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Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes.

Publication ,  Journal Article
Liang, Z-X; Kurnikov, IV; Nocek, JM; Mauk, AG; Beratan, DN; Hoffman, BM
Published in: Journal of the American Chemical Society
March 2004

Horse myoglobin (Mb) provides a convenient "workbench" for probing the effects of electrostatics on binding and reactivity in the dynamic [Mb, cytochrome b(5)] electron-transfer (ET) complex. We have combined mutagenesis and heme neutralization to prepare a suite of six Mb surface-charge variants: the [S92D]Mb and [V67R]Mb mutants introduce additional charges on the "front" face, and incorporation of the heme di-ester into each of these neutralizes the charge on the heme propionates which further increases the positive charge on the "front" face. For this set of mutants, the nominal charge of Mb changes by -1 to +3 units relative to that for native Mb. For each member of this set, we have measured the bimolecular quenching rate constant (k(2)) for the photoinitiated (3)ZnDMb --> Fe(3+)b(5) ET reaction as a function of ionic strength. We find: (i) a dramatic decoupling of binding and reactivity, in which k(2) varies approximately 10(3)-fold within the suite of Mbs without a significant change in binding affinity; (ii) the ET reaction occurs within the "thermodynamic" or "rapid exchange" limit of the "Dynamic Docking" model, in which a large ensemble of weakly bound protein-protein configurations contribute to binding, but only a few are reactive, as shown by the fact that the zero-ionic-strength bimolecular rate constant varies exponentially with the net charge on Mb; (iii) Brownian dynamic docking profiles allow us to visualize the microscopic basis of dynamic docking. To describe these results we present a new theoretical approach which mathematically combines PATHWAY donor/acceptor coupling calculations with Poisson-Boltzmann-based electrostatics estimates of the docking energetics in a Monte Carlo (MC) sampling framework that is thus specially tailored to the intermolecular ET problem. This procedure is extremely efficient because it targets only the functionally active complex geometries by introducing a "reactivity filter" into the computations themselves, rather than as a subsequent step. This efficiency allows us to employ more computationally expensive and accurate methods to describe the relevant intermolecular interaction energies and the protein-mediated donor/acceptor coupling interactions. It is employed here to compute the changes in the bimolecular rate constant for ET between Mb and cyt b(5) upon variations in the myoglobin surface charge, pH, and ionic strength.

Duke Scholars

Published In

Journal of the American Chemical Society

DOI

EISSN

1520-5126

ISSN

0002-7863

Publication Date

March 2004

Volume

126

Issue

9

Start / End Page

2785 / 2798

Related Subject Headings

  • Thermodynamics
  • Static Electricity
  • Osmolar Concentration
  • Myoglobin
  • Myocardium
  • Monte Carlo Method
  • Models, Molecular
  • Models, Chemical
  • Kinetics
  • Horses
 

Citation

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Liang, Z.-X., Kurnikov, I. V., Nocek, J. M., Mauk, A. G., Beratan, D. N., & Hoffman, B. M. (2004). Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes. Journal of the American Chemical Society, 126(9), 2785–2798. https://doi.org/10.1021/ja038163l
Liang, Zhao-Xun, Igor V. Kurnikov, Judith M. Nocek, A Grant Mauk, David N. Beratan, and Brian M. Hoffman. “Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes.Journal of the American Chemical Society 126, no. 9 (March 2004): 2785–98. https://doi.org/10.1021/ja038163l.
Liang Z-X, Kurnikov IV, Nocek JM, Mauk AG, Beratan DN, Hoffman BM. Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes. Journal of the American Chemical Society. 2004 Mar;126(9):2785–98.
Liang, Zhao-Xun, et al. “Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes.Journal of the American Chemical Society, vol. 126, no. 9, Mar. 2004, pp. 2785–98. Epmc, doi:10.1021/ja038163l.
Liang Z-X, Kurnikov IV, Nocek JM, Mauk AG, Beratan DN, Hoffman BM. Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes. Journal of the American Chemical Society. 2004 Mar;126(9):2785–2798.
Journal cover image

Published In

Journal of the American Chemical Society

DOI

EISSN

1520-5126

ISSN

0002-7863

Publication Date

March 2004

Volume

126

Issue

9

Start / End Page

2785 / 2798

Related Subject Headings

  • Thermodynamics
  • Static Electricity
  • Osmolar Concentration
  • Myoglobin
  • Myocardium
  • Monte Carlo Method
  • Models, Molecular
  • Models, Chemical
  • Kinetics
  • Horses