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Hagras MA. Respiratory Complex III: A Bioengine with a Ligand-Triggered Electron-Tunneling Gating Mechanism. J Phys Chem B 2024; 128:990-1000. [PMID: 38241470 DOI: 10.1021/acs.jpcb.3c07095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Respiratory complex III (a.k.a., the bc1 complex) plays a key role in the electron transport chain in aerobic cells. The bc1 complex exhibits multiple unique electron tunneling (ET) processes, such as ET-bifurcation at the Qo site and movement of the Rieske domain. Moreover, we previously discovered that electron tunneling in the low potential arm of the bc1 complex is regulated by a key phenylalanine residue (Phe90). The main goal of the current work is to study the dynamics of the key Phe90 residue in the electron tunneling reaction between heme bL and heme bH as a function of the occupancy of the Qo and Qi binding sites in the bc1 complex. We simulated the molecular dynamics of four model systems of respiratory complex III with different ligands bound at the Qo and Qi binding sites. In addition, we calculated the electron tunneling rate constants between heme bL and heme bH along the simulated molecular dynamics trajectories. The binding of aromatic ligands at the Qo site induces a conformational cascade that properly positions the Phe90 residue, reducing the through-space ET distance from ∼7 to ∼5.5 Å and thus enhancing the electron transfer rate between the heme bL and the heme bH redox pair. Also, the binding of aromatic ligands at the Qi site induces conformational changes that stabilize the Phe90 conformational variation from ∼1.5 to ∼0.5 Å. Hence, our molecular dynamics simulation results show an on-demand two-step conformational connection between the occupancy of the Qo and Qi binding sites and the conformational dynamics of the Phe90 residue. Additionally, our dynamic electron tunneling results confirm our previously reported findings that the Phe90 residue acts as an electron-tunneling gate or switch, controlling the electron transfer rate between the heme bL and heme bH redox systems.
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Affiliation(s)
- Muhammad A Hagras
- Department of Basic Sciences, University of Health Sciences and Pharmacy, St. Louis, Missouri 63110, United States
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Hagras MA, Stuchebrukhov AA. Concerted Two-Electron Reduction of Ubiquinone in Respiratory Complex I. J Phys Chem B 2019; 123:5265-5273. [DOI: 10.1021/acs.jpcb.9b04082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Muhammad A. Hagras
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
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Khani SK, Cundari TR. A comparison of the Simmons-Smith reaction with carbenoids to nitrenoids and oxenoids. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Foscato M, Venkatraman V, Occhipinti G, Alsberg BK, Jensen VR. Automated Building of Organometallic Complexes from 3D Fragments. J Chem Inf Model 2014; 54:1919-31. [DOI: 10.1021/ci5003153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Marco Foscato
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vishwesh Venkatraman
- Department
of Chemistry, Norwegian University of Science and Technology, Ho̷gskoleringen
1, N-7491 Trondheim, Norway
| | - Giovanni Occhipinti
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Bjørn K. Alsberg
- Department
of Chemistry, Norwegian University of Science and Technology, Ho̷gskoleringen
1, N-7491 Trondheim, Norway
| | - Vidar R. Jensen
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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Foscato M, Occhipinti G, Venkatraman V, Alsberg BK, Jensen VR. Automated Design of Realistic Organometallic Molecules from Fragments. J Chem Inf Model 2014; 54:767-80. [DOI: 10.1021/ci4007497] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Foscato
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Giovanni Occhipinti
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vishwesh Venkatraman
- Department
of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Bjørn K. Alsberg
- Department
of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Vidar R. Jensen
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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Ab initio, density functional theory, and semi-empirical calculations. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 924:3-27. [PMID: 23034743 DOI: 10.1007/978-1-62703-017-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented.
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Abstract
A first principles study of electronic tunneling along the chain of seven Fe/S clusters in respiratory complex I, a key enzyme in the respiratory electron transport chain, is described. The broken-symmetry states of the Fe/S metal clusters calculated at both DFT and semi-empirical ZINDO levels were utilized to examine both the extremely weak electronic couplings between Fe/S clusters and the tunneling pathways, which provide a detailed atomistic-level description of the charge transfer process in the protein. One-electron tunneling approximation was found to hold within a reasonable accuracy, with only a moderate induced polarization of the core electrons. The method is demonstrated to be able to calculate accurately the coupling matrix elements as small as 10-4 cm-1. A distinct signature of the wave properties of electrons is observed as quantum interferences of multiple tunneling pathways.
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Affiliation(s)
- Tomoyuki Hayashi
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616
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Abstract
We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. While the one-electron tunneling approximation is found to hold in electron tunneling between the antiferromagnetic binuclear and tetranuclear Fe/S clusters without major orbital or spin rearrangement of the core electrons, induced polarization of the core electrons contributes significantly to decrease the electron transfer rates to 19-56 %. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of the electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A signature of the wave properties of electrons is observed as distinct quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included is in good agreement with a reported phenomenological relation.
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Affiliation(s)
- Tomoyuki Hayashi
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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Abstract
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.
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Moens J, Jaque P, De Proft F, Geerlings P. A New View on the Spectrochemical and Nephelauxetic Series on the Basis of Spin-Polarized Conceptual DFT. Chemphyschem 2009; 10:847-54. [DOI: 10.1002/cphc.200800864] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Buda C, Flores A, Cundari TR. De novo prediction of the ground state structure of transition metal complexes using semiempirical and ab initio quantum mechanics. Coordination isomerism. J COORD CHEM 2007. [DOI: 10.1080/00958970500038258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Corneliu Buda
- a Department of Chemistry , University of North Texas , Denton, TX 76203, USA
| | - Alondra Flores
- b Department of Chemistry , University of Texas at Brownsville , Brownsville, TX 78520, USA
| | - Thomas R. Cundari
- a Department of Chemistry , University of North Texas , Denton, TX 76203, USA
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Stephens JC, Khan MA, Nicholas KM. Cyclopentadienyliron complexes of nitrosobenzene: Preparation, structure and reactivity with olefins. J Organomet Chem 2005. [DOI: 10.1016/j.jorganchem.2005.06.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Srivastava RS, Khan MA, Nicholas KM. Nitrosoarene−Cu(I) Complexes Are Intermediates in Copper-Catalyzed Allylic Amination. J Am Chem Soc 2005; 127:7278-9. [PMID: 15898753 DOI: 10.1021/ja044093m] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactions of nitrosobenzene and N,N'-diethyl-4-nitrosoaniline with [Cu(CH3CN)4]PF6 produce novel homoleptic Cu(I)-nitrosoarene complexes, [Cu(ArNO)3]PF6, 1 (Ar = Ph) and 2 (Ar = 4-Et2NC6H4NO). The X-ray structure of 2 reveals that the copper is coordinated in a severely distorted trigonal planar geometry to the N-atom of the nitrosoarene ligand. Reactions of the PhNO complex 1 with olefins and an olefin/diene mixture provide evidence for its role as an intermediate and possibly the active nitrogen transfer agent in the Cu-catalyzed allylic amination of olefins by aryl hydroxylamines.
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Buda C, Cundari TR. De novo prediction of ground state multiplicity and structural isomerism for transition metal complexes. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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DFT Computation of Relative Spin-State Energetics of Transition Metal Compounds. PRINCIPLES AND APPLICATIONS OF DENSITY FUNCTIONAL THEORY IN INORGANIC CHEMISTRY I 2004. [DOI: 10.1007/b97939] [Citation(s) in RCA: 212] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Buda C, Burt SK, Cundari TR, Shenkin PS. De novo structural prediction of transition metal complexes: application to technetium. Inorg Chem 2002; 41:2060-9. [PMID: 11952359 DOI: 10.1021/ic0109748] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
De novo structural prediction of transition metal complexes is investigated. Technetium complexes are chosen given their importance in medical imaging and nuclear waste remediation and for the chemical diversity they display. A new conformational searching algorithm (LIGB) for transition metals is described that allows one to search for different conformational and geometric isomers within a single simulation. In the preponderance of cases, both conformational searching techniques (LIGB and high-temperature molecular dynamics/simulated annealing) provide comparable results, while LIGB is superior for macrocyclic complexes. A genetic algorithm-optimized PM3(tm) parametrization for Tc is compared with the standard implementation and found to yield a significant improvement in predictive ability for the most prevalent Tc structural motifs. The utility of a coupled molecular mechanics-semiempirical quantum mechanics protocol is demonstrated for very rapid, efficient, and effective de novo prediction of transition metal complex geometries.
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Affiliation(s)
- Corneliu Buda
- Department of Chemistry, The University of Memphis, Computational Research on Materials Institute (CROMIUM), Memphis, Tennessee 38152, USA
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