1
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Dey A, Ghorai N, Das A, Ghosh HN. Effects of hydrogen bonding on intramolecular/intermolecular proton-coupled electron transfer using a Ruthenium-anthraquinone dyad in ultrafast time domain. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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2
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Ru X, Crane BR, Zhang P, Beratan DN. Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex? J Phys Chem B 2021; 125:7763-7773. [PMID: 34235935 DOI: 10.1021/acs.jpcb.1c05064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) complex (CcP:Cc) is used widely to study interprotein electron transfer (ET) mechanisms. Tryptophan 191 (Trp191) of CcP supports hole hopping charge recombination in the CcP:Cc complex. Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decrease. Theoretical analysis of these CcP:Cc complexes finds that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically to the Cc heme, and the structural disorder of the guest molecule in the binding pocket may contribute further to the lack of enzymatic activity. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine vs tryptophan oxidation accounts for the slower rate in the Tyr mutant. Thus, theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex. Favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in this protein-protein complex.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States
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3
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Fraggedakis D, McEldrew M, Smith RB, Krishnan Y, Zhang Y, Bai P, Chueh WC, Shao-Horn Y, Bazant MZ. Theory of coupled ion-electron transfer kinetics. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2020.137432] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Long distance electron transfer through the aqueous solution between redox partner proteins. Nat Commun 2018; 9:5157. [PMID: 30514833 PMCID: PMC6279779 DOI: 10.1038/s41467-018-07499-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 11/06/2018] [Indexed: 11/25/2022] Open
Abstract
Despite the importance of electron transfer between redox proteins in photosynthesis and respiration, the inter-protein electron transfer rate between redox partner proteins has never been measured as a function of their separation in aqueous solution. Here, we use electrochemical tunneling spectroscopy to show that the current between two protein partners decays along more than 10 nm in the solution. Molecular dynamics simulations reveal a reduced ionic density and extended electric field in the volume confined between the proteins. The distance-decay factor and the calculated local barrier for electron transfer are regulated by the electrochemical potential applied to the proteins. Redox partners could use electrochemically gated, long distance electron transfer through the solution in order to conciliate high specificity with weak binding, thus keeping high turnover rates in the crowded environment of cells. Electron transport chains rely on interactions between redox proteins, but the distance-dependence of the electron transfer rate through the solution is unknown. Here, the authors show that the current between two redox protein partners occurs at long distances and is electrochemically gated.
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5
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Greene BL, Stubbe J, Nocera DG. Photochemical Rescue of a Conformationally Inactivated Ribonucleotide Reductase. J Am Chem Soc 2018; 140:15744-15752. [PMID: 30347141 DOI: 10.1021/jacs.8b07902] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Class Ia ribonucleotide reductase (RNR) of Escherichia coli contains an unusually stable tyrosyl radical cofactor in the β2 subunit (Y122•) necessary for nucleotide reductase activity. Upon binding the cognate α2 subunit, loaded with nucleoside diphosphate substrate and an allosteric/activity effector, a rate determining conformational change(s) enables rapid radical transfer (RT) within the active α2β2 complex from the Y122• site in β2 to the substrate activating cysteine residue (C439) in α2 via a pathway of redox active amino acids (Y122[β] ↔ W48[β]? ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]) spanning >35 Å. Ionizable residues at the α2β2 interface are essential in mediating RT, and therefore control activity. One of these mutations, E350X (where X = A, D, Q) in β2, obviates all RT, though the mechanism of control by which E350 mediates RT remains unclear. Herein, we utilize an E350Q-photoβ2 construct to photochemically rescue RNR activity from an otherwise inactive construct, wherein the initial RT event (Y122• → Y356) is replaced by direct photochemical radical generation of Y356•. These data present compelling evidence that E350 conveys allosteric information between the α2 and β2 subunits facilitating conformational gating of RT that specifically targets Y122• reduction, while the fidelity of the remainder of the RT pathway is retained.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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6
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Suwa M, Imamura N, Awano P, Nakata E, Takashima H. Photoinduced electron-transfer reactions of tris(2,2′-bipyridine)ruthenium(II)-based carbonic anhydrase inhibitors tethering plural binding sites. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mikiko Suwa
- Department of Chemistry, Faculty of Science; Nara Women's University; Nara Japan
| | - Narumi Imamura
- Department of Chemistry, Faculty of Science; Nara Women's University; Nara Japan
| | - Pirika Awano
- Department of Chemistry, Faculty of Science; Nara Women's University; Nara Japan
| | - Eiji Nakata
- Institute of Advanced Energy; Kyoto University; Kyoto Japan
| | - Hiroshi Takashima
- Department of Chemistry, Faculty of Science; Nara Women's University; Nara Japan
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7
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Desai D, Kumar A, Bose D, Datta M. Ultrasensitive sensor for detection of early stage chronic kidney disease in human. Biosens Bioelectron 2018; 105:90-94. [DOI: 10.1016/j.bios.2018.01.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 12/20/2022]
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8
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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9
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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10
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Payne TM, Yee EF, Dzikovski B, Crane BR. Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c. Biochemistry 2016; 55:4807-22. [PMID: 27499202 PMCID: PMC5689384 DOI: 10.1021/acs.biochem.6b00262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The tryptophan 191 cation radical of cytochrome c peroxidase (CcP) compound I (Cpd I) mediates long-range electron transfer (ET) to cytochrome c (Cc). Here we test the effects of chemical substitution at position 191. CcP W191Y forms a stable tyrosyl radical upon reaction with peroxide and produces spectral properties similar to those of Cpd I but has low reactivity toward reduced Cc. CcP W191G and W191F variants also have low activity, as do redox ligands that bind within the W191G cavity. Crystal structures of complexes between Cc and CcP W191X (X = Y, F, or G), as well as W191G with four bound ligands reveal similar 1:1 association modes and heme pocket conformations. The ligands display structural disorder in the pocket and do not hydrogen bond to Asp235, as does Trp191. Well-ordered Tyr191 directs its hydroxyl group toward the porphyrin ring, with no basic residue in the range of interaction. CcP W191X (X = Y, F, or G) variants substituted with zinc-porphyrin (ZnP) undergo photoinduced ET with Cc(III). Their slow charge recombination kinetics that result from loss of the radical center allow resolution of difference spectra for the charge-separated state [ZnP(+), Cc(II)]. The change from a phenyl moiety at position 191 in W191F to a water-filled cavity in W191G produces effects on ET rates much weaker than the effects of the change from Trp to Phe. Low net reactivity of W191Y toward Cc(II) derives either from the inability of ZnP(+) or the Fe-CcP ferryl to oxidize Tyr or from the low potential of the resulting neutral Tyr radical.
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Affiliation(s)
- Thomas M. Payne
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Estella F. Yee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca 14850, USA
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States,To whom correspondence should be addressed , Tel (607) 254-8634 (B.R.C)
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11
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12
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Abstract
Many biomolecular interactions proceed via lowly populated, transient intermediates. Believed to facilitate formation of a productive complex, these short-lived species are inaccessible to conventional biophysical and structural techniques and, until recently, could only be studied by theoretical simulations. Recent development of experimental approaches sensitive to the presence of minor species--in particular paramagnetic relaxation enhancement (PRE) NMR spectroscopy--has enabled direct visualization and detailed characterization of such lowly populated states. Collectively referred to as an encounter complex, the binding intermediates are particularly important in transient protein interactions, such as those orchestrating signaling cascades or energy-generating electron transfer (ET) chains. Here I discuss encounter complexes of redox proteins mediating biological ET reactions, which are essential for many vital cellular activities including oxidative phosphorylation and photosynthesis. In particular, this Account focuses on the complex of cytochrome c (Cc) and cytochrome c peroxidase (CcP), which is a paradigm of biomolecular ET and an attractive system for studying protein binding and enzymatic catalysis. The Cc-CcP complex formation proceeds via an encounter state, consisting of multiple protein-protein orientations sampled in the search of the dominant, functionally active bound form and exhibiting a broad spatial distribution, in striking agreement with earlier theoretical simulations. At low ionic strength, CcP binds another Cc molecule to form a weak ternary complex, initially inferred from kinetics experiments and postulated to account for the measured ET activity. Despite strenuous efforts, the ternary complex could not be observed directly and remained eagerly sought for the past two decades. Very recently, we have solved its structure in solution and shown that it consists of two binding forms: the dominant, ET-inactive geometry and an ensemble of lowly populated species with short separations between Cc and CcP cofactors, which summarily account for the measured ET rate. Unlike most protein complexes, which require accurate alignment of the binding surfaces in a single, well-defined orientation to carry out their function, redox proteins can form multiple productive complexes. As fast ET will occur any time the redox centers of the binding partners are close enough to ensure efficient electron tunneling across the interface, many protein-protein orientations are expected to be ET active. The present analysis confirms that the low-occupancy states can support the functional ET activity and contribute to the stability of redox protein complexes. As illustrated here, boundaries between the dominant and the encounter forms become blurred for many dynamic ET systems, which are more aptly described by ensembles of functionally and structurally heterogeneous bound forms.
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Affiliation(s)
- Alexander N. Volkov
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, and Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
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13
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Erman JE, Vitello LB, Pearl NM, Jacobson T, Francis M, Alberts E, Kou A, Bujarska K. Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry. Biochemistry 2015. [PMID: 26212209 DOI: 10.1021/acs.biochem.5b00686] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, we constructed, expressed, and purified 46 charge-reversal mutants of yeast cytochrome c peroxidase (CcP) and determined their electronic absorption spectra, their reaction with H2O2, and their steady-state catalytic properties [ Pearl , N. M. et al. (2008) Biochemistry 47 , 2766 - 2775 ]. Forty-four of the mutants involve the conversion of either an aspartate or glutamate residue to a lysine residue, while two are positive-to-negative mutations, R31E and K149D. In this paper, we report on a calorimetric study of the interaction of each charge-reversal mutant (excluding the internal mutants D76K and D235K) with recombinant yeast iso-1 ferricytochrome c(C102T) (yCc) under conditions where only one-to-one yCc/CcP complex formation is observed. Thirteen of the 44 surface-site charge-reversal mutants decrease the binding affinity for yCc by a factor of 2 or more. Eight of the 13 mutations (E32K, D33K, D34K, E35K, E118K, E201K, E290K, E291K) occur within, or on the immediate periphery, of the crystallographically defined yCc binding site [ Pelletier , H. and Kraut , J. (1992) Science 258 , 1748 - 1755 ], three of the mutations (D37K, E98K, E209K) are slightly removed from the crystallographic site, and two of the mutations (D165K, D241K) occur on the "back-side" of CcP. The current study is consistent with a model for yCc binding to CcP in which yCc binds predominantly near the region defined by crystallographic structure of the 1:1 yCc-CcP complex, whether as a stable electron-transfer active complex or as part of a dynamic encounter complex.
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Affiliation(s)
- James E Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Lidia B Vitello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Naw May Pearl
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Timothy Jacobson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Meka Francis
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Erik Alberts
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Allen Kou
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Kathy Bujarska
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
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14
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Properties of the indole ring in metal complexes. A comparison with the phenol ring. J Inorg Biochem 2015; 148:105-15. [DOI: 10.1016/j.jinorgbio.2015.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 11/20/2022]
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15
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The low-affinity complex of cytochrome c and its peroxidase. Nat Commun 2015; 6:7073. [PMID: 25944250 PMCID: PMC4432590 DOI: 10.1038/ncomms8073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/30/2015] [Indexed: 01/07/2023] Open
Abstract
The complex of yeast cytochrome c peroxidase and cytochrome c is a paradigm of the biological electron transfer (ET). Building on seven decades of research, two different models have been proposed to explain its functional redox activity. One postulates that the intermolecular ET occurs only in the dominant, high-affinity protein–protein orientation, while the other posits formation of an additional, low-affinity complex, which is much more active than the dominant one. Unlike the high-affinity interaction—extensively studied by X-ray crystallography and NMR spectroscopy—until now the binding of cytochrome c to the low-affinity site has not been observed directly, but inferred mainly from kinetics experiments. Here we report the structure of this elusive, weak protein complex and show that it consists of a dominant, inactive bound species and an ensemble of minor, ET-competent protein–protein orientations, which summarily account for the experimentally determined value of the ET rate constant. The redox activity of cytochrome c in complex with its peroxidase has been rationalized by two possible models; a readily observable high-affinity complex and a more elusive but potentially more active low-affinity complex. Here, the authors provide an NMR-based structural mapping of this low-affinity complex.
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16
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Page TR, Hoffman BM. Control of cyclic photoinitiated electron transfer between cytochrome c peroxidase (W191F) and cytochrome c by formation of dynamic binary and ternary complexes. Biochemistry 2015; 54:1188-97. [PMID: 25629200 DOI: 10.1021/bi500888y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Extensive studies of the physiological protein-protein electron-transfer (ET) complex between yeast cytochrome c peroxidase (CcP) and cytochrome c (Cc) have left unresolved questions about how formation and dissociation of binary and ternary complexes influence ET. We probe this issue through a study of the photocycle of ET between Zn-protoporphyrin IX-substituted CcP(W191F) (ZnPCcP) and Cc. Photoexcitation of ZnPCcP in complex with Fe(3+)Cc initiates the photocycle: charge-separation ET, [(3)ZnPCcP, Fe(3+)Cc] → [ZnP(+)CcP, Fe(2+)Cc], followed by charge recombination, [ZnP(+)CcP, Fe(2+)Cc] → [ZnPCcP, Fe(3+)Cc]. The W191F mutation eliminates fast hole hopping through W191, enhancing accumulation of the charge-separated intermediate and extending the time scale for binding and dissociation of the charge-separated complex. Both triplet quenching and the charge-separated intermediate were monitored during titrations of ZnPCcP with Fe(3+)Cc, Fe(2+)Cc, and redox-inert CuCc. The results require a photocycle that includes dissociation and/or recombination of the charge-separated binary complex and a charge-separated ternary complex, [ZnP(+)CcP, Fe(2+)Cc, Fe(3+)Cc]. The expanded kinetic scheme formalizes earlier proposals of "substrate-assisted product dissociation" within the photocycle. The measurements yield the thermodynamic affinity constants for binding the first and second Cc: KI = 10(-7) M(-1), and KII = 10(-4) M(-1). However, two-site analysis of the thermodynamics of formation of the ternary complex reveals that Cc binds at the weaker-binding site with much greater affinity than previously recognized and places upper bounds on the contributions of repulsion between the two Cc's of the ternary complex. In conjunction with recent nuclear magnetic resonance studies, the analysis further suggests a dynamic view of the ternary complex, wherein neither Cc necessarily faithfully adopts the crystal-structure configuration because of Cc-Cc repulsion.
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Affiliation(s)
- Taylor R Page
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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17
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Tron A, Rocher M, Thornton PJ, Tucker JHR, McClenaghan ND. Supramolecular Architectures Incorporating Hydrogen-Bonding Barbiturate Receptors. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201402243] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Tezcan FA, Kaiser JT, Howard JB, Rees DC. Structural evidence for asymmetrical nucleotide interactions in nitrogenase. J Am Chem Soc 2014; 137:146-9. [PMID: 25522159 PMCID: PMC4304452 DOI: 10.1021/ja511945e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
roles of ATP hydrolysis in electron-transfer (ET) reactions
of the nitrogenase catalytic cycle remain obscure. Here, we present
a new structure of a nitrogenase complex crystallized with MgADP and
MgAMPPCP, an ATP analogue. In this structure the two nucleotides are
bound asymmetrically by the Fe-protein subunits connected to the two
different MoFe-protein subunits. This binding mode suggests that ATP
hydrolysis and phosphate release may proceed by a stepwise mechanism.
Through the associated Fe-protein conformational changes, a stepwise
mechanism is anticipated to prolong the lifetime of the Fe-protein-MoFe-protein
complex and, in turn, could orchestrate the sequence of intracomplex
ET required for substrate reduction.
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Affiliation(s)
- F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States
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19
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Yau ST, Xu Y, Song Y, Feng Y, Wang J. Voltage-controlled enzyme-catalyzed glucose-gluconolactone conversion using a field-effect enzymatic detector. Phys Chem Chem Phys 2014; 15:20134-9. [PMID: 24158463 DOI: 10.1039/c3cp52004h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field-effect enzymatic detection (FEED) technique was used to control the kinetics of the enzymatic conversion of glucose to gluconolactone. The glucose-gluconolactone conversion occurring at an enzyme-immobilized electrode, a well-studied process, was confirmed using mass spectrometry. Electrochemical studies showed that the glucose oxidation current depends on the gating voltage VG and the ion concentration of the sample solution. Additionally, the depletion of glucose in the sample also showed a dependence on VG. FEED was used to detect H2O2 on the zepto-molar level in order to show the ultrasensitive detection capability of the technique. These results, while providing evidence for the proposed mechanism of FEED, indicate that VG controls the conversion process. The effect of VG on the glucose-gluconolactone conversion was demonstrated by the observed VG-dependent kinetic parameters of the conversion process.
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Affiliation(s)
- Siu-Tung Yau
- Department of Electrical and Computer Engineering, Cleveland State University, Cleveland, Ohio 44115, USA.
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20
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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21
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Kinetic studies on cyclopalladation in palladium(II) complexes containing an indole moiety. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Various Pd–C complexes have been developed to date, affording deep insights into the reaction intermediates in useful catalytic reactions in organic syntheses. Cyclopalladation is one of the most famous Pd–C bond formation reactions to generate the palladacycles. Indole is an electron-rich aromatic ring involved in the side chain of an essential amino acid, tryptophan (Trp), and Trp and its derivatives are important in biological systems, such as electron transfer in protein, cofactors for conversion of biological molecules and so on. Pd catalysts are also useful for syntheses of such indole derivatives, and the mechanisms are considered to be through the Pd–C intermediates. However, the detailed properties and formation mechanisms of Pd–indole species are still unclear. With these points in mind, we focus on Pd(II)–indole-C2 carbon bond formations using various Pd(II) complexes having an indole moiety, especially on the recent studies on the kinetic analyses for these cyclopalladation reactions and their detailed mechanisms.
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22
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Wang D, Böckmann A, Dolenc J, Meier BH, van Gunsteren WF. On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water. J Phys Chem B 2013; 117:11433-47. [PMID: 23998392 DOI: 10.1021/jp400655v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NMR experiments have shown that water molecules in the crystal of the protein Crh are still mobile at temperatures well below 273 K. In order to investigate this water anomaly, a molecular dynamics (MD) simulation study of crystalline Crh was carried out to determine the mobility of water in this crystal. The simulations were carried out at three temperatures, 150, 200, and 291 K. Simulations of bulk water at these temperatures were also done to obtain the properties of the simple point charge (SPC) water model used at these temperatures and to allow a comparison of the properties of water in the Crh crystal with those of bulk water at the same temperatures. According to the simulations, water is immobilized at 150 K both in crystal and in bulk water. As expected, at 291 K it diffuses and rotates more slowly in the protein crystal than in bulk water. However, at 200 K, the translational and rotational mobility of the water molecules is larger in the crystal than in bulk water. The enhancement of water mobility in the crystal at 200 K was further investigated by MD simulations in which the backbone or all protein atoms were positionally restrained, and in which additionally the electrostatic protein-water interactions were removed. Of these changes in the environment of the water molecules, rigidifying the protein backbones slightly enhanced water diffusion, while it slowed down rotation. In contrast, removal of electrostatic protein-water interactions did not change water diffusion but enhanced rotational motion significantly. Further investigations are required to delineate particular features of the protein crystal that induce the anomalous behavior of water at 200 K.
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Affiliation(s)
- Dongqi Wang
- Laboratory of Physical Chemistry, ETH Zürich , CH-8093 Zürich, Switzerland
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23
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Jiang N, Kuznetsov A, Nocek JM, Hoffman BM, Crane BR, Hu X, Beratan DN. Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies. J Phys Chem B 2013; 117:9129-41. [PMID: 23895339 PMCID: PMC3809023 DOI: 10.1021/jp401551t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and in complexes with four mutants of the Cc protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:Cc interface for the F82Y(I) mutants compared to that the WT and F82S(W) complexes are predicted to change the reorganization energies for the CcP:Cc ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor-acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, Duke University, Durham, NC 27708
| | | | - Judith M. Nocek
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, NC 27708
- Department of Biochemistry, Duke University, Durham, NC 27708
- Department of Physics, Duke University, Durham, NC 27708
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24
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Wallrapp FH, Voityuk AA, Guallar V. In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c. PLoS Comput Biol 2013; 9:e1002990. [PMID: 23555224 PMCID: PMC3605091 DOI: 10.1371/journal.pcbi.1002990] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/28/2013] [Indexed: 11/28/2022] Open
Abstract
The fast development of software and hardware is notably helping in closing the gap between macroscopic and microscopic data. Using a novel theoretical strategy combining molecular dynamics simulations, conformational clustering, ab-initio quantum mechanics and electronic coupling calculations, we show how computational methodologies are mature enough to provide accurate atomistic details into the mechanism of electron transfer (ET) processes in complex protein systems, known to be a significant challenge. We performed a quantitative study of the ET between Cytochrome c Peroxidase and its redox partner Cytochrome c. Our results confirm the ET mechanism as hole transfer (HT) through residues Ala194, Ala193, Gly192 and Trp191 of CcP. Furthermore, our findings indicate the fine evolution of the enzyme to approach an elevated turnover rate of 5.47×106 s−1 for the ET between Cytc and CcP through establishment of a localized bridge state in Trp191. We have developed a protocol capable of describing long-range electron transfer mechanisms at an atomic detailed level. We demonstrate the maturity of the computational techniques in obtaining a quantitative view of the Cytochrome c Peroxidase/Cytochrome c electron transfer process, known to be a significant challenge. In excellent agreement with experimental data, our results allow for the description of the electron transfer pathway, its mechanism and the electron transfer rate at a quantitative level. The overall protocol is free of parameterization and can be applied to any complex electron transfer process. Furthermore, the results reveal the fine enzyme evolution of this protein-protein complex to optimize its electron transfer rate by a localized bridge state.
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Affiliation(s)
- Frank H. Wallrapp
- Department of Life Sciences, Barcelona Supercomputing Center, Nexus II Building, Barcelona, Spain
| | - Alexander A. Voityuk
- Department of Computational Chemistry, University of Girona, Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Victor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center, Nexus II Building, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail:
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25
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Takashima H, Fukuda M, Nakagaki F, Ogata T, Tsukahara K. Photoinduced Electron-Transfer Reactions of Carbonic Anhydrase Inhibitor Containing Tris(2,2′-bipyridine)ruthenium(II) Analogue. J Phys Chem B 2013; 117:2625-35. [DOI: 10.1021/jp310604w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan
| | - Misa Fukuda
- Department of Chemistry, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan
| | - Fumie Nakagaki
- Department of Chemistry, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan
| | - Tomoko Ogata
- Department of Chemistry, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan
| | - Keiichi Tsukahara
- Department of Chemistry, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan
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26
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Yin G. Understanding the oxidative relationships of the metal oxo, hydroxo, and hydroperoxide intermediates with manganese(IV) complexes having bridged cyclams: correlation of the physicochemical properties with reactivity. Acc Chem Res 2013. [PMID: 23194251 DOI: 10.1021/ar300208z] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple transition metal functional groups including metaloxo, hydroxo, and hydroperoxide groups play significant roles in various biological and chemical oxidations such as electron transfer, oxygen transfer, and hydrogen abstraction. Further studies that clarify their oxidative relationships and the relationship between their reactivity and their physicochemical properties will expand our ability to predict the reactivity of the intermediate in different oxidative events. As a result researchers will be able to provide rational explanations of poorly understood oxidative phenomena and design selective oxidation catalysts. This Account summarizes results from recent studies of oxidative relationships among manganese(IV) molecules that include pairs of hydroxo/oxo ligands. Changes in the protonation state may simultaneously affect the net charge, the redox potential, the metal-oxygen bond order (M-O vs M═O), and the reactivity of the metal ion. In the manganese(IV) model system, [Mn(IV)(Me(2)EBC)(OH)(2)](PF(6))(2), the Mn(IV)-OH and Mn(IV)═O moieties have similar hydrogen abstraction capabilities, but Mn(IV)═O abstracts hydrogen at a more than 40-fold faster rate than the corresponding Mn(IV)-OH. However, after the first hydrogen abstraction, the reduction product, Mn(III)-OH(2) from the Mn(IV)-OH moiety, cannot transfer a subsequent OH group to the substrate radical. Instead the Mn(III)-OH from the Mn(IV)═O moiety reforms the OH group, generating the hydroxylated product. In the oxygenation of substrates such as triarylphosphines, the reaction with the Mn(IV)═O moiety proceeds by concerted oxygen atom transfer, but the reaction with the Mn(IV)-OH functional group proceeds by electron transfer. In addition, the manganese(IV) species with a Mn(IV)-OH group has a higher redox potential and demonstrates much more facile electron transfer than the one that has the Mn(IV)═O group. Furthermore, an increase in the net charge of the Mn(IV)-OH further accelerates its electron transfer rate. But its influence on hydrogen abstraction is minor because charge-promoted electron transfer does not enhance hydrogen abstraction remarkably. The Mn(IV)-OOH moiety with an identical coordination environment is a more powerful oxidant than the corresponding Mn(IV)-OH and Mn(IV)═O moieties in both hydrogen abstraction and oxygen atom transfer. With this full understanding of the oxidative reactivity of the Mn(IV)-OH and Mn(IV)═O moieties, we have clarified the correlation between the physicochemical properties of these active intermediates, including net charge, redox potential, and metal-oxygen bond order, and their reactivities. The reactivity differences between the metal oxo and hydroxo moieties on these manganese(IV) functional groups after the first hydrogen abstraction have provided clues for understanding their occurrence and functions in metalloenzymes. The P450 enzymes require an iron(IV) oxo form rather than an iron(IV) hydroxo form to perform substrate hydroxylation. However, the lipoxygenases use an iron(III) hydroxo group to dioxygenate unsaturated fatty acids rather than an iron(III) oxo species, a moiety that could facilitate hydroxylation reactions. These distinctly different physicochemical properties and reactivities of the metal oxo and hydroxo moieties could provide clues to understand these elusive oxidation phenomena and provide the foundation for the rational design of novel oxidation catalysts.
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Affiliation(s)
- Guochuan Yin
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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27
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Elschenbroich C, Lu F, Harms K, Pietzonka C. Intermolecular hydrogen bonds directed tetramer and intramolecular electronic communication: paramagnetic di([5]trovacenyl)arsinous acid. CrystEngComm 2013. [DOI: 10.1039/c3ce40246k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Saen-Oon S, Lucas MF, Guallar V. Electron transfer in proteins: theory, applications and future perspectives. Phys Chem Chem Phys 2013; 15:15271-85. [DOI: 10.1039/c3cp50484k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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Volkov AN, van Nuland NAJ. Electron transfer interactome of cytochrome C. PLoS Comput Biol 2012; 8:e1002807. [PMID: 23236271 PMCID: PMC3516563 DOI: 10.1371/journal.pcbi.1002807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/12/2012] [Indexed: 01/31/2023] Open
Abstract
Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility. A number of vital cellular processes such as respiration, photosynthesis, and multifarious metabolic conversions rely on a long-range electron transfer (ET) among protein molecules. Full understanding of the biological ET requires accurate description of the redox protein complexes, which is hampered by their pronounced mobility and short lifetimes. Here we used a simple computational approach to predict the ET properties of the physiological protein complexes of cytochrome c (Cc) – a small electron carrier that coordinates the electron flow among different redox partners. By performing extensive conformational sampling of the possible binding geometries, we mapped out functional epitopes in the Cc complexes and assessed their ET properties. Our study suggests that protein dynamics within redox complexes is the rate-limiting step in the intermolecular ET and indicates that the functional epitope size correlates with the extent of dynamics in the Cc complexes. We believe that the latter finding can be used as a diagnostic tool for protein mobility and expect that this work will engender future studies of the intermolecular ET in biological networks.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Belgium.
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30
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DAS MOUSUMI. ELECTRON TRANSFER THROUGH NON-HYDROGEN AND HYDROGEN BONDED INTERMOLECULAR TUNNEL JUNCTIONS: A COMPUTATIONAL STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nature of electron transfer through intermolecular tunnel junctions has been studied. Intermolecular junctions feature non-hydrogen and hydrogen bonded interactions and are defined by the end groups of pairs of functionalized conjugated alkenes. We compared the distant dependent electron transfer from donor to acceptor group attached to the other sides of those functionalized conjugated alkenes. Study shows electron transfer coupling matrix element for these intermolecular junctions decays exponentially as a function of junction separation and quite substantial in energetically favourable hydrogen bonded intermolecular junctions.
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Affiliation(s)
- MOUSUMI DAS
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur Campus, Mohanpur - 741252, Nadia, West Bengal, India
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31
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Yagati AK, Lee T, Min J, Choi JW. Electrochemical performance of gold nanoparticle–cytochrome c hybrid interface for H2O2 detection. Colloids Surf B Biointerfaces 2012; 92:161-7. [DOI: 10.1016/j.colsurfb.2011.11.035] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/18/2011] [Accepted: 11/17/2011] [Indexed: 10/14/2022]
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32
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Conductivity by Electron Pairs. Chem Phys 2012. [DOI: 10.1201/b11524-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Simultaneous true, gated, and coupled electron-transfer reactions and energetics of protein rearrangement. J Inorg Biochem 2012; 106:143-50. [DOI: 10.1016/j.jinorgbio.2011.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 09/06/2011] [Accepted: 09/09/2011] [Indexed: 11/19/2022]
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34
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Volkov AN, Nicholls P, Worrall JA. The complex of cytochrome c and cytochrome c peroxidase: The end of the road? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1482-503. [DOI: 10.1016/j.bbabio.2011.07.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 11/25/2022]
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35
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Mononuclear nickel and copper complexes with indolecarboxamide ligands: Synthesis, properties and electrochemistry. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.02.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Takashima H, Kitano M, Hirai C, Murakami H, Tsukahara K. Photophysical and DNA-binding properties of cytochrome c modified with a platinum(II) complex. J Phys Chem B 2011; 114:13889-96. [PMID: 20936831 DOI: 10.1021/jp106121n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c (cyt c) derivatives modified with a platinum(II) complex at the lysine residue, cyt c(III)-[Pt(bpy)(dapap)](1) {bpy = 2,2'-bipyridine, and dapap = 3-(2,3-diaminopropionylamino)propionic acid}, have been prepared. The modified residues are Lys8, Lys13, Lys55, Lys60, Lys73, and Lys88. In the case of the cyt c(III)-[Pt(bpy)(dapap)](1) dyad, the photoexcited singlet state of (1)([Pt(bpy)(dapap)](1))* was quenched by the heme Fe(III) moiety through the intramolecular photoinduced energy-transfer reaction via a through-space mechanism. Next, in the presence of calf thymus (CT)-DNA, the DNA-responsive fluorescence properties of cyt c(III)-[Pt(bpy)(dapap)](1) isomers were investigated. The order of the obtained binding constants between the cyt c(III)-[Pt(bpy)(dapap)](1) isomer and CT-DNA in an aqueous solution suggested that the electrostatic interaction is one of the important factors to stabilize the cyt c-DNA complex. Finally, we discussed the rotational motion of the [Pt(bpy)(dapap)](2+) moiety at the surface of cyt c by fluorescence anisotropy measurement. The increase in the anisotropy parameter, r, for each cyt c isomer clearly revealed that the noncovalent recognition of the [Pt(bpy)(dapap)](2+) moiety by CT-DNA is an essential event in the formation of the cyt c-DNA complex and generation of DNA-sensitive fluorescence signals.
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Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara, 630-8506 Japan.
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37
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Loget G, Chevance S, Poriel C, Simonneaux G, Lagrost C, Rault-Berthelot J. Direct Electron Transfer of Hemoglobin and Myoglobin at the Bare Glassy Carbon Electrode in an Aqueous BMI.BF4 Ionic-Liquid Mixture. Chemphyschem 2011; 12:411-8. [DOI: 10.1002/cphc.201000779] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Indexed: 11/10/2022]
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38
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Tsukiji S, Hamachi I. Semisynthetic Hemoproteins Using Cofactor Engineering: Toward Supramolecular Protein-based Photosynthetic System. Supramol Chem 2010. [DOI: 10.1080/10610270290026031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Shinya Tsukiji
- a Department of Chemistry and Biochemistry, Graduate School of Engineering , Kyushu University , Fukuoka , 812-8581 , Japan
| | - Itaru Hamachi
- b Institute for Fundamental Research of Organic Chemistry (IFOC) , Kyushu University , Fukuoka , 812-8581 , Japan
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39
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Dinuclear Ni(II) and Cu(II) complexes with indolecarboxamide ligand: Synthesis, structure and properties. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.04.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Murata K, Kajiya K, Nukaga M, Suga Y, Watanabe T, Nakamura N, Ohno H. A Simple Fabrication Method for Three-Dimensional Gold Nanoparticle Electrodes and Their Application to the Study of the Direct Electrochemistry of Cytochromec. ELECTROANAL 2010. [DOI: 10.1002/elan.200900323] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Chen X, Zhang L, Zhang L, Wang J, Liu H, Bu Y. Proton-Regulated Electron Transfers from Tyrosine to Tryptophan in Proteins: Through-Bond Mechanism versus Long-Range Hopping Mechanism. J Phys Chem B 2009; 113:16681-8. [DOI: 10.1021/jp9077689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Xiaohua Chen
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Laibin Zhang
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Liang Zhang
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Jun Wang
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Haiying Liu
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Yuxiang Bu
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
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42
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Qi Y, Rao F, Luo Z, Liang ZX. A flavin cofactor-binding PAS domain regulates c-di-GMP synthesis in AxDGC2 from Acetobacter xylinum. Biochemistry 2009; 48:10275-85. [PMID: 19785462 DOI: 10.1021/bi901121w] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cytoplasmic protein AxDGC2 regulates cellulose synthesis in the obligate aerobe Acetobacter xylinum by controlling the cellular concentration of the cyclic dinucleotide messenger c-di-GMP. AxDGC2 contains a Per-Arnt-Sim (PAS) domain and two putative catalytic domains (GGDEF and EAL) for c-di-GMP metabolism. We found that the PAS domain of AxDGC2 binds a flavin adenine dinucleotide (FAD) cofactor noncovalently. The redox status of the FAD cofactor modulates the catalytic activity of the GGDEF domain for c-di-GMP synthesis, with the oxidized form exhibiting higher catalytic activity and stronger substrate inhibition. The results suggest that AxDGC2 is a signaling protein that regulates the cellular c-di-GMP level in response to the change in cellular redox status or oxygen concentration. Moreover, several residues predicated to be involved in FAD binding and signal transduction were mutated to examine the impact on redox potential and catalytic activity. Despite the minor perturbation of redox potential and unexpected modification of FAD in one of the mutants, none of the single mutations was able to completely disrupt the transmission of the signal to the GGDEF domain, indicating that the change in the FAD redox state can still trigger structural changes in the PAS domain probably by using substituted hydrogen-bonded water networks. Meanwhile, although the EAL domain of AxDGC2 was found to be catalytically inactive toward c-di-GMP, it was capable of hydrolyzing some phosphodiester bond-containing nonphysiological substrates. Together with the previously reported oxygen-dependent activity of the homologous AxPDEA1, the results provided new insight into relationships among oxygen level, c-di-GMP concentration, and cellulose synthesis in A. xylinum.
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Affiliation(s)
- Yaning Qi
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Clore GM, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 2009; 109:4108-39. [PMID: 19522502 DOI: 10.1021/cr900033p] [Citation(s) in RCA: 588] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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Takashima H, Shibata S, Sekiguchi Y, Imai Y, Tsukahara K. Direct Comparison of Chiral Substituent Effects for Viologens in Stereoselective Photoinduced Electron-Transfer Reactions with Zinc Myoglobin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.1250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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45
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Zhang Y, Straub JE. Diversity of solvent dependent energy transfer pathways in heme proteins. J Phys Chem B 2009; 113:825-30. [PMID: 19115811 DOI: 10.1021/jp807499y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The time scales and pathways of heme cooling in both reduced cytochrome c and oxidized cytochrome c following heme photoexcitation were studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol, and a nonpolar solvent, were used in the simulation. Single exponential decay of the excess kinetic energy of the heme following photoexcitation was observed in all systems studied. The simulated time scale for heme cooling in normal water agrees with recent experimental results. In contrast to heme cooling in myoglobin, no solvent dependence was observed for the time scale for heme cooling in cytochrome c. The diversity of solvent dependence results from the different local heme environments in the two proteins. In myoglobin, it has been established that the dominant mechanism for heme cooling is direct energy transfer from the heme to the solvent. In cytochrome c, direct interaction between heme and protein residues forms the dominant energy transfer pathway. This distinction is dictated by protein topology and linked to function.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215, USA
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46
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Takashima H, Kawahara H, Kitano M, Shibata S, Murakami H, Tsukahara K. Metal ion-dependent fluorescent dynamics of photoexcited zinc-porphyrin and zinc-myoglobin modified with ethylenediaminetetraacetic acid. J Phys Chem B 2009; 112:15493-502. [PMID: 18991435 DOI: 10.1021/jp807692w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reconstituted zinc-myoglobin (ZnMb) dyads, ZnMb-[M(II)(edta)], have been prepared by incorporating a zinc-porphyrin (ZnP) cofactor modified with ethylenediaminetetraacetic acid (H(4)edta) into apo-Mb. In case of the monomeric ZnP(edta) cofactor coordinated by one pyridine molecule, ZnP(py)(edta), a spontaneous 1:1 complex with a transient metal ion was formed in an aqueous solvent, and the photoexcited singlet state of ZnP, (1)(ZnP)*, was quenched by the [Cu(II)(edta)] moiety through intramolecular photoinduced electron-transfer (ET) reaction. The rate constant for the intramolecular quenching ET (k(q)) at 25 degrees C was successfully obtained as k(q) = 5.1 x 10(9) s(-1). In the case of Co(2+), Ni(2+), and Mn(2+), intersystem crossing by paramagnetic effect was mainly considered between (1)(ZnP)* and the [M(II)(edta)] complex. For the ZnMb-[M(II)(edta)] systems, the intramolecular ET reaction between the excited singlet state of (1)(ZnMb)* and the [Cu(II)(edta)] moieties provided the slower quenching rate constant, k(q) = 2.1 x 10(8) s(-1), compared with that of the ZnP(py)(edta) one. Kinetic studies also presented the efficient fluorescence quenching of the (1)(ZnMb)*-[Co(II)(edta)] dyad. Our study clearly demonstrates that wrapping of the ZnP cofactor by the apoprotein matrix and synthetic manipulation at the Mb surface ensure metal ion-sensitive fluorescent dynamics of ZnMb and provides valuable information to elucidate the complicated mechanism of the biological photoinduced ET reactions of hemoproteins.
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Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara, 630-8506 Japan.
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47
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Fukuzumi S. Roles of Metal Ions in Controlling Bioinspired Electron-Transfer Systems. Metal Ion-Coupled Electron Transfer. PROGRESS IN INORGANIC CHEMISTRY 2009. [DOI: 10.1002/9780470440124.ch2] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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48
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Shimazaki Y, Yajima T, Takani M, Yamauchi O. Metal complexes involving indole rings: Structures and effects of metal–indole interactions. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2008.04.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Shimazaki Y, Takani M, Yamauchi O. Metal complexes of amino acids and amino acid side chain groups. Structures and properties. Dalton Trans 2009:7854-69. [PMID: 19771344 DOI: 10.1039/b905871k] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Volkov AN, Bashir Q, Worrall JAR, Ubbink M. Binding hot spot in the weak protein complex of physiological redox partners yeast cytochrome C and cytochrome C peroxidase. J Mol Biol 2008; 385:1003-13. [PMID: 19026661 DOI: 10.1016/j.jmb.2008.10.091] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/16/2008] [Accepted: 10/30/2008] [Indexed: 10/21/2022]
Abstract
Transient protein interactions mediate many vital cellular processes such as signal transduction or intermolecular electron transfer. However, due to difficulties associated with their structural characterization, little is known about the principles governing recognition and binding in weak transient protein complexes. In particular, it has not been well established whether binding hot spots, which are frequently found in strong static complexes, also govern transient protein interactions. To address this issue, we have investigated an electron transfer complex of physiological partners from yeast: yeast iso-1-cytochrome c (Cc) and yeast cytochrome c peroxidase (CcP). Using isothermal titration calorimetry and NMR spectroscopy, we show that Cc R13 is a hot-spot residue, as R13A mutation has a strong destabilizing effect on binding. Furthermore, we employ a double-mutant cycle to illustrate that Cc R13 interacts with CcP Y39. The present results, in combination with those of earlier mutational studies, have enabled us to outline the extent of the energetically important Cc-CcP binding region. Based on our analysis, we propose that binding energy hot spots, which are prevalent in static protein complexes, could also govern transient protein interactions.
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Affiliation(s)
- Alexander N Volkov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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