1
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Cheng L, Chen H, Ren Y, Cheng Z, Fan M, Liu Y, Shen Z, Yuan T. Study on enhancement of hemoglobin antitoxic ability modified with chromium and ruthenium. Int J Biol Macromol 2023; 242:124756. [PMID: 37178891 DOI: 10.1016/j.ijbiomac.2023.124756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/17/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Hemoglobin is essential for carrying oxygen (O2) in the blood. However, its ability to bind excessively to carbon monoxide (CO) makes it susceptible to CO poisoning. To reduce the risk of CO poisoning, Cr-based heme and Ru-based heme were selected from among many transition metal-based hemes based on their characteristics of adsorption conformation, binding intensity, spin multiplicity, and electronic properties. The results showed that hemoglobin modified by Cr-based heme and Ru-based heme had strong anti-CO poisoning abilities. The Cr-based heme and Ru-based heme exhibited much stronger affinity for O2 (-190.67 kJ/mol and -143.18 kJ/mol, respectively) than Fe-based heme (-44.60 kJ/mol). Moreover, Cr-based heme and Ru-based heme exhibited much weaker affinity for CO (-121.50 kJ/mol and -120.88 kJ/mol, respectively) than their affinity for O2, suggesting that they were less likely to cause CO poisoning. The electronic structure analysis also supported this conclusion. Additionally, molecular dynamics analysis showed that hemoglobin modified by Cr-based heme and Ru-based heme was stable. Our findings offer a novel and effective strategy for enhancing the reconstructed hemoglobin's ability to bind O2 and reduce its potential for CO poisoning.
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Affiliation(s)
- Luwei Cheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hongjiang Chen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yuanyang Ren
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhiwen Cheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai Academy of Environment Sciences, Shanghai 200233, PR China
| | - Maohong Fan
- College of Engineering & Applied Science, University of Wyoming, Laramie 82070, WY, USA
| | - Yawei Liu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhemin Shen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai 200233, PR China; Shanghai Engineering Research Center of Solid Waste Treatment and Resource Recovery, Shanghai 200240, China.
| | - Tao Yuan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai 200233, PR China; Shanghai Engineering Research Center of Solid Waste Treatment and Resource Recovery, Shanghai 200240, China
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2
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Trana EN, Nocek JM, Woude JV, Span I, Smith SM, Rosenzweig AC, Hoffman BM. Charge-Disproportionation Symmetry Breaking Creates a Heterodimeric Myoglobin Complex with Enhanced Affinity and Rapid Intracomplex Electron Transfer. J Am Chem Soc 2016; 138:12615-28. [PMID: 27646786 DOI: 10.1021/jacs.6b07672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report rapid photoinitiated intracomplex electron transfer (ET) within a "charge-disproportionated" myoglobin (Mb) dimer with greatly enhanced affinity. Two mutually supportive Brownian Dynamics (BD) interface redesign strategies, one a new "heme-filtering" approach, were employed to "break the symmetry" of a Mb homodimer by pairing Mb constructs with complementary highly positive and highly negative net surface charges, introduced through D/E → K and K → E mutations, respectively. BD simulations using a previously developed positive mutant, Mb(+6) = Mb(D44K/D60K/E85K), led to construction of the complementary negative mutant Mb(-6) = Mb(K45E, K63E, K95E). Simulations predict the pair will form a well-defined complex comprising a tight ensemble of conformations with nearly parallel hemes, at a metal-metal distance ∼18-19 Å. Upon expression and X-ray characterization of the partners, BD predictions were verified through ET photocycle measurements enabled by Zn-deuteroporphyrin substitution, forming the [ZnMb(-6), Fe(3+)Mb(+6)] complex. Triplet ET quenching shows charge disproportionation increases the binding constant by no less than ∼5 orders of magnitude relative to wild-type Mb values. All progress curves for charge separation (CS) and charge recombination (CR) are reproduced by a generalized kinetic model for the interprotein ET photocycle. The intracomplex ET rate constants for both CS and CR are increased by over 5 orders of magnitude, and their viscosity independence is indicative of true interprotein ET, rather than dynamic gating as seen in previous studies. The complex displays an unprecedented timecourse for CR of the CS intermediate I. After a laser flash, I forms through photoinduced CS, accumulates to a maximum concentration, then dies away through CR. However, before completely disappearing, I reappears without another flash and reaches a second maximum before disappearing completely.
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Affiliation(s)
- Ethan N Trana
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Judith M Nocek
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Jon Vander Woude
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Ingrid Span
- Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Stephen M Smith
- Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
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3
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Owens CP, Katz FEH, Carter CH, Luca MA, Tezcan FA. Evidence for Functionally Relevant Encounter Complexes in Nitrogenase Catalysis. J Am Chem Soc 2015; 137:12704-12. [PMID: 26360912 PMCID: PMC4809638 DOI: 10.1021/jacs.5b08310] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nitrogenase is the only enzyme that can convert atmospheric dinitrogen (N2) into biologically usable ammonia (NH3). To achieve this multielectron redox process, the nitrogenase component proteins, MoFe-protein (MoFeP) and Fe-protein (FeP), repeatedly associate and dissociate in an ATP-dependent manner, where one electron is transferred from FeP to MoFeP per association. Here, we provide experimental evidence that encounter complexes between FeP and MoFeP play a functional role in nitrogenase catalysis. The encounter complexes are stabilized by electrostatic interactions involving a positively charged patch on the β-subunit of MoFeP. Three single mutations (βAsn399Glu, βLys400Glu, and βArg401Glu) in this patch were generated in Azotobacter vinelandii MoFeP. All of the resulting variants displayed decreases in specific catalytic activity, with the βK400E mutation showing the largest effect. As simulated by the Thorneley-Lowe kinetic scheme, this single mutation lowered the rate constant for FeP-MoFeP association 5-fold. We also found that the βK400E mutation did not affect the coupling of ATP hydrolysis with electron transfer (ET) between FeP and MoFeP. These data suggest a mechanism where FeP initially forms encounter complexes on the MoFeP β-subunit surface en route to the ATP-activated, ET-competent complex over the αβ-interface.
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Affiliation(s)
- Cedric P. Owens
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - Faith E. H. Katz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - Cole H. Carter
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - Maria A. Luca
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
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4
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Yu Y, Cui C, Liu X, Petrik ID, Wang J, Lu Y. A Designed Metalloenzyme Achieving the Catalytic Rate of a Native Enzyme. J Am Chem Soc 2015; 137:11570-3. [PMID: 26318313 PMCID: PMC4676421 DOI: 10.1021/jacs.5b07119] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Terminal
oxidases catalyze four-electron reduction of oxygen to
water, and the energy harvested is utilized to drive the synthesis
of adenosine triphosphate. While much effort has been made to design
a catalyst mimicking the function of terminal oxidases, most biomimetic
catalysts have much lower activity than native oxidases. Herein we
report a designed oxidase in myoglobin with an O2 reduction
rate (52 s–1) comparable to that of a native cytochrome
(cyt) cbb3 oxidase (50 s–1) under identical conditions. We achieved this goal by engineering
more favorable electrostatic interactions between a functional oxidase
model designed in sperm whale myoglobin and its native redox partner,
cyt b5, resulting in a 400-fold electron
transfer (ET) rate enhancement. Achieving high activity equivalent
to that of native enzymes in a designed metalloenzyme offers deeper
insight into the roles of tunable processes such as ET in oxidase
activity and enzymatic function and may extend into applications such
as more efficient oxygen reduction reaction catalysts for biofuel
cells.
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Affiliation(s)
| | | | - Xiaohong Liu
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences , 15 Datun Road, Chaoyang District, Beijing 100101, P. R. China
| | | | - Jiangyun Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences , 15 Datun Road, Chaoyang District, Beijing 100101, P. R. China
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5
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Bashir Q, Meulenbroek EM, Pannu NS, Ubbink M. Engineering specificity in a dynamic protein complex with a single conserved mutation. FEBS J 2014; 281:4892-905. [DOI: 10.1111/febs.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Qamar Bashir
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | | | - Navraj S. Pannu
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
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6
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Co NP, Young RM, Smeigh AL, Wasielewski MR, Hoffman BM. Symmetrized photoinitiated electron flow within the [myoglobin:cytochrome b₅] complex on singlet and triplet time scales: energetics vs dynamics. J Am Chem Soc 2014; 136:12730-6. [PMID: 25133915 PMCID: PMC4160274 DOI: 10.1021/ja506388c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report here that photoinitiated electron flow involving a metal-substituted (M = Mg, Zn) myoglobin (Mb) and its physiological partner protein, cytochrome b5 (cyt b5) can be "symmetrized": the [Mb:cyt b5] complex stabilized by three D/E → K mutations on Mb (D44K/D60K/E85K, denoted MMb) exhibits both oxidative and reductive ET quenching of both the singlet and triplet photoexcited MMb states, the direction of flow being determined by the oxidation state of the cyt b5 partner. The first-excited singlet state of MMb ((1)MMb) undergoes ns-time scale reductive ET quenching by Fe(2+)cyt b5 as well as ns-time scale oxidative ET quenching by Fe(3+)cyt b5, both processes involving an ensemble of structures that do not interconvert on this time scale. Despite a large disparity in driving force favoring photooxidation of (1)MMb relative to photoreduction (δ(-ΔG(0)) ≈ 0.4 eV, M = Mg; ≈ 0.2 eV, M = Zn), for each M the average rate constants for the two reactions are the same within error, (1)k(f) > 10(8) s(-1). This surprising observation is explained by considering the driving-force dependence of the Franck-Condon factor in the Marcus equation. The triplet state of the myoglobin ((3)MMb) created by intersystem crossing from (1)MMb likewise undergoes reductive ET quenching by Fe(2+)cyt b5 as well as oxidative ET quenching by Fe(3+)cyt b5. As with singlet ET, the rate constants for oxidative ET quenching and reductive ET quenching on the triplet time scale are the same within error, (3)k(f) ≈ 10(5) s(-1), but here the equivalence is attributable to gating by intracomplex conversion among a conformational ensemble.
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Affiliation(s)
- Nadia Petlakh Co
- Department of Chemistry and ‡Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University , Evanston, Illinois 60208-3113, United States
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7
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Schilder J, Löhr F, Schwalbe H, Ubbink M. The cytochrome c peroxidase and cytochrome c encounter complex: the other side of the story. FEBS Lett 2014; 588:1873-8. [PMID: 24726731 DOI: 10.1016/j.febslet.2014.03.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/18/2014] [Accepted: 03/26/2014] [Indexed: 11/18/2022]
Abstract
Formation of an encounter complex is important for efficient protein complex formation. The encounter state consists of an ensemble of orientations of two proteins in the complex. Experimental description of such ensembles inherently suffers from insufficient data availability. We have measured paramagnetic relaxation enhancements (PRE) on cytochrome c peroxidase (CcP) caused by its partner cytochrome c (Cc) carrying a spin label. The data complement earlier PRE data of spin labelled CcP, identifying several new interactions. This work demonstrates the need of obtaining as many independent data sets as possible to achieve the most accurate description of an encounter complex.
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Affiliation(s)
- Jesika Schilder
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Frank Löhr
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Centre for Biomolecular Magnetic Resonance, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular Magnetic Resonance, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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8
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Khoshtariya DE, Dolidze TD, Shushanyan M, van Eldik R. Long-range electron transfer with myoglobin immobilized at Au/mixed-SAM junctions: mechanistic impact of the strong protein confinement. J Phys Chem B 2014; 118:692-706. [PMID: 24369906 DOI: 10.1021/jp4101569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Horse muscle myoglobin (Mb) was tightly immobilized at Au-deposited ~15-Å-thick mixed-type (1:1) alkanethiol SAMs, HS-(CH₂)₁₁-COOH/HS-(CH₂)₁₁-OH, and placed in contact with buffered H₂O or D₂O solutions. Fast-scan cyclic voltammetry (CV) and a Marcus-equation-based analysis were applied to determine unimolecular standard rate constants and reorganization free energies for electron transfer (ET), under variable-temperature (15-55 °C) and -pressure (0.01-150 MPa) conditions. The CV signal was surprisingly stable and reproducible even after multiple temperature and pressure cycles. The data analysis revealed the following values: standard rate constant, 33 s⁻¹ (25 °C, 0.01 MPa, H₂O); reorganization free energy, 0.5 ± 0.1 eV (throughout); activation enthalpy, 12 ± 3 kJ mol⁻¹; activation volume, -3.1 ± 0.2 cm³ mol⁻¹; and pH-dependent solvent kinetic isotope effect (k(H)⁰/k(D)⁰), 0.7-1.4. Furthermore, the values for the rate constant and reorganization free energy are very similar to those previously found for cytochrome c electrostatically immobilized at the monocomponent Au/HS-(CH₂)₁₁-COOH junction. In vivo, Mb apparently forms a natural electrostatic complex with cytochrome b₅ (cyt-b₅) through the "dynamic" (loose) docking pattern, allowing for a slow ET that is intrinsically coupled to the water's removal from the "defective" heme iron (altogether shaping the biological repair mechanism for Mb's "met" form). In contrary, our experiments rather mimic the case of a "simple" (tight) docking of the redesigned (mutant) Mb with cyt-b₅ (Nocek et al. J. Am. Chem. Soc. 2010, 132, 6165-6175). According to our analysis, in this configuration, Mb's distal pocket (linked to the "ligand channel") seems to be arrested within the restricted configuration, allowing the rate-determining reversible ET process to be coupled only to the inner-sphere reorganization (minimal elongation/shortening of an Fe-OH₂ bond) rather than the pronounced detachment (rebinding) of water and, hence, to be much faster.
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Affiliation(s)
- Dimitri E Khoshtariya
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg , 91058 Erlangen, Germany
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9
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Schilder J, Ubbink M. Formation of transient protein complexes. Curr Opin Struct Biol 2013; 23:911-8. [PMID: 23932200 DOI: 10.1016/j.sbi.2013.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/11/2013] [Accepted: 07/11/2013] [Indexed: 01/16/2023]
Abstract
The encounter complex of two proteins is a dynamic intermediate state that guides proteins to their binding site, thus enhancing the rate of complex formation. It is particularly useful for complexes that must balance a biological requirement for high turnover with the need for specific binding, such as electron transfer complexes. Here, we describe the current methods for studying and visualizing encounter complexes. We discuss recent developments in mapping the energy landscapes, the role of hydrophobic interactions during encounter complex formation and the discovery of futile encounter complexes. These studies have not only provided insight into encounter complexes of electron transfer proteins, but also opened up new questions and approaches for studying encounter complexes in other weakly associated proteins.
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Affiliation(s)
- Jesika Schilder
- Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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10
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Takematsu K, Williamson H, Blanco-Rodríguez AM, Sokolová L, Nikolovski P, Kaiser JT, Towrie M, Clark IP, Vlček A, Winkler JR, Gray HB. Tryptophan-accelerated electron flow across a protein-protein interface. J Am Chem Soc 2013; 135:15515-25. [PMID: 24032375 PMCID: PMC3855362 DOI: 10.1021/ja406830d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new metallolabeled blue copper protein, Re126W122Cu(I) Pseudomonas aeruginosa azurin, which has three redox sites at well-defined distances in the protein fold: Re(I)(CO)3(4,7-dimethyl-1,10-phenanthroline) covalently bound at H126, a Cu center, and an indole side chain W122 situated between the Re and Cu sites (Re-W122(indole) = 13.1 Å, dmp-W122(indole) = 10.0 Å, Re-Cu = 25.6 Å). Near-UV excitation of the Re chromophore leads to prompt Cu(I) oxidation (<50 ns), followed by slow back ET to regenerate Cu(I) and ground-state Re(I) with biexponential kinetics, 220 ns and 6 μs. From spectroscopic measurements of kinetics and relative ET yields at different concentrations, it is likely that the photoinduced ET reactions occur in protein dimers, (Re126W122Cu(I))2 and that the forward ET is accelerated by intermolecular electron hopping through the interfacial tryptophan: *Re//←W122←Cu(I), where // denotes a protein-protein interface. Solution mass spectrometry confirms a broad oligomer distribution with prevalent monomers and dimers, and the crystal structure of the Cu(II) form shows two Re126W122Cu(II) molecules oriented such that redox cofactors Re(dmp) and W122-indole on different protein molecules are located at the interface at much shorter intermolecular distances (Re-W122(indole) = 6.9 Å, dmp-W122(indole) = 3.5 Å, and Re-Cu = 14.0 Å) than within single protein folds. Whereas forward ET is accelerated by hopping through W122, BET is retarded by a space jump at the interface that lacks specific interactions or water molecules. These findings on interfacial electron hopping in (Re126W122Cu(I))2 shed new light on optimal redox-unit placements required for functional long-range charge separation in protein complexes.
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Affiliation(s)
- Kana Takematsu
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Heather Williamson
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ana María Blanco-Rodríguez
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, United Kingdom
| | - Lucie Sokolová
- Institute of Physical and Theoretical Chemistry, Goethe-Universität, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Pavle Nikolovski
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jens T. Kaiser
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0FA, UK
| | - Ian P. Clark
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0FA, UK
| | - Antonín Vlček
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, United Kingdom
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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11
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Ferreiro DN, Boechi L, Estrin DA, Martí MA. The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin. J Inorg Biochem 2012; 119:75-84. [PMID: 23220591 DOI: 10.1016/j.jinorgbio.2012.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
Abstract
Flavohemoglobins (FHbs) are members of the globin superfamily, widely distributed among prokaryotes and eukaryotes that have been shown to carry out nitric oxide dioxygenase (NOD) activity. In prokaryotes, such as Escherichia coli, NOD activity is a defence mechanism against the NO release by the macrophages of the hosts' immune system during infection. Because of that, FHbs have been studied thoroughly and several drugs have been developed in an effort to fight infectious processes. Nevertheless, the protein's structural determinants involved in the NOD activity are still poorly understood. In this context, the aim of the present work is to unravel the molecular basis of FHbs structural dynamics-to-function relationship using state of the art computer simulation tools. In an effort to fulfill this goal, we studied three key processes that determine NOD activity, namely i) ligand migration into the active site ii) stabilization of the coordinated oxygen and iii) intra-protein electron transfer (ET). Our results allowed us to determine key factors related to all three processes like the presence of a long hydrophobic tunnel for ligand migration, the presence of a water mediated hydrogen bond to stabilize the coordinated oxygen and therefore achieve a high affinity, and the best possible ET paths between the FAD and the heme, where water molecules play an important role. Taken together the presented results close an important gap in our understanding of the wide and diverse globin structural-functional relationships.
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Affiliation(s)
- Dardo N Ferreiro
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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12
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Keinan S, Nocek JM, Hoffman BM, Beratan DN. Interfacial hydration, dynamics and electron transfer: multi-scale ET modeling of the transient [myoglobin, cytochrome b5] complex. Phys Chem Chem Phys 2012; 14:13881-9. [PMID: 22955681 PMCID: PMC3490627 DOI: 10.1039/c2cp41949a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formation of a transient [myoglobin (Mb), cytochrome b(5) (cyt b(5))] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b(5)] complex exhibits dynamic docking (DD), with its cyt b(5) partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble. An electrostatically-guided brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (T(DA)) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated T(DA) values to compute ET rates for the [Mb(wt), cyt b(5)] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E → K charge-reversal mutations, [Mb(3M), cyt b(5)]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher T(DA) values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface remodeling that screens the repulsion between the negatively-charged propionates of the two hemes.
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Affiliation(s)
- Shahar Keinan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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13
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Trana EN, Nocek JM, Knutson AK, Hoffman BM. Evolving the [myoglobin, cytochrome b(5)] complex from dynamic toward simple docking: charging the electron transfer reactive patch. Biochemistry 2012; 51:8542-53. [PMID: 23067206 DOI: 10.1021/bi301134f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe photoinitiated electron transfer (ET) from a suite of Zn-substituted myoglobin (Mb) variants to cytochrome b(5) (b(5)). An electrostatic interface redesign strategy has led to the introduction of positive charges into the vicinity of the heme edge through D/E → K charge-reversal mutation combinations at "hot spot" residues (D44, D60, and E85), augmented by the elimination of negative charges from Mb or b(5) by neutralization of heme propionates. These variations create an unprecedentedly large range in the product of the ET partners' total charges (-5 < -q(Mb)q(b(5)) < 40). The binding affinity (K(a)) increases 1000-fold as -q(Mb)q(b(5)) increases through this range and exhibits a surprisingly simple, exponential dependence on -q(Mb)q(b(5)). This is explained in terms of electrostatic interactions between a "charged reactive patch" (crp) on each partner's surface, defined as a compact region around the heme edge that (i) contains the total protein charge of each variant and (ii) encompasses a major fraction of the "reactive region" (Rr) comprising surface atoms with large matrix elements for electron tunneling to the heme. As -q(Mb)q(b(5)) increases, the complex undergoes a transition from fast to slow-exchange dynamics on the triplet ET time scale, with a correlated progression in the rate constants for intracomplex (k(et)) and bimolecular (k(2)) ET. This progression is analyzed by integrating the crp and Rr descriptions of ET into the textbook steady-state treatment of reversible binding between partners that undergo intracomplex ET and found to encompass the full range of behaviors predicted by the model. The generality of this approach is demonstrated by its application to the extensive body of data for the ET complex between the photosynthetic reaction center and cytochrome c(2). Deviations from this model also are discussed.
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Affiliation(s)
- Ethan N Trana
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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Scanu S, Förster J, Finiguerra MG, Shabestari MH, Huber M, Ubbink M. The complex of cytochrome f and plastocyanin from Nostoc sp. PCC 7119 is highly dynamic. Chembiochem 2012; 13:1312-8. [PMID: 22619165 PMCID: PMC3569876 DOI: 10.1002/cbic.201200073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Indexed: 01/23/2023]
Abstract
Cytochrome f (Cyt f) and plastocyanin (Pc) form a highly transient complex as part of the photosynthetic redox chain. The complex from Nostoc sp. PCC 7119 was studied by NMR relaxation spectroscopy with the aim of determining the orientation of Pc relative to Cyt f. Chemical-shift-perturbation analysis showed that the presence of spin labels on the surface of Cyt f does not significantly affect the binding of Pc. The paramagnetic relaxation enhancement results are not consistent with a single orientation of Pc, thus indicating that multiple orientations must occur and suggesting that an encounter state represents a large fraction of the complex.
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Affiliation(s)
- Sandra Scanu
- Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Feng C. Mechanism of Nitric Oxide Synthase Regulation: Electron Transfer and Interdomain Interactions. Coord Chem Rev 2012; 256:393-411. [PMID: 22523434 PMCID: PMC3328867 DOI: 10.1016/j.ccr.2011.10.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Nitric oxide synthase (NOS), a flavo-hemoprotein, tightly regulates nitric oxide (NO) synthesis and thereby its dual biological activities as a key signaling molecule for vasodilatation and neurotransmission at low concentrations, and also as a defensive cytotoxin at higher concentrations. Three NOS isoforms, iNOS, eNOS and nNOS (inducible, endothelial, and neuronal NOS), achieve their key biological functions by tight regulation of interdomain electron transfer (IET) process via interdomain interactions. In particular, the FMN-heme IET is essential in coupling electron transfer in the reductase domain with NO synthesis in the heme domain by delivery of electrons required for O(2) activation at the catalytic heme site. Compelling evidence indicates that calmodulin (CaM) activates NO synthesis in eNOS and nNOS through a conformational change of the FMN domain from its shielded electron-accepting (input) state to a new electron-donating (output) state, and that CaM is also required for proper alignment of the domains. Another exciting recent development in NOS enzymology is the discovery of importance of the the FMN domain motions in modulating reactivity and structure of the catalytic heme active site (in addition to the primary role of controlling the IET processes). In the absence of a structure of full-length NOS, an integrated approach of spectroscopic (e.g. pulsed EPR, MCD, resonance Raman), rapid kinetics (laser flash photolysis and stopped flow) and mutagenesis methods is critical to unravel the molecular details of the interdomain FMN/heme interactions. This is to investigate the roles of dynamic conformational changes of the FMN domain and the docking between the primary functional FMN and heme domains in regulating NOS activity. The recent developments in understanding of mechanisms of the NOS regulation that are driven by the combined approach are the focuses of this review. An improved understanding of the role of interdomain FMN/heme interaction and CaM binding may serve as the basis for the design of new selective inhibitors of NOS isoforms.
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Affiliation(s)
- Changjian Feng
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, NM 87131 (USA) , Tel: 505-925-4326
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Xiong P, Nocek JM, Vura-Weis J, Lockard JV, Wasielewski MR, Hoffman BM. Faster interprotein electron transfer in a [myoglobin, b⁵] complex with a redesigned interface. Science 2010; 330:1075-8. [PMID: 21097931 DOI: 10.1126/science.1197054] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Direct measurements of electron transfer (ET) within a protein-protein complex with a redesigned interface formed by physiological partner proteins myoglobin (Mb) and cytochrome b(5) (b(5)) reveal interprotein ET rates comparable to those observed within the photosynthetic reaction center. Brownian dynamics simulations show that Mb in which three surface acid residues are mutated to lysine binds b(5) in an ensemble of configurations distributed around a reactive most-probable structure. Correspondingly, charge-separation ET from a photoexcited singlet zinc porphyrin incorporated within Mb to the heme of b(5) and the follow-up charge-recombination exhibit distributed kinetics, with median rate constants, k(f)(s) = 2.1 × 10(9) second(-1) and k(b)(s) = 4.3 × 10(10) second(-1), respectively. The latter approaches that for the initial step in photosynthetic charge separation, k = 3.3 × 10(11) second(-1).
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Affiliation(s)
- Peng Xiong
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
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