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Biophysical Journal 87:498-512 (2004)
© 2004 The Biophysical Society

Modeling the Backbone Dynamics of Reduced and Oxidized Solvated Rat Microsomal Cytochrome b5

Andrea Giachetti *, Giovanni La Penna * {dagger}, Angelo Perico {dagger} and Lucia Banci *

* Magnetic Resonance Center, University of Florence, Florence, Italy; and {dagger} National Research Council, Institute for Macromolecular Studies, Genoa, Italy

Correspondence: Address reprint requests to Lucia Banci, Magnetic Resonance Center, University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy. E-mail: banci{at}cerm.unifi.it.

In this article, a description of the statistics and dynamics of cytochrome b5 in both reduced and oxidized forms is given. Results of molecular dynamics computer simulations in the explicit solvent have been combined with mode-coupling diffusion models including and neglecting the molecule-solvent correlations. R1 and R1{rho} nuclear magnetic relaxation parameters of 15N in the protein backbone have been calculated and compared with experiments. Slight changes in charge density in the heme upon oxidation produces a cascade of changes in charge distributions from heme propionates up to charged residues ~1.5 nm from Fe. These changes in charge distributions modify the molecular surface and the water shell surrounding the protein. The statistical changes upon oxidation can be included in diffusive models that physically explain the upper and lower limits of R1{rho} relaxation parameters at high off-resonance fields.




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E. Caballero-Manrique, J. K. Bray, W. A. Deutschman, F. W. Dahlquist, and M. G. Guenza
A Theory of Protein Dynamics to Predict NMR Relaxation
Biophys. J., December 15, 2007; 93(12): 4128 - 4140.
[Abstract] [Full Text] [PDF]


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