.M.G., Lin Y., Mayne L., Walter Englander S. Intimate view of a kinetic protein folding intermediate: residue-resolved structure, interactions, stability, folding and unfolding rates, homogeneity. J. Mol. Biol. 334:2003;501-513
19. Fersht A.R. A kinetically significant intermediate in the folding of barnase. Proc. Natl Acad. Sci. USA. 97:2000;14121-14126
20. Jemth P., Gianni S., Day R., Li B., Johnson C.M., Daggett V., Fersht A.R. Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. Proc. Natl Acad. Sci. USA. 101:2004;6450-6455
21. Myers J.K., Oas T.G. Mechanism of fast protein folding. Annu. Rev. Biochem. 71:2002;783-815
22. Ferguson N., Fersht A.R. Early events in protein folding. Curr. Opin. Struct. Biol. 13:2003;75-81
23. Fersht A.R., Daggett V. Protein folding and unfolding at atomic resolution. Cell. 108:2002;573-582
24. Horovitz A. Double-mutant cycles: a powerful tool for analyzing protein structure and function. Fold. Des. 1:1996;R121-R126
25. Englander S.W. Protein folding intermediates and pathways studied by hydrogen exchange. Annu. Rev. Biophys. Biomol. Struct. 29:2000;213-238
26. Chamberlain A.K., Marqusee S. Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms. Advan. Protein Chem. 53:2000;283-328
27. Gorski S.A., Le Duff C.S., Capaldi A.P., Kalverda A.P., Beddard G.S., Moore G.R., Radford S.E. Equilibrium hydrogen exchange reveals extensive hydrogen bonded secondary structure in the on-pathway intermediate of Im7. J. Mol. Biol. 337:2004;183-193
28. Dennis C.A., Videler H., Pauptit R.A., Wallis R., James R., Moore G.R., Kleanthous C. A structural comparison of the colicin immunity proteins Im7 and Im9 gives new insights into the molecular determinants of immunity-protein specificity. Biochem. J. 333:1998;183-191
29. Li W., Dennis C.A., Moore G.R., James R., Kleanthous C. Protein-protein interaction specificity of Im9 for the endonuclease toxin colicin E9 defined by homologue-scanning mutagenesis. J. Biol. Chem. 272:1997;22253-22258
30. Siedlecka M., Goch G., Ejchart A., Sticht H., Bierzyski A. Alpha-helix nucleation by a calcium-binding peptide loop. Proc. Natl Acad. Sci. USA. 96:1999;903-908
31. Chen Y.H., Yang J.T., Chau K.H. Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry. 13:1974;3350-3359
32. Woody R.W., Tinoco I. Jr. Optical rotation of oriented helices.3. Calculation of rotatory dispersion and circular dichroism of alpha- and 310-helix. J. Chem. Phys. 46:1967;4927-4945
33. Semisotnov G.V., Rodionova N.A., Razgulyaev O.I., Uversky V.N., Gripas A.F., Gilmanshin R.I. Study of the "molten globule" intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers. 31:1991;119-128
34. Arai M., Kuwajima K. Role of the molten globule state in protein folding. Advan. Protein Chem. 53:2000;209-282
35. Ramboarina S., Redfield C. Structural characterisation of the human alpha-lactalbumin molten globule at high temperature. J. Mol. Biol. 330:2003;1177-1188
36. Redfield C., Schulman B.A., Milhollen M.A., Kim P.S., Dobson C.M. Alpha-lactalbumin forms a compact molten globule in the absence of disulfide bonds. Nature Struct. Biol. 6:1999;948-952
37. Gorski S.A., Capaldi A.P., Kleanthous C., Radford S.E. Acidic conditions stabilise intermediates populated during the folding of im7 and Im9. J. Mol. Biol. 312:2001;849-863
38. Myers J.K., Pace C.N., Scholtz J.M. Denaturant m-values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4:1995;2138-2148
39. Paci E., Friel C.T., Lindorff-Larsen K., Radford S.E., Karplus M., Vendruscolo M. Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with φ value restraints. Proteins: Struct. Funct. Genet. 54:2004;513-525
40. Gill S.C., von Hippel P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:1989;319-326
41. Stafford W.F. III. Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Anal. Biochem. 203:1992;295-301
42. Philo J.S. A method for directly fitting the time derivative of sedimentation velocity data and an alternative algorithm for calculating sedimentation coefficient distribution functions. Anal. Biochem. 279:2000;151-163
43. Hwang T.-L., Shaka A.J. Water suppression that works. Excitation sculpting using arbitary waveforms and pulsed field gradients. J. Magn. Res. ser. A. 112:1995;275-279
44. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., Bax A. NMRpipe: A multidimensional spectral processing system based on unix pipes. J. Biomol. NMR. 6:1995;277-293
45. Altieri A.S., Hinton D.P., Byrd R.A. Association of biomolecular systems via pulsed field gradient NMR self-diffusion measurements. J. Am. Chem. Soc. 117:1995;7566-7567
46. Wilkins D.K., Grimshaw S.B., Receveur V., Dobson C.M., Jones J.A., Smith L.J. Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques. Biochemistry. 38:1999;16424-16431
47. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
48. Merrit E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524