Conservation of folding pathways in evolutionarily distant globin sequences

Nature Structural Biology

Volumn 7, Issue 8, 2000, Pages 679-686

  Nishimura, Chiaki ^a   Prytulla, Stefan ^b   Dyson, H Jane ^a   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF GRAZ   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

APOMYOGLOBIN; GLOBIN; HEMOGLOBIN DERIVATIVE; LEGHEMOGLOBIN;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; CIRCULAR DICHROISM; EVOLUTION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE;

AMINO ACID SEQUENCE; ANIMALS; APOPROTEINS; CIRCULAR DICHROISM; EVOLUTION, MOLECULAR; GLOBINS; HEMEPROTEINS; HYDROGEN-ION CONCENTRATION; KINETICS; LEGHEMOGLOBIN; MASS SPECTROMETRY; MICROSCOPY, FLUORESCENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYOGLOBIN; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN RENATURATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT; THERMODYNAMICS; UREA;

EID: 0033871703     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/77985     Document Type: Article

References (39)

1. Lesk, A.M. & Chothia, C. How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins. J. Mol. Biol. 136, 225-270 (1980).
2. Bashford, D., Chothia, C. & Lesk, A.M. Determinants of a protein fold. Unique features of the globin amino acid sequence. J. Mol. Biol. 196, 199-216 (1987).
3. Hollecker, M. & Creighton, T.E. Evolutionary conservation and variation of protein folding pathways. J. Mol. Biol. 168, 409-437 (1983).
4. Krebs, H., Schmid, F.X. & Jaenicke, R. Folding of homologous proteins. J. Mol. Biol. 169, 619-635 (1983).
5. Stackhouse, T.M., Onuffer, J.J., Matthews, C.R., Ahmed, S.A. & Miles, E.W. Folding of homologous proteins: Conservation of the folding mechanism of the a subunit of tryptophan synthase from Escherichia coli, Salmonella typhimurium, and five interspecies hybrids. Biochemistry 27, 824-832 (1988).
6. Jaenicke, R. Folding and association of proteins. Prog. Biophys. Mol. Biol. 49, 117-237 (1987).
7. Plaxco, K.W., Spitzfaden, C., Campbell, I.D. & Dobson, C.M. A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules. J. Mol. Biol. 270, 763-770 (1997).
8. Chiti, F., et al. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Struct. Biol. 6, 1005-1009 (1999).
9. Riddle, D.S., Grantcharova, V.P., Santiago, J.V., Alm, E., Ruczinski, I. & Baker, D. Experiment and theory highlight role of native state topology in SH3 folding. Nature Struct. Biol. 6, 1016-1024 (1999).
10. Martinez, J.C. & Serrano, L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nature Struct. Biol. 6, 1010-1016 (1999).
11. Ptitsyn, O.B. & Ting, K.L. Non-functional conserved residues in globins and their possible role as a folding nucleus. J. Mol. Biol. 291, 671-682 (1999).
12. Appleby, C.A. Leghemoglobin and Rhizobium respiration. Annu. Rev. Plant Physiol. 35, 443-478 (1984).
13. Appleby, C.A. The origin and functions of hemoglobin in plants. Sci. Progr. 76, 365-398 (1992).
14. Landsmann, J., Dennis, E.S., Higgins, T.J.V., Appleby, C.A., Kortt, A.A. & Peacock, W.J. Common evolutionary origin of legume and non-legume plant haemoglobins. Nature 324, 166-168 (1986).
15. Callaway, D.J.E. Solvent-induced organization: A physical model of folding myoglobin. Proteins 20, 124-138 (1994).
16. Chelvanayagam, G., Reich, Z., Bringas, R. & Argos, P. Prediction of protein folding pathways. J. Mol. Biol. 227, 901-916 (1992).
17. Hargrove, M.S., et al. Characterization of recombinant soybean leghemoglobin a and apolar distal histidine mutants. J. Mol. Biol. 266, 1032-1042 (1997).
18. Ellis, P.J., Appleby, C.A., Guss, J.M., Hunter, W.N., Ollis, D.L. & Freeman, H.C. The crystal structure of ferric soybean leghemoglobin a nicotinate at 2.3 Å resolution. Acta Crystallogr. D 53, 302-310 (1997).
19. Kuriyan, J., Wilz, S., Karplus, M. & Petsko, G.A. X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 Å resolution. J. Mol. Biol. 192, 133-154 (1986).
20. Morikis, D. & Wright, P.E. Hydrogen exchange in the carbon monoxide complex of soybean leghemoglobin. Eur. J. Biochem. 237, 212-220 (1996).
21. Tsui, V., Garcia, C., Cavagnero, S., Siuzdak, G., Dyson, H.J. & Wright, P.E. Quenchflow experiments combined with mass spectrometry show apomyoglobin folds through an obligatory intermediate. Protein Sci. 8, 45-49 (1999).
22. Jennings, P.A. & Wright, P.E. Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262, 892-896 (1993).
23. Hughson, F.M., Wright, P.E. & Baldwin, R.L. Structural characterization of a partly folded apomyoglobin intermediate. Science 249, 1544-1548 (1990).
24. Eliezer, D., Yao, J., Dyson, H.J. & Wright, P.E. Structural and dynamic characterization of partially folded states of myoglobin and implications for protein folding. Nature Struct. Biol. 5, 148-155 (1998).
25. Jamin, M. & Baldwin, R.L. Refolding and unfolding kinetics of the equilibrium folding intermediate of apomyoglobin. Nature Struct. Biol. 3, 613-618 (1996).
26. Luo, Y., Kay, M.S. & Baldwin, R.L. Cooperativity of folding of the apomyoglobin pH 4 intermediate studied by glycine and proline mutations. Nature Struct. Biol. 4, 925-930 (1997).
27. Cavagnero, S., Dyson, H.J. & Wright, P.E. Effect of H helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin. J. Mol. Biol. 285, 269-282 (1999).
28. Garcia, C., Nishimura, C., Cavagnero, S., Dyson, H.J. & Wright, P.E. Changes in the apomyoglobin folding pathway caused by mutations of the distal histidine residue. Biochemistry in the press (2000).
29. Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. & Zehfus, M.H. Hydrophobicity of amino acid residues in globular proteins. Science 229, 834-838 (1985).
30. Muñoz, V. & Serrano, L. Development of the multiple sequence approximation within the AGADIR model of α-helix formation: Comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers 41, 495-509 (1997).
31. Waltho, J.P., Feher, V.A., Merutka, G., Dyson, H.J. & Wright, P.E. Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G-and H-helices of myoglobin. Biochemistry 32, 6337-6347 (1993).
32. Shin, H.-C., Merutka, G., Waltho, J.P., Tennant, L.L., Dyson, H.J. & Wright, P.E. Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin. Biochemistry 32, 6356-6364 (1993).
33. Dalessio, P.M. & Ropson, I.J. β-sheet proteins with nearly identical structures have different folding intermediates. Biochemistry 39, 860-871 (2000).
34. 13C resonances of soybean leghemoglobin. FEBS Lett. 399, 283-289 (1996).
35. Ellfolk, N. & Sievers, G. Circular dichroism of soybean leghemoglobin. Biochim. Biophys. Acta 405, 213-227 (1975).
36. Delaglio, F., Grzesiek, S., Vuister, G.W., Guang, Z., Pfeifer, J. & Bax, A. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 (1995).
37. 1H resonance assignments and secondary structure of the carbon monoxide complex of soybean leghemoglobin determined by homonuclear two-dimensional and three-dimensional NMR spectroscopy. Eur. J. Biochem. 219, 611-626 (1994).
38. Miranker, A., Robinson, C.V., Radford, S.E. & Dobson, C.M. Investigation of protein folding by mass spectrometry. FASEB J. 10, 93-101 (1996).
39. 1H NMR spectra. Protein Sci. 9, 186-193 (2000).