Dynamic Docking and Electron-Transfer between Cytochrome<i> b</i><sub>5</sub> and a Suite of Myoglobin Surface-Charge Mutants. Introduction of a Functional-Docking Algorithm for Protein−Protein Complexes

Liang, Zhao‐Xun; Kurnikov, Igor V.; Nocek, Judith M.; Mauk, A. Grant; Beratan, David N.; Hoffman, Brian M.

doi:10.1021/ja038163l

Cited by 73 publications

(141 citation statements)

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“…Unlike the hybrids, results to date suggest that intracomplex ET may not persist as the viscosity increases without bound (38). (4,14). These studies showed that the bimolecular, 3 ZnDMb 3 Fe 3ϩ b 5 forward ET rate constant, k f2 , increases dramatically as the positive charge on Mb is changed by the nominal amounts, Ϫ1 Յ ⌬q nom Յ ϩ3, but without a substantial increase in the binding affinity (4).…”

Section: Methodsmentioning

confidence: 95%

“…Samples for ET studies were prepared in the dark under a N 2 atmosphere as described (4,14). Briefly, protein stock solutions for flash photolysis were exchanged into working buffers: 10 For the experiments with the Hb hybrid and the [ZnCcP(W191F),Fe 3ϩ Cc] complex, cryosolvents of varying viscosity were made at a selected (vol͞vol) composition of glycerol and deionized water.…”

Section: Methodsmentioning

confidence: 99%

“…1 A Right (4,14). This paradigm in protein-protein ET was revealed through the decoupling of binding and reactivity: increasing the surface charge on Mb caused the second-order rate for ET from 3 ZnMb to Fe 3ϩ b 5 to increase by nearly three orders of magnitude without significantly varying Mb's binding affinity for Fe 3ϩ b 5 .…”

mentioning

confidence: 99%

“…Much of this work seeks to understand the electron transfer (ET) process itself. However, when the ET event involves a dynamic protein-protein interface, the observed kinetics frequently are controlled not by the ET process itself, but by the dynamics of recognition and binding and͞or conversion within an ensemble of bound configurations (3,4).…”

mentioning

confidence: 99%

“…Recent studies of ET between myoglobin (Mb) and cytochrome b 5 (Fe 3ϩ b 5 ), which bind to each other by weak electrostatic interactions, disclosed a new dynamic docking paradigm in protein-protein reaction dynamics: the landscape involves numerous configurations of similar affinity, only a subset of which is active in ET ( Fig. 1 A Right) (4,14).…”

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confidence: 99%

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Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface

Hoffman

Celis²,

Cull³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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We propose that the forward and reverse halves of a flash-induced protein-protein electron transfer (ET) photocycle should exhibit differential responses to dynamic interconversion of configurations when the most stable configuration is not the most reactive, because the reactants exist in different initial configurations: the flash-photoinitiated forward ET process begins with the protein partners in an equilibrium ensemble of configurations, many of which have little or no reactivity, whereas the reactant of the thermal back ET (the charge-separated intermediate) is formed in a nonequilibrium, ''activated'' protein configuration. We report evidence for this proposal in measurements on (i) mixed-metal hemoglobin hybrids, (ii) the complex between cytochrome c peroxidase and cytochrome c, and (iii and iv) the complexes of myoglobin and isolated hemoglobin ␣-chains with cytochrome b 5. For all three systems, forward and reverse ET does respond differently to modulation of dynamic processes; further, the response to changes in viscosity is different for each system. cytochrome c ͉ dynamics ͉ hemoglobin ͉ myoglobin ͉ cytochrome c peroxidase T he long-range transfer of a single electron from donor to acceptor in a condensed phase is a fascinating and widely studied process (1, 2). Much of this work seeks to understand the electron transfer (ET) process itself. However, when the ET event involves a dynamic protein-protein interface, the observed kinetics frequently are controlled not by the ET process itself, but by the dynamics of recognition and binding and͞or conversion within an ensemble of bound configurations (3, 4).Studies of interprotein ET (3, 5-10) began with the implicit assumption of a protein-protein binding-energy landscape with a single reactive complex (Fig. 1A Left), implying a direct correlation between binding and reactivity. When the landscape for complex formation has several discrete minima ( Fig. 1 A Center) the reactive conformation may differ from the most stable one, in which case the observed ET kinetics are controlled by the rates and͞or energetics of conformational conversion within a complex (11-13). Recent studies of ET between myoglobin (Mb) and cytochrome b 5 (Fe 3ϩ b 5 ), which bind to each other by weak electrostatic interactions, disclosed a new dynamic docking paradigm in protein-protein reaction dynamics: the landscape involves numerous configurations of similar affinity, only a subset of which is active in ET (Fig. 1 A Right) (4, 14).A majority of these studies have used a photocycle in which laser-flash excitation of the metallo-porphyrin in a metalsubstituted (M ϭ Zn or Mg) hemoprotein to its triplet excited state ( 3 D) triggers ET from the triplet to the metal center of an acceptor protein (A) across a protein-protein interface, with rate constant, k f , Eq. 1:[1]The acceptor metal center of A typically is a ferri-heme center, Given the exponentially steep fall-off in the matrix element for ET between the two redox centers (19,20), there will be only a subset of conformation...

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Section: Methodsmentioning

confidence: 95%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface

Hoffman

Celis²,

Cull³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Post‐Crystal Engineering of Zinc‐Substituted Myoglobin to Construct a Long‐Lived Photoinduced Charge‐Separation System

et al. 2011

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Photoinduced electron transfer (ET) in native photosynthesis reactions is efficiently achieved by the accumulation of different types of redox cofactors within protein assemblies immobilized in cell membranes. [1][2][3] The precise arrangement of each cofactor in the molecular spaces enables them to retain the long-lived charge-separated state, which promotes multistep reactions in biological systems. To elucidate the mechanism of the biological ET reactions and to develop light energy conversion systems, artificial ET proteins have been constructed using de novo proteins, chemical modification of native cofactors, photocatalytic reaction centers engineered into protein assemblies, and design of synthetic metal complexes immobilized in protein-protein ET systems. [4][5][6][7][8][9][10][11][12] The reported systems have provided insights into control of ET rates in terms of the distance between donors and acceptors, hydrogen-bonding interactions, reorganization energy of cofactors, and other factors. [4][5][6][7][8][9][10][11][12] Control of the dense accumulation of the different redox cofactors observed in natural photosystems required to achieve long-lived charge-separated state has caused difficulties in efforts to duplicate this process using artificial protein systems in solution. [13] Thus, the design of novel protein frameworks that allow construction of a dense array of various cofactors is a worthwhile goal.Protein crystals can be regarded as excellent candidates for the development of artificial ET reaction systems because the crystal lattices are expected to allow different types of cofactors to be arranged in three-dimensional frameworks that mimic the native ET systems. ET reactions in single protein crystals have been investigated for the dependence of long-range ET on the structures and orientations of redox centers within proteins. [14][15][16] Gray et al. constructed photochemically-initiated protein-protein ET reactions in protein crystals containing zinc-substituted cytochrome c peroxidase or ruthenium-modified azurin. [14][15][16] Moreover, protein crystals provide nanosized spaces for the fixation of metal ions, metal complexes, and the diffusion of organic molecules. [17][18][19][20][21][22] For instance, accumulation of metal ions and metal complexes in a protein crystal lattice spaces was accomplished simply by soaking of the crystals in a solution containing their precursors. [17][18][19] Anisotropic diffusion of small molecules in hen egg-white lysozyme (HEWL) crystals has been investigated by experimental and simulation approaches. [21,22] The results suggest that these features are governed by steric repulsion and electrostatic interaction induced by amino acid residues located on the internal surface of the crystal lattices. Thus, if we can precisely arrange donor and acceptor molecules and mediators in protein crystals, it is expected that the novel three-dimensional framework will allow us to achieve a longlived charge-separated state.Herein, we construct an artificial long-lived ph...

show abstract

Post‐Crystal Engineering of Zinc‐Substituted Myoglobin to Construct a Long‐Lived Photoinduced Charge‐Separation System

et al. 2011

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Photoinduced electron transfer (ET) in native photosynthesis reactions is efficiently achieved by the accumulation of different types of redox cofactors within protein assemblies immobilized in cell membranes. [1][2][3] The precise arrangement of each cofactor in the molecular spaces enables them to retain the long-lived charge-separated state, which promotes multistep reactions in biological systems. To elucidate the mechanism of the biological ET reactions and to develop light energy conversion systems, artificial ET proteins have been constructed using de novo proteins, chemical modification of native cofactors, photocatalytic reaction centers engineered into protein assemblies, and design of synthetic metal complexes immobilized in protein-protein ET systems. [4][5][6][7][8][9][10][11][12] The reported systems have provided insights into control of ET rates in terms of the distance between donors and acceptors, hydrogen-bonding interactions, reorganization energy of cofactors, and other factors. [4][5][6][7][8][9][10][11][12] Control of the dense accumulation of the different redox cofactors observed in natural photosystems required to achieve long-lived charge-separated state has caused difficulties in efforts to duplicate this process using artificial protein systems in solution.[13] Thus, the design of novel protein frameworks that allow construction of a dense array of various cofactors is a worthwhile goal. Protein crystals can be regarded as excellent candidates for the development of artificial ET reaction systems because the crystal lattices are expected to allow different types of cofactors to be arranged in three-dimensional frameworks that mimic the native ET systems. ET reactions in single protein crystals have been investigated for the dependence of long-range ET on the structures and orientations of redox centers within proteins. [14][15][16] Gray et al. constructed photochemically-initiated protein-protein ET reactions in protein crystals containing zinc-substituted cytochrome c peroxidase or ruthenium-modified azurin. [14][15][16] Moreover, protein crystals provide nanosized spaces for the fixation of metal ions, metal complexes, and the diffusion of organic molecules. [17][18][19][20][21][22] For instance, accumulation of metal ions and metal complexes in a protein crystal lattice spaces was accomplished simply by soaking of the crystals in a solution containing their precursors. [17][18][19] Anisotropic diffusion of small molecules in hen egg-white lysozyme (HEWL) crystals has been investigated by experimental and simulation approaches. [21,22] The results suggest that these features are governed by steric repulsion and electrostatic interaction induced by amino acid residues located on the internal surface of the crystal lattices. Thus, if we can precisely arrange donor and acceptor molecules and mediators in protein crystals, it is expected that the novel three-dimensional framework will allow us to achieve a longlived charge-separated state.Herein, we construct an artificial long-lived ph...

show abstract

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

Cited by 73 publications

References 76 publications

Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface

Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface

Post‐Crystal Engineering of Zinc‐Substituted Myoglobin to Construct a Long‐Lived Photoinduced Charge‐Separation System

Post‐Crystal Engineering of Zinc‐Substituted Myoglobin to Construct a Long‐Lived Photoinduced Charge‐Separation System

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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

Cited by 73 publications

References 76 publications

Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface

Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface

Post‐Crystal Engineering of Zinc‐Substituted Myoglobin to Construct a Long‐Lived Photoinduced Charge‐Separation System

Post‐Crystal Engineering of Zinc‐Substituted Myoglobin to Construct a Long‐Lived Photoinduced Charge‐Separation System

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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