Heme–copper oxidases use tunneling pathways

Beratan, David N.; Balabin, Ilya A.

doi:10.1073/pnas.0711343105

Cited by 34 publications

(41 citation statements)

References 17 publications

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“…All of these results seem to be inconsistent with previous experiments' conclusions that the single-stranded helical molecules, such as ssDNA, may not polarize the electrons (5). We note that the electron transport/transfer has been widely investigated in many proteins (19)(20)(21)(22)(23)(24)(25)(26). However, to our knowledge, the underlying physics is still unclear for spin-selective phenomenon observed in the α-helical protein and for the contradictory behaviors between the protein and the ssDNA.…”

mentioning

confidence: 99%

Spin-dependent electron transport in protein-like single-helical molecules

Guo

Sun

2014

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

198

249

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We report on a theoretical study of spin-dependent electron transport through single-helical molecules connected by two nonmagnetic electrodes, and explain the experiment of significant spin-selective phenomenon observed in α-helical protein and the contradictory results between the protein and single-stranded DNA. Our results reveal that the α-helical protein is an efficient spin filter and the spin polarization is robust against the disorder. These results are in excellent agreement with recent experiments [Mishra D, et al. (2013) S pintronics is a multidisciplinary field that manipulates the electron spin transport in solid-state systems and has been receiving much attention among the physics, chemistry, and biology communities (1-4). Recent experiments have made significant progress in this research field, finding that doublestranded DNA (dsDNA) molecules are highly efficient spin filters (5-7). This chiral-induced spin selectivity (CISS) is surprising because the DNA molecules are nonmagnetic and their spin-orbit couplings (SOCs) are small. Additionally, the CISS effect opens new opportunities for using chiral molecules in spintronic applications and could provide a deeper understanding of the spin effects in biological processes. For the above reasons, there has been considerable interest in the spin transport along various chiral systems including dsDNA (8-11), single-stranded DNA (ssDNA) (12-15), and carbon nanotubes (16). However, no spin selectivity was measured in the ssDNA above the experimental noise (5).Very recently, spin-dependent electron transmission and electrochemical experiments were performed on bacteriorhodopsinan α-helical protein of which the structure is single helicalembedded in purple membrane which was physisorbed on a variety of substrates (17). It was reported by means of two distinct techniques that the electrons transmitted through the membrane are spin polarized, independent of the experimental environments, implying that this α-helical protein can exhibit the ability of spin filtering. Meanwhile, a chiral-based magnetic memory device was fabricated by using self-assembled monolayer of another α-helical protein called polyalanine (18). All of these results seem to be inconsistent with previous experiments' conclusions that the single-stranded helical molecules, such as ssDNA, may not polarize the electrons (5). We note that the electron transport/transfer has been widely investigated in many proteins (19)(20)(21)(22)(23)(24)(25)(26). However, to our knowledge, the underlying physics is still unclear for spin-selective phenomenon observed in the α-helical protein and for the contradictory behaviors between the protein and the ssDNA.In this paper, we propose a model Hamiltonian to explore the spin transport through single-helical molecules connected by two nonmagnetic electrodes, and provide an unambiguous physical mechanism for efficient spin selectivity observed in the protein and for the contrary experimental results between the protein and the ssDNA. Our results reveal that t...

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mentioning

confidence: 99%

Spin-dependent electron transport in protein-like single-helical molecules

Guo

Sun

2014

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

198

249

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“…The question of whether specific paths or residues were selected for electron transfer in proteins is still vigorously debated in the literature (34,37,38). Calculations on frozen structures clearly predict localization of the tunneling fluxes to specific structural elements of the protein.…”

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Electron tunneling in respiratory complex I

Hayashi

Stuchebrukhov

2010

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

115

120

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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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“…6A). Thus, Ser 47 , Gly 48 , and water residues contribute to define the ET pathway during the whole trajectory, they being involved in around 28, 42, and 29% of the ET pathways. A series of representative ET pathways sampled at the end of the trajectory are shown in Fig.…”

Section: Molecular Docking and Identification Of Reactive Configuratimentioning

confidence: 99%

“…A detailed analysis of the pathways reveals that the ET from the FAD isoalloxazine ring to the heme follows three major pathways (Fig. 6B): (i) a direct transfer through the backbone of Ser 47 and/or Gly 48 residues, (ii) assisted by a water molecule prior to transfer to residues in the CD loop, and (iii) directly through a water molecule. This latter pathway agrees with the trends found for the ET in E. coli flavoHb (38), where a water molecule was found to assist the ET from the isoalloxazine ring to the heme (37).…”

Section: Molecular Docking and Identification Of Reactive Configuratimentioning

confidence: 99%

“…Site-directed Mutagenesis of CD Loop of MtbHbN-Because structural and MD simulation studies supported the involvement of CD loop residues Ser 47 , Gly 48 , and Thr 49 in defining the ET pathway, the role of these residues was further checked by site-directed mutagenesis. Thus, Ser 47 , Gly 48 , and Thr 49 were mutated to Trp, Ile, and Trp, respectively, to generate HbN mutants, HbN S47W , HbN G48I , and HbN T49W , and the efficiency of these mutants for reduction of heme in the presence of FdR was determined and compared with the wild type protein.…”

Section: Role Of CD Loop Of Mtb Hbn In Protein-protein Interactions Amentioning

confidence: 99%

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Mechanistic Insight into the Enzymatic Reduction of Truncated Hemoglobin N of Mycobacterium tuberculosis

Singh

Thakur

Oliveira

et al. 2014

Journal of Biological Chemistry

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Background:The HbN of Mycobacterium tuberculosis carries a potent nitric-oxide dioxygenase activity despite lacking a reductase domain. Results:The NADH-ferredoxin reductase system acts as an efficient partner for the reduction of HbN. Conclusion:The interactions of HbN with the reductase are modulated by its CD loop and the Pre-A region. Significance: The present study provides new insights into the mechanism of electron transfer during nitric oxide detoxification by HbN.

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Heme–copper oxidases use tunneling pathways

Cited by 34 publications

References 17 publications

Spin-dependent electron transport in protein-like single-helical molecules

Spin-dependent electron transport in protein-like single-helical molecules

Electron tunneling in respiratory complex I

Mechanistic Insight into the Enzymatic Reduction of Truncated Hemoglobin N of Mycobacterium tuberculosis

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