Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

FEBS Letters

Volumn 581, Issue 25, 2007, Pages 4965-4971

  Modig, Kristofer ^a   Jürgensen, Vibeke W ^a,b   Lindorff Larsen, Kresten ^a   Fieber, Wolfgang ^a   Bohr, Henrik G ^b   Poulsen, Flemming M ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Chemical shift; Intrinsic random coil chemical shifts; NMR; Protein folding; Residual dipolar coupling; Unfolded states

Indexed keywords

ACID; ACYL COENZYME A; BINDING PROTEIN; CARBON;

AMINO ACID SEQUENCE; ARTICLE; METHODOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

ACYL COENZYME A; AMINO ACID SEQUENCE; CARRIER PROTEINS; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT;

EID: 35148842435     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.09.027     Document Type: Article

References (33)

1. Kragelund B.B., Robinson C.V., Knudsen J., Dobson C.M., and Poulsen F.M. Folding of a 4-helix bundle - studies of acyl-coenzyme A binding protein. Biochemistry 34 (1995) 7217-7224
2. Teilum K., Maki K., Kragelund B.B., Poulsen F.M., and Roder H. Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing. Proc. Nat. Acad. Sci. USA 99 (2002) 9807-9812
3. Teilum K., Poulsen F.M., and Akke M. The inverted chevron plot measured by NMR relaxation reveals a native-like unfolding intermediate in acyl-CoA binding protein. Proc. Nat. Acad. Sci. USA 103 (2006) 6877-6882
4. Kragelund B.B., Osmark P., Neergaard T.B., Schiodt J., Kristiansen K., Knudsen J., and Poulsen F.M. The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP. Nat. Struct. Biol. 6 (1999) 594-601
5. Teilum K., Thormann T., Caterer N.R., Poulsen H.I., Jensen P.H., Knudsen J., Kragelund B.B., and Poulsen F.M. Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles. Proteins-Struct. Funct. Bioinformat. 59 (2005) 80-90
6. Teilum K., Kragelund B.B., Knudsen J., and Poulsen F.M. Formation of hydrogen bonds precedes the rate-limiting formation of persistent structure in the folding of ACBP. J. Mol. Biol. 301 (2000) 1307-1314
7. Fieber W., Kristjansdottir S., and Poulsen F.M. Short-range, long-range and transition state interactions in the denatured state of ACBP from residual dipolar couplings. J. Mol. Biol. 339 (2004) 1191-1199
8. Thomsen J.K., Kragelund B.B., Teilum K., Knudsen J., and Poulsen F.M. Transient intermediary states with high and low folding probabilities in the apparent two-state folding equilibrium of ACBP at low pH. J. Mol. Biol. 318 (2002) 805-814
9. Lindorff-Larsen K., Kristjansdottir S., Teilum K., Fieber W., Dobson C.M., Poulsen F.M., and Vendruscolo M. Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme A binding protein. J. Am. Chem. Soc. 126 (2004) 3291-3299
10. Kristjansdottir S., Lindorff-Larsen K., Fieber W., Dobson C.M., Vendruscolo M., and Poulsen F.M. Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies. J. Mol. Biol. 347 (2005) 1053-1062
11. Schwarzinger S., Kroon G.J., Foss T.R., Chung J., Wright P.E., and Dyson H.J. Sequence-dependent correction of random coil NMR chemical shifts. J. Am. Chem. Soc. 123 (2001) 2970-2978
12. Schwarzinger S., Kroon G.J., Foss T.R., Wright P.E., and Dyson H.J. Random coil chemical shifts in acidic 8 M urea: implementation of random coil shift data in NMRView. J. Biomol. NMR 18 (2000) 43-48
13. Bundi A., and Wüthrich K. NMR parameters of the common amino-acid residues measured in aqueous-solutions of the linear tetrapeptides h-Gly-Gly-x-l-Ala-OH. Biopolymers 18 (1979) 285-297
14. Spera S., and Bax A. Empirical correlation between protein backbone conformation and C-alpha and C-beta C-13 nuclear-magnetic-resonance chemical-shifts. J. Am. Chem. Soc. 113 (1991) 5490-5492
15. Wishart D.S., Sykes B.D., and Richards F.M. Simple techniques for the quantification of protein secondary structure by H-1-NMR spectroscopy. J. Mol. Biol. 222 (1991) 311-333
16. Braun D., Wider G., and Wüthrich K. Sequence-corrected N-15 random coil chemical-shifts. J. Am. Chem. Soc. 116 (1994) 8466-8469
17. Wishart D.S., Bigam C.G., Holm A., Hodges R.S., and Sykes B.D. H-1, C-13 and N-15 random coil NMR chemical-shifts of the common amino-acids 1. Investigations of nearest-neighbor effects. J. Biomol. NMR 5 (1995) 67-81
18. Neal S., Nip A.M., Zhang H., and Wishart D.S. Rapid and accurate calculation of protein H-1, C-13 and N-15 chemical shifts. J. Biomol. NMR 26 (2003) 215-240
19. Wishart D.S., Sykes B.D., and Richards F.M. The chemical-shift index - a fast and simple method for the assignment of protein secondary structure through NMR-spectroscopy. Biochemistry 31 (1992) 1647-1651
20. Wishart D.S., and Sykes B.D. The C-13 chemical-shift index - a simple method for the identification of protein secondary structure using C-13 chemical-shift data. J. Biomol. NMR 4 (1994) 171-180
21. Logan T.M., Thériault Y., and Fesik S.W. Structural characterization of the fk506 binding-protein unfolded in urea and guanidine-hydrochloride. J. Mol. Biol. 236 (1994) 637-648
22. Buck M., Schwalbe H., and Dobson C.M. Characterization of conformational preferences in a partly folded protein by heteronuclear NMR-spectroscopy - assignment and secondary structure-analysis of hen egg-white lysozyme in trifluoroethanol. Biochemistry 34 (1995) 13219-13232
23. Kuwata K., Hoshino M., Era S., Batt C.A., and Goto Y.J. Alpha → beta transition of beta-lactoglobulin as evidenced by heteronuclear NMR. Mol. Biol. 283 (1998) 731-739
24. Schwarzinger S., Wright P.E., and Dyson H.J. Molecular hinges in protein folding: the urea-denatured state of apomyoglobin. Biochemistry 41 (2002) 12681-12686
25. Klein-Seetharaman J., Oikawa M., Grimshaw S.B., Wirmer J., Duchardt E., Ueda T., Imoto T., Smith L.J., Dobson C.M., and Schwalbe H. Long-range interactions within a non-native protein. Science 295 (2002) 1719-1722
26. Flory P.J. Statistical Mechanics of Chain Molecules (1969), Interscience Publishers, New York
27. Pappu R.V., Srinivasan R., and Rose G.D. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding. Proc. Nat. Acad. Sci. USA 97 (2000) 12565-12570
28. Pace C.N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131 (1986) 266-280
29. Seavey B.R., Farr E.A., Westler W.M., and Markley J.L. A relational database for sequence-specific protein NMR data. J. Biomol. NMR 1 (1991) 217-236
30. Mandrup S., Hojrup P., Kristiansen K., and Knudsen J. Gene synthesis, expression in Escherichia coli, purification and characterization of the recombinant bovine acyl-CoA binding protein. Biochem. J. 276 (1991) 817-823
31. Fieber W., Kragelund B.B., Meldal M., and Poulsen F.M. Reversible dimerization of acid-denatured ACBP controlled by helix A4. Biochemistry 44 (2005) 1375-1384
32. Nozaki Y. The preparation of guanidine hydrochloride. Methods Enzymol. 26 (1972) 43-50
33. Markley J.L., Bax A., Arata Y., Hilbers C.W., Kaptein R., Sykes B.D., Wright P.E., and Wüthrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids - IUPAC-IUBMB-IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. J. Biomol. NMR 12 (1998) 1-23