Toward Ab Initio Theory of Longdistance Electron Tunneling in Proteins: Tunneling Currents Approach

Stuchebrukhov, Alexei A.

doi:10.1002/9780470141786.ch1

Cited by 32 publications

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“…treats many-electron wave functions explicitly by incorporating both the tunneling electron orbitals and the induced polarization of core electrons. By assuming single Slater determinant manyelectron wave functions of the donor and acceptor diabatic states, the donor and acceptor tunneling orbitals that carry the tunneling electron are obtained as biorthogonal donor and acceptor orbitals with the smallest overlap (29,31). The rest of the orbitals undergoing induced polarization in the tunneling transition give rise to the electronic Franck-Condon factor (30,31).…”

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confidence: 99%

“…The simulations of electron transfer between redox centers are based on the tunneling current theory (29,30), which had been successfully applied to several systems previously. The theory This article is a PNAS Direct Submission.…”

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confidence: 99%

“…Tunneling matrix element T DA is calculated by using the tunneling flux theorem as the total flux across the dividing plane between the donor and acceptor (see Fig. S1) (29,30):…”

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Electron tunneling in respiratory complex I

Hayashi

Stuchebrukhov

2010

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

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NADH:ubiquinone oxidoreductase (complex I) plays a central role in the respiratory electron transport chain by coupling the transfer of electrons from NADH to ubiquinone to the creation of the proton gradient across the membrane necessary for ATP synthesis. Here the atomistic details of electronic wiring of all Fe/S clusters in complex I are revealed by using the tunneling current theory and computer simulations; both density functional theory and semiempirical electronic structure methods were used to examine antiferromagnetically coupled spin states and corresponding tunneling wave functions. Distinct electron tunneling pathways between neighboring Fe/S clusters are identified; the pathways primarily consist of two cysteine ligands and one additional key residue. Internal water between protein subunits is identified as an essential mediator enhancing the overall electron transfer rate by almost three orders of magnitude to achieve a physiologically significant value. The identified key residues are further characterized by sensitivity of electron transfer rates to their mutations, examined in simulations, and their conservation among complex I homologues. The unusual electronic structure properties of Fe 4 S 4 clusters in complex I explain their remarkable efficiency of electron transfer.electron transfer in proteins | respiratory chain | iron-sulfur clusters N ADH:ubiquinone oxidoreductase (complex I) is a large L-shaped membrane-bound enzyme involved in cellular respiration that catalyzes the oxidation of NADH and the reduction of ubiquinone in mitochondria and respiring bacteria (1-3). This reaction involves the transfer of electrons over approximately 90 Å from NADH bound to the hydrophilic domain to ubiquinone in or near the hydrophobic membrane-bound domain of complex I (4). In turn, the reaction provides the driving force for translocation of four protons across the membrane, thus generating, in part, the proton gradient necessary for ATP synthesis (5). Complex I defects are the cause of several neurodegenerative diseases including Parkinson disease, Alzheimer's disease, and Huntington disease (6).The transfer of electrons from NADH to ubiquinone is facilitated by flavin mononucleotide (FMN), two binuclear (2Fe-2S) iron-sulfur clusters (N1a and N1b), and six tetranuclear (4Fe-4S) iron-sulfur clusters (N3, N4, N5, N6a, N6b, and N2) (Fig. 1A). NADH, a two-electron donor, initially passes both electrons, as hydride, to the FMN cofactor. From FMN one electron enters a transport chain leading to the ubiquinone-binding site; the second electron enters a side path to N1a that appears to serve as a control mechanism to prevent generation of superoxide ions (4).The crystal structure of hydrophilic domain of complex I from Thermus thermophilus was reported in 2006 (4), and recently the whole architecture of the enzyme has been revealed (7); however, until now, the atomistic details of electron transfer along the chain of Fe/S metal clusters have remained unknown. Recently, a hopping (stepwise) electron transfer (...

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Electron tunneling in respiratory complex I

Hayashi

Stuchebrukhov

2010

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

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115

120

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“…Numerous theoretical methods can be applied to calculate electron transfer couplings [112][113][114][115][116][117][118][119][120][121]. However, it is not trivial to extract the coupling from experimental data to check the quality of a theoretical method.…”

Section: Electron Transfer Couplingmentioning

confidence: 99%

Chapter 2. Absorption of Light, Excitation Energy Transfer and Electron Transfer Reactions

Renger¹

2007

Comprehensive Series in Photochemical &Amp; Photobiological Sciences

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The present chapter gives an overview of photophysical principles underlying the primary photosynthetic reactions in pigment-protein complexes, i.e., the absorption of light, excitation energy transfer and electron transfer reactions. From a common viewpoint the description of the above reactions requires theories that can include both the pigment-pigment (electronic) as well as the pigment-protein (electron-vibrational) coupling in an appropriate manner. Different theories are classified according to the relative strength of the two types of couplings. In the weak electronic coupling limit, a semiclassical and a quantum Fermi's Golden Rule type rate constant and their relation are discussed and applied to absorption and fluorescence, excitation energy transfer, and electron transfer, yielding the standard results by Lax/Kubo, Fo¨rster, and Marcus, respectively. Whereas for electron transfer reactions the weak electronic coupling limit is appropriate, in the case of excitation energy transfer and optical spectra, usually, the pigment-pigment coupling is of the same strength or even stronger than the pigmentprotein coupling, a situation that is treated by theories that take into account delocalized excited states of the pigments. Multilevel Redfield theory describes excitation energy relaxation between different delocalized states and relates the relaxation times to optical line widths. In non-Markovian density matrix theories, besides a life time broadening due to exciton relaxation, vibrational sidebands of the optical lines are included. Another extension of Redfield theory, the modified Redfield theory, takes into account the reorganization of nuclei during exciton relaxation between different delocalized states. The generalized Fo¨rster theory allows a description of transfer between aggregates with strong intra-and weak inter-aggregate couplings. How the parameters (couplings, energies and spectral densities) of the dynamical theories can be extracted from experimental data and independent calculations is outlined also.

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“…[26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45] Quite detailed studies of tunneling in alkane chains have illuminated the nature of interference effects, [26][27][28][29][30]45 but still validate the treatment of chemical units as leading to (nearly) equivalent decays with distance as the chain between donor and acceptor becomes elongated. A number of experimental studies have also investigated the impact of nonbonded contacts on the electronic coupling element and seen significant contributions to the coupling from weak interactions.…”

Section: Introductionmentioning

confidence: 99%

Tunneling through Weak Interactions: Comparison of Through-Space-, H-Bond-, and Through-Bond-Mediated Tunneling

Kurlancheek

Cave

2006

J. Phys. Chem. A

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Results from ab initio electronic structure theory calculations on model systems allow for the detailed comparison of tunneling through covalently bonded contacts, hydrogen bonds, and van der Waals contacts. Considerable geometrical sensitivity as well as an exponential distance dependence of the tunneling is observed for tunneling through various nonbonded contacts. However, the fundamental result from the present study is that at most a modest difference is observed between tunneling mediated by H-bonds and tunneling mediated by van der Waals contacts at typical distances for each type of interaction. These results are considered in relation to the pathways model of Beratan and Onuchic, and implications for understanding long-range tunneling in biological systems are discussed.

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Toward Ab Initio Theory of Longdistance Electron Tunneling in Proteins: Tunneling Currents Approach

Cited by 32 publications

References 80 publications

Electron tunneling in respiratory complex I

Electron tunneling in respiratory complex I

Chapter 2. Absorption of Light, Excitation Energy Transfer and Electron Transfer Reactions

Tunneling through Weak Interactions: Comparison of Through-Space-, H-Bond-, and Through-Bond-Mediated Tunneling

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