The C terminus of apocytochrome b562 undergoes fast motions and slow exchange among ordered conformations resembling the folded state.
The present work describes the dynamics of the apo form of cytochrome b(562), a small soluble protein consisting of 106 amino acid residues [Itagaki, E., and Hager, L. P. (1966) J. Biol. Chem. 241, 3687-3695]. The presence of exchange in the millisecond time scale is demonstrated for the last part of helix IV (residues 95-105 in the holo form). The chemical shift index analysis [Wishart, D. S., and Sykes, B. D. (1994) J. Biomol. NMR 4, 171-180] based on H(alpha), C(alpha), C(beta), and C' chemical shifts suggests a larger helical content than shown in the NMR structure based on NOEs. These results indicate the presence of helical-like conformations participating in the exchange process. This hypothesis is consistent with amide deuterium exchange rates and the presence of some hydrogen bonds identified from amide chemical shift temperature coefficients [Baxter, N. J., and Williamson, M. P. (1997) J. Biomol. NMR 9, 359-369]. (15)N relaxation indicates limited mobility for the amide protons of this part of the helix in the picosecond time scale. A 30 ns stochastic dynamics simulation shows small fluctuations around the helical conformation on this time scale. These fluctuations, however, do not result in a significant decrease of the calculated order parameters which are consistent with the experimental (15)N relaxation data. These results resolve an apparent discrepancy in the NMR structures between the disorder observed in helix IV due to a lack of NOEs and the secondary structure predictions based on H(alpha) chemical shifts [Feng, Y., Wand, A. J., and Sligar, S. G. (1994) Struct. Biol. 1, 30-35].
D'Amelio
Nicola
N
NMR Department of the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands.
Bonvin
Alexandre M J J
AM
Czisch
Michael
M
Barker
Paul
P
Kaptein
Rob
R
D000577:Amides / Q000737:chemistry; D001059:Apoproteins / Q000737:chemistry*; D002247:Carbon Isotopes; D002248:Carbon Monoxide / Q000737:chemistry; D003573:Cytochrome b Group / Q000737:chemistry*; D003903:Deuterium; D004926:Escherichia coli / Q000201:enzymology; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D011522:Protons; D013696:Temperature; D013816:Thermodynamics
D000577:Amides; D001059:Apoproteins; D002247:Carbon Isotopes; D003573:Cytochrome b Group; D009587:Nitrogen Isotopes; D010446:Peptide Fragments; D011522:Protons; D002248:Carbon Monoxide; D003903:Deuterium