Erratum: Discerning the structure and energy of multiple transition states in protein folding using ψ-analysis (Journal of Molecular Biology (2004) 337 (463-475) DOI: 10.1016/j.jmb.2004.01.018);Discerning the structure and energy of multiple transition states in protein folding using ψ-analysis

Journal of Molecular Biology

Volumn 337, Issue 2, 2004, Pages 463-475

  Krantz, Bryan A ^a,c   Dothager, Robin S ^a   Sosnick, Tobin R ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

BiHis, engineered bi histidine divalent metal ion binding site; CO, contact order; F value, fractional metal binding energy realized at the transition state; Metal ion binding; Protein folding; Transition state; Ubiquitin; analysis

Indexed keywords

POLYPEPTIDE; UBIQUITIN;

ARTICLE; COMPLEX FORMATION; COVALENT BOND; ENERGY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; SIMULATION; THEORETICAL STUDY;

EID: 1442348207     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.01.001     Document Type: Erratum

References (43)

1. Fersht A.R., Itzhaki L.S., elMasry N.F., Matthews J.M., Otzen D.E. Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. Proc. Natl Acad. Sci. USA. 91:1994;10426-10429.
2. Oliveberg M., Tan Y.J., Silow M., Fersht A.R. The changing nature of the protein folding transition state: implications for the shape of the free-energy profile for folding. J. Mol. Biol. 277:1998;933-943.
3. Martinez J.C., Pisabarro M.T., Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nature Struct. Biol. 5:1998;721-729.
4. Otzen D.E., Kristensen O., Proctor M., Oliveberg M. Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry. 38:1999;6499-6511.
5. Grantcharova V.P., Riddle D.S., Baker D. Long-range order in the src SH3 folding transition state. Proc. Natl Acad. Sci. USA. 97:2000;7084-7089.
6. Sanchez I.E., Kiefhaber T. Hammond behavior versus ground state effects in protein folding: evidence for narrow free energy barriers and residual structure in unfolded states. J. Mol. Biol. 327:2003;867-884.
7. Wright C.F., Lindorff-Larsen K., Randles L.G., Clarke J. Parallel protein-unfolding pathways revealed and mapped. Nature Struct. Biol. 10:2003;658-662.
8. Moran L.B., Schneider J.P., Kentsis A., Reddy G.A., Sosnick T.R. Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking. Proc. Natl Acad. Sci. USA. 96:1999;10699-10704.
9. Matthews C.R. Effects of point mutations on the folding of globular proteins. Methods Enzymol. 154:1987;498-511.
10. Fersht A.R., Matouschek A., Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224:1992;771-782.
11. Sanchez I.E., Kiefhaber T. Origin of unusual phi-values in protein folding: evidence against specific nucleation sites. J. Mol. Biol. 334:2003;1077-1085.
12. Kim D.E., Yi Q., Gladwin S.T., Goldberg J.M., Baker D. The single helix in protein L is largely disrupted at the rate-limiting step in folding. J. Mol. Biol. 284:1998;807-815.
13. Ozkan S.B., Bahar I., Dill K.A. Transition states and the meaning of Phi-values in protein folding kinetics. Nature Struct. Biol. 8:2001;765-769.
14. Bulaj G., Goldenberg D.P. Phi-values for BPTI folding intermediates and implications for transition state analysis. Nature Struct. Biol. 8:2001;326-330.
15. Krantz B.A., Sosnick T.R. Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nature Struct. Biol. 8:2001;1042-1047.
16. Northey J.G., Maxwell K.L., Davidson A.R. Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J. Mol. Biol. 320:2002;389-402.
17. Horovitz A., Amir A., Danziger O., Kafri G. Phi value analysis of heterogeneity in pathways of allosteric transitions: evidence for parallel pathways of ATP-induced conformational changes in a GroEL ring. Proc. Natl Acad. Sci. USA. 99:2002;14095-14097.
18. Krantz B.A., Sosnick T.R. Distinguishing between two-state and three-state models for ubiquitin folding. Biochemistry. 39:2000;11696-11701.
19. 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.
20. A Brønsted J.N., Pedersen K. The catalytic decomposition of nitramide and its physico-chemical applications. Z. Phys. Chem. 108:1924;185-235.
21. 2+ binding on the folding kinetics of alpha-lactalbumin. J. Mol. Biol. 206:1989;547-561.
22. Pan Y., Briggs M.S. Hydrogen exchange in native and alcohol forms of ubiquitin. Biochemistry. 31:1992;11405-11412.
23. Kuwajima K. The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins: Struct. Funct. Genet. 6:1989;87-103.
24. Sosnick T.R., Mayne L., Englander S.W. Molecular collapse: the rate-limiting step in two-state cytochrome c folding. Proteins: Struct. Funct. Genet. 24:1996;413-426.
25. Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:1998;985-994.
26. Abkevich V.I., Gutin A.M., Shakhnovich E.I. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 33:1994;10026-10036.
27. Khorasanizadeh S., Peters I.D., Roder H. Evidence for a 3-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nature Struct. Biol. 3:1996;193-205.
28. Munoz V., Serrano L. Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers. 41:1997;495-509.
29. Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4:1997;19.
30. Shakhnovich E.I. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Fold. Des. 3:1998;R108-R111.
31. Thirumalai D., Klimov D.K. Fishing for folding nuclei in lattice models and proteins. Fold. Des. 3:1998;R112-R118.
32. Socci N.D., Onuchic J.N., Wolynes P.G. Protein folding mechanisms and the multidimensional folding funnel. Proteins: Struct. Funct. Genet. 32:1998;136-158.
33. Dinner A.R., Sali A., Smith L.J., Dobson C.M., Karplus M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci. 25:2000;331-339.
34. Zerella R., Chen P.Y., Evans P.A., Raine A., Williams D.H. Structural characterization of a mutant peptide derived from ubiquitin: implications for protein folding. Protein Sci. 9:2000;2142-2150.
35. Krantz B.A., Srivastava A.K., Nauli S., Baker D., Sauer R.T., Sosnick T.R. Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature Struct. Biol. 9:2002;458-463.
36. Makarov D.E., Keller C.A., Plaxco K.W., Metiu H. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc. Natl Acad. Sci. USA. 99:2002;3535-3539.
37. Zhou H., Zhou Y. Folding rate prediction using total contact distance. Biophys. J. 82:2002;458-463.
38. Gong H., Isom D.G., Srinivasan R., Rose G.D. Local secondary structure content predicts folding rates for simple, two-state proteins. J. Mol. Biol. 327:2003;1149-1154.
39. Makarov D.E., Plaxco K.W. The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci. 12:2003;17-26.
40. Kaya H., Chan H.S. Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins: Struct. Funct. Genet. 52:2003;524-533.
41. Riddle D.S., Grantcharova V.P., Santiago J.V., Alm E., Ruczinski I.I., Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nature Struct. Biol. 6:1999;1016-1024.
42. Chen P.Y., Gopalacushina B.G., Yang C.C., Chan S.I., Evans P.A. The role of a beta-bulge in the folding of the beta-hairpin structure in ubiquitin. Protein Sci. 10:2001;2063-2074.
43. Vijay-Kumar S., Bugg C.E., Wilkinson K.D., Vierstra R.D., Hatfield P.M., Cook W.J. Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin. J. Biol. Chem. 262:1987;6396-6399.