Abstract
The apoprotein is an important intermediate on the folding pathways of many haem proteins, yet a detailed structure of such an intermediate has remained elusive. Here we present the structure of apocytochrome b562 obtained by NMR spectroscopy. The apoprotein has a topology similar to the holoprotein. Nevertheless, significant differences in helix–helix packing between the two are evident. Much of the haem binding pocket in the apoprotein is preserved but exposed to solvent creating a large cavern. As apocytochrome b562 displays many of the physical characteristics ascribed to the molten globule state, these results help ellucidate the origin of several properties of the protein molten globule.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Get just this article for as long as you need it
$39.95
Prices may be subject to local taxes which are calculated during checkout
References
Creighton, T.E. The disulphide folding pathway of BPTI. Science 256, 111–112 (1992).
Oas, T. & Kim, P.S. A peptide model of a protein folding intermediate. Nature 336, 42–48 (1988).
Hughson, F.M., Barrick, D. & Baldwin, R.L. Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis. Biochemistry 30, 4113–4118 (1991).
Baum, J., Dobson, C.E., Evans, P.A. & Hanley, C. Characterization of a partly folded protein by NMR methods: Studies on the molten globule state of guinea pig α-lactalbumin. Biochemisty 28, 7–13 (1989).
Jeng, M.-F., Englander, S.W., Elove, G.A., Wand, A.J. & Roder, H. Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry 29, 10433–10437 (1990).
Jeng, M.-F. & Englander, S.W. Stable submolecular folding units in a non-compact form of cytochrome c. J. molec. Biol. 221, 1045–1061 (1991).
Ikeguchi, M., Kuwajima, K. & Sugai, S. Ca2+-induced alteration in the unfolding behavior of α-lactalbumin. J. Biochem. 99, 1191–1201 (1986).
Moore, C.D. & Lecomte, J.T.J. Structural properties of apocytochrome b5: Presence of a stable native core. Biochemistry 29, 1984–1989 (1990).
Cocco, M.J. & Lecomte, J.T.J. Characterization of hydrophobic cores in apomyoglobin: A proton NMR spectroscopy study. Biochemistry 29, 11067–11072 (1990).
Hughson, F.M., Wright, P.E. & Baldwin, R.L. Structural characterization of a partly folded apomyoglobin intermediate. Science 249, 1544–1548 (1990).
Feng, Y. & Sligar, S.G. Effect of heme binding on the structure and stability of Escherichia coli apocytochrome b562 . Biochemistry 30, 10150–10155 (1991).
Hughson, F.M. & Baldwin, R.L. Use of site-directed mutagenesis to destabilize native apomyoglobin relative to folding intermediates. Biochemistry 28, 4415–4422 (1989).
Cocco, M.J., Kao, Y-H., Phillips, A.T. & Lecomte, J.T.J. Structural comparison of apomyoglobin and metaquomyoglobin: pH titration histidines by NMR spectroscopy. Biochemistry 31, 6481–6491 (1992).
Moore, C.D., AI-Misky, O.N. & Lecomte, J.T. Similarities in structure in structure between holocytochrome b5 and apocytochrome b5: NMR studies of histidine residues. Biochemistry 30, 8357–8365 (1991).
Lecomte, J.T.J. & Moore, C.D. Helix formation in apocytochrome b5: The role of a neutral histidine at the N-cap position. J. Am. chem. Soc. 113, 9663–9665 (1991).
Feng, Y., Wand, A.J. & Sligar, S.G. 1H and 15N NMR resonance assignments and preliminary structural characterization of Escherichia coli apocytochrome b562 . Biochemistry 30, 7711–7717 (1991).
Robinson, C. & Sligar, S.G. Electrostatic stabilization in four helix bundle proteins. Protein Science 2, 826–837 (1993).
Macura, S. & Ernst, R.R. Elucidation of cross relaxation in liquids by two-dimensional NMR spectroscopy. Molec. Phys. 61, 95–119 (1980).
Wüthrich, K., Billeter, M. & Braun, W. Polypeptide secondary structure determination by NMR observation of short proton-proton distances J. molec. Biol. 180, 715–740 (1984).
Englander, S.W. & Wand, A.J. Main chain directed strategy for the assignment of 1H NMR spectra of proteins. Biochemistry 28, 5953–5958 (1987).
Wand, A.J. & Nelson, S.J. Refinement of the main chain directed assignment strategy for the analysis of 1H NMR spectra of proteins. Biophys. J. 59, 1301–1112 (1991).
Clore, G.M. & Gronenborn, A.M. A. Rev. Biophys. biophys. Chem. 20, 29–63 (1991).
Lederer, F., Glatigny, A., Bethge, P.H., Bellamy, H.D. & Mathews, F.S. Improvement of the 2.5 Å resolution model of cytochrome b562 by redetermining the primary structure and using molecular graphics. J. molec. Biol. 148, 427–448 (1981).
Lee, B. & Richards, F. The interpretation of protein structures: Estimation of static accessibility. J. molec. Biol. 55, 379–400 (1971).
Spolar, R.S., Ha, J.-H. & Record, M.T. Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc. natn. Acad. Sci. U.S.A. 86, 8382–8385 (1989).
Privalov, P.L. & Makhatadze, G.I. Heat capacity of proteins. 2. Partial molar heat capacity of the unfolded polypeptide cahin of proteins- protein unfolding effects. J. molec. Biol. 213, 385–391 (1990).
Haynie, D.T. & Freire, E. Structural energetics of the molten globule state. Proteins 16, 115–140 (1993).
Kuwajima, K. The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins 6, 87–103 (1989).
Kim, P.S. & Baldwin, R.L. Intermediates in the folding reactions of small proteins. A. Rev. Biochem. 59, 631–660 (1990).
Baldwin, R.L. Molten globules: Specific or nonspecific folding intermediates? Chemtracts-Biochemistry & Molecular Biology 2, 379–389 (1991).
Barrick, D. & Baldwin, R.L. The molten globule intermediate of apomyoglobin and the process of protein folding. Protein Science 2, 869–876 (1993).
Stockman, B.J., Euvrard, A. & Scahill, T.A. Heteronuclear three-dimensional NMR spectroscopy of a partially denatured protein: The A-state of human ubiquitin. J. biomolecular NMR 3, 285–296 (1993).
Chyan, C.-L., Wormald, C., Dobson, C.M., Evans, P.A., Baum, J. Biochemistry 29, 5681–5691 (1992).
Nikkila, H., Gennis, R. & Sligar, S.G. Cloning and expression of the gene encoding the soluble cytochrome b562 of Escherichia coli. Eur. J. Biochem. 202, 309–313 (1991).
Teale, F.W.J. Cleavage of the haem-protein link by acid methylethylketone. Biochem. biophys. Acta. 35, 543 (1959).
Kay, L.E., Marion, D. & Bax, A. Practical aspects of 3D heteronuclear NMR of proteins. J. magn. Reson. 84, 72–84 (1989).
Kay, L.E. & Bax, A. New methods for the measurement of NH-CaH coupling constants in 15N-labeled proteins. J. magn. Reson. 86, 110–126 (1990).
Pardi, A., Wagner, G. & Wüthrich, K. Calibration of the angular dependence of the amide proton-C α-proton coupling constants 3JHNα, in a globular protein J. molec. Biol. 180, 741–751 (1984).
Nerdal, W., Hare, D.R. & Reid, B.R. 3-dimensional structure of the wild-type Lac Pribinov promoter DNA in solution- two dimensional nuclear magnetic resonance studies and distance geometry calculations. J. molec. Biol. 201, 717–721 (1988).
Weber, P.L., Morrison, R. & Hare, D.R. Determining the stereo-specific 1H nuclear magnetic resonance assignments from distance geometry calculations. J. molec. Biol. 204, 483–487 (1988).
Brünger, A.T., Clore, G.M., Gronenborn, A.M. & Karplus, M. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin. Proc. natn. Acad. Sci. U.S.A. 83, 3801–3805 (1986).
Carson, M. Ribbon models of macromolecules. J. molec. Graphics 5, 103–106 (1987).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Feng, Y., Sligar, S. & Wand, A. Solution structure of apocytochrome b562. Nat Struct Mol Biol 1, 30–35 (1994). https://doi.org/10.1038/nsb0194-30
Issue Date:
DOI: https://doi.org/10.1038/nsb0194-30
This article is cited by
-
Bipartite structure of the α-lactalbumin molten globule
Nature Structural & Molecular Biology (1995)
-
Partially folded, molten globule and molten coil states of bovine pancreatic trypsin inhibitor
Nature Structural & Molecular Biology (1995)
-
Molten globular characteristics of the native state of apomyoglobin
Nature Structural & Molecular Biology (1994)
-
The connective tissue connection
Nature Structural & Molecular Biology (1994)
-
Snapshots of the 'molten globule'
Nature (1994)