1
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Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
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Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
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2
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Gibbs C, Fedoretz-Maxwell BP, MacNeil GA, Walsby CJ, Warren JJ. Proximal Methionine Amino Acid Residue Affects the Properties of Redox-Active Tryptophan in an Artificial Model Protein. ACS OMEGA 2023; 8:19798-19806. [PMID: 37305310 PMCID: PMC10249128 DOI: 10.1021/acsomega.3c01589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/11/2023] [Indexed: 06/13/2023]
Abstract
Redox-active amino acid residues are at the heart of biological electron-transfer reactions. They play important roles in natural protein functions and are implicated in disease states (e.g., oxidative-stress-associated disorders). Tryptophan (Trp) is one such redox-active amino acid residue, and it has long been known to serve a functional role in proteins. Broadly speaking, there is still much to learn about the local features that make some Trp redox active and others inactive. Herein, we describe a new protein model system where we investigate how a methionine (Met) residue proximal to a redox-active Trp affects its reactivity and spectroscopy. We use an artificial variant of azurin from Pseudomonas aeruginosa to produce these models. We employ a series of UV-visible spectroscopy, electrochemistry, electron paramagnetic resonance, and density functional theory experiments to demonstrate the effect that placing Met near Trp radicals has in the context of redox proteins. The introduction of Met proximal to Trp lowers its reduction potential by ca. 30 mV and causes clear shifts in the optical spectra of the corresponding radicals. While the effect may be small, it is significant enough to be a way for natural systems to tune Trp reactivity.
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3
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Stathi P, Fotou E, Moussis V, Tsikaris V, Louloudi M, Deligiannakis Y. Control of Tyrosyl Radical Stabilization by {SiO 2@Oligopeptide} Hybrid Biomimetic Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9799-9809. [PMID: 35915965 DOI: 10.1021/acs.langmuir.2c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tyrosine radicals are notoriously short-lived/unstable in solution, while they present an impressive degree of stability and versatility in bioenzymes. Herein, we have developed a library of hybrid biomimetic materials (HBMs), which consists of tyrosine-containing oligopeptides covalently grafted on SiO2 nanoparticles, and studied the formation, lifetime, and redox properties of tyrosyl radicals. Using electron paramagnetic resonance spectroscopy, we have studied the radical-spin distribution as a probe of the local microenvironment of the tyrosyl radicals in the HBMs. We find that the lifetime of the tyrosyl radical can be enhanced by up to 6 times, by adjusting three factors, namely, a proximal histidine, the length of the oligopeptide, and the interface with the SiO2 nanomatrix. This is shown to be correlated to a significant lowering of E1/2 from +736 mV, in free tyrosine, to +548 mV in the {12-peptide}@SiO2 material. Moreover, we show that grafting on SiO2 lowers the E1/2 of tyrosine radicals by ∼50 mV in all oligopeptides. Analysis of the spin-distribution by EPR reveals that the positioning of a histidine at a H-bonding distance from the tyrosine further favors tyrosine radical stabilization.
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Affiliation(s)
- Panagiota Stathi
- Department of Chemistry, Laboratory of Biomimetic Catalysis & Hybrid Materials, University of Ioannina, Ioannina 4550, Greece
| | - Evgenia Fotou
- Department of Chemistry, Laboratory of Protein and Peptide Chemistry, University of Ioannina, Ioannina 4550, Greece
| | - Vassilios Moussis
- Department of Chemistry, Laboratory of Protein and Peptide Chemistry, University of Ioannina, Ioannina 4550, Greece
| | - Vassilios Tsikaris
- Department of Chemistry, Laboratory of Protein and Peptide Chemistry, University of Ioannina, Ioannina 4550, Greece
| | - Maria Louloudi
- Department of Chemistry, Laboratory of Biomimetic Catalysis & Hybrid Materials, University of Ioannina, Ioannina 4550, Greece
| | - Yiannis Deligiannakis
- Department of Physics, Laboratory of Physical Chemistry of Materials & Environment, University of Ioannina, Ioannina 4550, Greece
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4
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Abstract
Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, activate the substrate molecules, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α3X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals.
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Affiliation(s)
- Cecilia Tommos
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA;
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5
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Yoon JH, Kulesha AV, Lengyel-Zhand Z, Volkov AN, Rempillo JJ, D'Souza A, Costeas C, Chester C, Caselle ER, Makhlynets OV. Uno Ferro, a de novo Designed Protein, Binds Transition Metals with High Affinity and Stabilizes Semiquinone Radical Anion. Chemistry 2019; 25:15252-15256. [PMID: 31509280 DOI: 10.1002/chem.201904020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Indexed: 11/07/2022]
Abstract
Metalloenzymes often utilize radicals in order to facilitate chemical reactions. Recently, DeGrado and co-workers have discovered that model proteins can efficiently stabilize semiquinone radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC) in the presence of two zinc ions. Here, we show that the number and the nature of metal ions have relatively minor effect on semiquinone stabilization in model proteins, with a single metal ion being sufficient for radical stabilization. The radical is stabilized by both metal ion, hydrophobic sequestration, and interactions with the hydrophilic residues in the protein interior resulting in a remarkable, nearly 500 mV change in the redox potential of the SQ. - /catechol couple compared to bulk aqueous solution. Moreover, we have created 4G-UFsc, a single metal ion-binding protein with pm affinity for zinc that is higher than any other reported model systems and is on par with many natural zinc-containing proteins. We expect that the robust and easy-to-modify DFsc/UFsc family of proteins will become a versatile tool for mechanistic model studies of metalloenzymes.
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Affiliation(s)
- Jennifer H Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Alona V Kulesha
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels, 1050, Belgium.,Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium
| | - Joel J Rempillo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Christos Costeas
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Cara Chester
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Elizabeth R Caselle
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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6
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Grayson KJ, Anderson JLR. Designed for life: biocompatible de novo designed proteins and components. J R Soc Interface 2019; 15:rsif.2018.0472. [PMID: 30158186 PMCID: PMC6127164 DOI: 10.1098/rsif.2018.0472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
A principal goal of synthetic biology is the de novo design or redesign of biomolecular components. In addition to revealing fundamentally important information regarding natural biomolecular engineering and biochemistry, functional building blocks will ultimately be provided for applications including the manufacture of valuable products and therapeutics. To fully realize this ambitious goal, the designed components must be biocompatible, working in concert with natural biochemical processes and pathways, while not adversely affecting cellular function. For example, de novo protein design has provided us with a wide repertoire of structures and functions, including those that can be assembled and function in vivo. Here we discuss such biocompatible designs, as well as others that have the potential to become biocompatible, including non-protein molecules, and routes to achieving full biological integration.
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Affiliation(s)
- Katie J Grayson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK .,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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7
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Roy A, Seidel R, Kumar G, Bradforth SE. Exploring Redox Properties of Aromatic Amino Acids in Water: Contrasting Single Photon vs Resonant Multiphoton Ionization in Aqueous Solutions. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.7b11762] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anirban Roy
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Robert Seidel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Gaurav Kumar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Stephen E. Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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8
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Streit BR, Celis AI, Moraski GC, Shisler KA, Shepard EM, Rodgers KR, Lukat-Rodgers GS, DuBois JL. Decarboxylation involving a ferryl, propionate, and a tyrosyl group in a radical relay yields heme b. J Biol Chem 2018; 293:3989-3999. [PMID: 29414780 DOI: 10.1074/jbc.ra117.000830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/01/2018] [Indexed: 01/02/2023] Open
Abstract
The H2O2-dependent oxidative decarboxylation of coproheme III is the final step in the biosynthesis of heme b in many microbes. However, the coproheme decarboxylase reaction mechanism is unclear. The structure of the decarboxylase in complex with coproheme III suggested that the substrate iron, reactive propionates, and an active-site tyrosine convey a net 2e-/2H+ from each propionate to an activated form of H2O2 Time-resolved EPR spectroscopy revealed that Tyr-145 formed a radical species within 30 s of the reaction of the enzyme-coproheme complex with H2O2 This radical disappeared over the next 270 s, consistent with a catalytic intermediate. Use of the harderoheme III intermediate as substrate or substitutions of redox-active side chains (W198F, W157F, or Y113S) did not strongly affect the appearance or intensity of the radical spectrum measured 30 s after initiating the reaction with H2O2, nor did it change the ∼270 s required for the radical signal to recede to ≤10% of its initial intensity. These results suggested Tyr-145 as the site of a catalytic radical involved in decarboxylating both propionates. Tyr-145• was accompanied by partial loss of the initially present Fe(III) EPR signal intensity, consistent with the possible formation of Fe(IV)=O. Site-specifically deuterated coproheme gave rise to a kinetic isotope effect of ∼2 on the decarboxylation rate constant, indicating that cleavage of the propionate Cβ-H bond was partly rate-limiting. The inferred mechanism requires two consecutive hydrogen atom transfers, first from Tyr-145 to the substrate Fe/H2O2 intermediate and then from the propionate Cβ-H to Tyr-145•.
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Affiliation(s)
- Bennett R Streit
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Arianna I Celis
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Garrett C Moraski
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Krista A Shisler
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Eric M Shepard
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Kenton R Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Gudrun S Lukat-Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
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9
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Ravichandran KR, Zong AB, Taguchi AT, Nocera DG, Stubbe J, Tommos C. Formal Reduction Potentials of Difluorotyrosine and Trifluorotyrosine Protein Residues: Defining the Thermodynamics of Multistep Radical Transfer. J Am Chem Soc 2017; 139:2994-3004. [PMID: 28171730 DOI: 10.1021/jacs.6b11011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redox-active tyrosines (Ys) play essential roles in enzymes involved in primary metabolism including energy transduction and deoxynucleotide production catalyzed by ribonucleotide reductases (RNRs). Thermodynamic characterization of Ys in solution and in proteins remains a challenge due to the high reduction potentials involved and the reactive nature of the radical state. The structurally characterized α3Y model protein has allowed the first determination of formal reduction potentials (E°') for a Y residing within a protein (Berry, B. W.; Martı́nez-Rivera, M. C.; Tommos, C. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 9739-9743). Using Schultz's technology, a series of fluorotyrosines (FnY, n = 2 or 3) was site-specifically incorporated into α3Y. The global protein properties of the resulting α3(3,5)F2Y, α3(2,3,5)F3Y, α3(2,3)F2Y and α3(2,3,6)F3Y variants are essentially identical to those of α3Y. A protein film square-wave voltammetry approach was developed to successfully obtain reversible voltammograms and E°'s of the very high-potential α3FnY proteins. E°'(pH 5.5; α3FnY(O•/OH)) spans a range of 1040 ± 3 mV to 1200 ± 3 mV versus the normal hydrogen electrode. This is comparable to the potentials of the most oxidizing redox cofactors in nature. The FnY analogues, and the ability to site-specifically incorporate them into any protein of interest, provide new tools for mechanistic studies on redox-active Ys in proteins and on functional and aberrant hole-transfer reactions in metallo-enzymes. The former application is illustrated here by using the determined α3FnY ΔE°'s to model the thermodynamics of radical-transfer reactions in FnY-RNRs and to experimentally test and support the key prediction made.
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Affiliation(s)
| | - Allan B Zong
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | | | - Cecilia Tommos
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
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10
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Larson BC, Pomponio JR, Shafaat HS, Kim RH, Leigh BS, Tauber MJ, Kim JE. Photogeneration and Quenching of Tryptophan Radical in Azurin. J Phys Chem B 2015; 119:9438-49. [PMID: 25625660 PMCID: PMC5092234 DOI: 10.1021/jp511523z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan and tyrosine can form radical intermediates that enable long-range, multistep electron transfer (ET) reactions in proteins. This report describes the mechanisms of formation and quenching of a neutral tryptophan radical in azurin, a blue-copper protein that contains native tyrosine (Y108 and Y72) and tryptophan (W48) residues. A long-lived neutral tryptophan radical W48• is formed upon UV-photoexcitation of a zinc(II)-substituted azurin mutant in the presence of an external electron acceptor. The quantum yield of W48• formation (Φ) depends upon the tyrosine residues in the protein. A tyrosine-deficient mutant, Zn(II)Az48W, exhibited a value of Φ = 0.080 with a Co(III) electron acceptor. A nearly identical quantum yield was observed when the electron acceptor was the analogous tyrosine-free, copper(II) mutant; this result for the Zn(II)Az48W:Cu(II)Az48W mixture suggests there is an interprotein ET path. A single tyrosine residue at one of the native positions reduced the quantum yield to 0.062 (Y108) or 0.067 (Y72). Wild-type azurin with two tyrosine residues exhibited a quantum yield of Φ = 0.045. These data indicate that tyrosine is able to quench the tryptophan radical in azurin.
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Affiliation(s)
- Bethany C. Larson
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jennifer R. Pomponio
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | | | - Rachel H. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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11
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Glover SD, Jorge C, Liang L, Valentine KG, Hammarström L, Tommos C. Photochemical tyrosine oxidation in the structurally well-defined α3Y protein: proton-coupled electron transfer and a long-lived tyrosine radical. J Am Chem Soc 2014; 136:14039-51. [PMID: 25121576 PMCID: PMC4195373 DOI: 10.1021/ja503348d] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Tyrosine oxidation–reduction involves proton-coupled electron
transfer (PCET) and a reactive radical state. These properties are
effectively controlled in enzymes that use tyrosine as a high-potential,
one-electron redox cofactor. The α3Y model protein
contains Y32, which can be reversibly oxidized and reduced in voltammetry
measurements. Structural and kinetic properties of α3Y are presented. A solution NMR structural analysis reveals that
Y32 is the most deeply buried residue in α3Y. Time-resolved
spectroscopy using a soluble flash-quench generated [Ru(2,2′-bipyridine)3]3+ oxidant provides high-quality Y32–O•
absorption spectra. The rate constant of Y32 oxidation (kPCET) is pH dependent: 1.4 × 104 M–1 s–1 (pH 5.5), 1.8 × 105 M–1 s–1 (pH 8.5), 5.4
× 103 M–1 s–1 (pD
5.5), and 4.0 × 104 M–1 s–1 (pD 8.5). kH/kD of Y32 oxidation is 2.5 ± 0.5 and 4.5 ± 0.9 at
pH(D) 5.5 and 8.5, respectively. These pH and isotope characteristics
suggest a concerted or stepwise, proton-first Y32 oxidation mechanism.
The photochemical yield of Y32–O• is 28–58% versus
the concentration of [Ru(2,2′-bipyridine)3]3+. Y32–O• decays slowly, t1/2 in the range of 2–10 s, at both pH 5.5 and 8.5,
via radical–radical dimerization as shown by second-order kinetics
and fluorescence data. The high stability of Y32–O•
is discussed relative to the structural properties of the Y32 site.
Finally, the static α3Y NMR structure cannot explain
(i) how the phenolic proton released upon oxidation is removed or
(ii) how two Y32–O• come together to form dityrosine.
These observations suggest that the dynamic properties of the protein
ensemble may play an essential role in controlling the PCET and radical
decay characteristics of α3Y.
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Affiliation(s)
- Starla D Glover
- Department of Chemistry, Ångström Laboratory, Uppsala University , Box 523, SE75120 Uppsala, Sweden
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12
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Ravichandran KR, Liang L, Stubbe J, Tommos C. Formal reduction potential of 3,5-difluorotyrosine in a structured protein: insight into multistep radical transfer. Biochemistry 2013; 52:8907-15. [PMID: 24228716 DOI: 10.1021/bi401494f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The reversible Y-O•/Y-OH redox properties of the α3Y model protein allow access to the electrochemical and thermodynamic properties of 3,5-difluorotyrosine. The unnatural amino acid has been incorporated at position 32, the dedicated radical site in α3Y, by in vivo nonsense codon suppression. Incorporation of 3,5-difluorotyrosine gives rise to very minor structural changes in the protein scaffold at pH values below the apparent pK (8.0±0.1) of the unnatural residue. Square-wave voltammetry on α3(3,5)F2Y provides an E°'(Y-O•/Y-OH) of 1026±4 mV versus the normal hydrogen electrode (pH 5.70±0.02) and shows that the fluoro substitutions lower the E°' by -30±3 mV. These results illustrate the utility of combining the optimized α3Y tyrosine radical system with in vivo nonsense codon suppression to obtain the formal reduction potential of an unnatural aromatic residue residing within a well-structured protein. It is further observed that the protein E°' values differ significantly from peak potentials derived from irreversible voltammograms of the corresponding aqueous species. This is notable because solution potentials have been the main thermodynamic data available for amino acid radicals. The findings in this paper are discussed relative to recent mechanistic studies of the multistep radical-transfer process in Escherichia coli ribonucleotide reductase site-specifically labeled with unnatural tyrosine residues.
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Affiliation(s)
- Kanchana R Ravichandran
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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13
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Tommos C, Valentine KG, Martínez-Rivera MC, Liang L, Moorman VR. Reversible phenol oxidation and reduction in the structurally well-defined 2-Mercaptophenol-α₃C protein. Biochemistry 2013; 52:1409-18. [PMID: 23373469 DOI: 10.1021/bi301613p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2-Mercaptophenol-α₃C serves as a biomimetic model for enzymes that use tyrosine residues in redox catalysis and multistep electron transfer. This model protein was tailored for electrochemical studies of phenol oxidation and reduction with specific emphasis on the redox-driven protonic reactions occurring at the phenol oxygen. This protein contains a covalently modified 2-mercaptophenol-cysteine residue. The radical site and the phenol compound were specifically chosen to bury the phenol OH group inside the protein. A solution nuclear magnetic resonance structural analysis (i) demonstrates that the synthetic 2-mercaptophenol-α₃C model protein behaves structurally as a natural protein, (ii) confirms the design of the radical site, (iii) reveals that the ligated phenol forms an interhelical hydrogen bond to glutamate 13 (phenol oxygen-carboxyl oxygen distance of 3.2 ± 0.5 Å), and (iv) suggests a proton-transfer pathway from the buried phenol OH (average solvent accessible surface area of 3 ± 5%) via glutamate 13 (average solvent accessible surface area of the carboxyl oxygens of 37 ± 18%) to the bulk solvent. A square-wave voltammetry analysis of 2-mercaptophenol-α₃C further demonstrates that (v) the phenol oxidation-reduction cycle is reversible, (vi) formal phenol reduction potentials can be obtained, and (vii) the phenol-O(•) state is long-lived with an estimated lifetime of ≥180 millisecond. These properties make 2-mercaptophenol-α₃C a unique system for characterizing phenol-based proton-coupled electron transfer in a low-dielectric and structured protein environment.
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Affiliation(s)
- Cecilia Tommos
- Graduate Group in Biochemistry and Molecular Biophysics and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, United States.
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14
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Sheth S, Baron A, Herrero C, Vauzeilles B, Aukauloo A, Leibl W. Light-induced tryptophan radical generation in a click modular assembly of a sensitiser-tryptophan residue. Photochem Photobiol Sci 2013; 12:1074-8. [DOI: 10.1039/c3pp50021g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Prabhulkar S, Tian H, Wang X, Zhu JJ, Li CZ. Engineered proteins: redox properties and their applications. Antioxid Redox Signal 2012; 17:1796-822. [PMID: 22435347 PMCID: PMC3474195 DOI: 10.1089/ars.2011.4001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices.
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Affiliation(s)
- Shradha Prabhulkar
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
| | - Hui Tian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Xiaotang Wang
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Jun-Jie Zhu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chen-Zhong Li
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
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16
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Reversible voltammograms and a Pourbaix diagram for a protein tyrosine radical. Proc Natl Acad Sci U S A 2012; 109:9739-43. [PMID: 22675121 DOI: 10.1073/pnas.1112057109] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reversible voltammograms and a voltammetry half-wave potential versus solution pH diagram are described for a protein tyrosine radical. This work required a de novo designed tyrosine-radical protein displaying a unique combination of structural and electrochemical properties. The α(3)Y protein is structurally stable across a broad pH range. The redox-active tyrosine Y32 resides in a desolvated and well-structured environment. Y32 gives rise to reversible square-wave and differential pulse voltammograms at alkaline pH. The formal potential of the Y32-O(•)/Y32-OH redox couple is determined to 918 ± 2 mV versus the normal hydrogen electrode at pH 8.40 ± 0.01. The observation that Y32 gives rise to fully reversible voltammograms translates into an estimated lifetime of ≥30 ms for the Y32-O(•) state. This illustrates the range of tyrosine-radical stabilization that a structured protein can offer. Y32 gives rise to quasireversible square-wave and differential pulse voltammograms at acidic pH. These voltammograms represent the Y32 species at the upper edge of the quasirevesible range. The square-wave net potential closely approximates the formal potential of the Y32-O(•)/Y32-OH redox couple to 1,070 ± 1 mV versus the normal hydrogen electrode at pH 5.52 ± 0.01. The differential pulse voltammetry half-wave potential of the Y32-O(•)/Y32-OH redox pair is measured between pH 4.7 and 9.0. These results are described and analyzed.
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17
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Martínez-Rivera MC, Berry BW, Valentine KG, Westerlund K, Hay S, Tommos C. Electrochemical and structural properties of a protein system designed to generate tyrosine Pourbaix diagrams. J Am Chem Soc 2011; 133:17786-95. [PMID: 22011192 DOI: 10.1021/ja206876h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This report describes a model protein specifically tailored to electrochemically study the reduction potential of protein tyrosine radicals as a function of pH. The model system is based on the 67-residue α(3)Y three-helix bundle. α(3)Y contains a single buried tyrosine at position 32 and displays structural properties inherent to a protein. The present report presents differential pulse voltammograms obtained from α(3)Y at both acidic (pH 5.6) and alkaline (pH 8.3) conditions. The observed Faradaic response is uniquely associated with Y32, as shown by site-directed mutagenesis. This is the first time voltammetry is successfully applied to detect a redox-active tyrosine residing in a structured protein environment. Tyrosine is a proton-coupled electron-transfer cofactor making voltammetry-based pH titrations a central experimental approach. A second set of experiments was performed to demonstrate that pH-dependent studies can be conducted on the redox-active tyrosine without introducing large-scale structural changes in the protein scaffold. α(3)Y was re-engineered with the specific aim to place the imidazole group of a histidine close to the Y32 phenol ring. α(3)Y-K29H and α(3)Y-K36H each contain a histidine residue whose protonation perturbs the fluorescence of Y32. We show that these variants are stable and well-folded proteins whose helical content, tertiary structure, solution aggregation state, and solvent-sequestered position of Y32 remain pH insensitive across a range of at least 3-4 pH units. These results confirm that the local environment of Y32 can be altered and the resulting radical site studied by voltammetry over a broad pH range without interference from long-range structural effects.
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Affiliation(s)
- Melissa C Martínez-Rivera
- Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, 905 Stellar-Chance Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, United States
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18
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Sinha RK, Maître P, Piccirillo S, Chiavarino B, Crestoni ME, Fornarini S. Cysteine radical cation: A distonic structure probed by gas phase IR spectroscopy. Phys Chem Chem Phys 2010; 12:9794-800. [DOI: 10.1039/c003576a] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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19
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Westerlund K, Moran SD, Privett HK, Hay S, Jarvet J, Gibney BR, Tommos C. Making a single-chain four-helix bundle for redox chemistry studies. Protein Eng Des Sel 2008; 21:645-52. [PMID: 18755707 DOI: 10.1093/protein/gzn043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The construction and characteristics of the stable and well-structured alpha(4)W protein are described. The 117-residue, single-chain protein has a molecular weight of 13.1 kDa and is designed to fold into a four-helix bundle. Experimental characterization of the expressed and purified protein shows a 69.8 +/- 0.8% helical content over a 5.5-10.0 pH range. The protein is thermostable with a T(M) > 355 K and has a free energy of unfolding as measured by chemical denaturation of -4.7 kcal mol(-1) at 25 degrees C and neutral pH. One-dimensional (1D) proton and 2D (15)N-HSQC spectra show narrow, well-dispersed spectral lines consistent with a uniquely structured alpha-helical protein. Analytical ultracentrifugation and NMR data show that the protein is monomeric over a broad protein concentration range. The 324 nm emission maximum of the unique Trp-106 is consistent with a sequestered position of the aromatic residue. Additionally, differential pulse voltammetry characterization indicates an elevated peak potential for Trp-106 when the protein is folded (pH range 7.0-8.5) relative to partly unfolded (pH range 11.4-13.2). The oxidation of Trp-106 is coupled to proton release as shown by a 53 +/- 3 mV/pH unit dependence of the peak potential over the 7.0-8.5 pH range.
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Affiliation(s)
- Kristina Westerlund
- Department of Biochemistry and Biophysics, University of Pennsylvania, 905 Stellar-Chance Laboratories, Philadelphia, PA 19104-6059, USA
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20
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Costanzo F, Sulpizi M, Guido Della Valle R, Sprik M. First Principles Study of Alkali−Tyrosine Complexes: Alkali Solvation and Redox Properties. J Chem Theory Comput 2008; 4:1049-56. [DOI: 10.1021/ct8000415] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Costanzo
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Marialore Sulpizi
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Raffaele Guido Della Valle
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Michiel Sprik
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
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21
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Wydrzynski T, Hillier W, Conlan B. Engineering model proteins for Photosystem II function. PHOTOSYNTHESIS RESEARCH 2007; 94:225-233. [PMID: 17955341 DOI: 10.1007/s11120-007-9271-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 10/04/2007] [Indexed: 05/25/2023]
Abstract
Our knowledge of Photosystem II and the molecular mechanism of oxygen production are rapidly advancing. The time is now ripe to exploit this knowledge and use it as a blueprint for the development of light-driven catalysts, ultimately for the splitting of water into O2 and H2. In this article, we outline the background and our approach to this technological application through the reverse engineering of Photosystem II into model proteins.
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Affiliation(s)
- Tom Wydrzynski
- Research School of Biological Sciences, Australian National University, Canberra, ACT, 0200, Australia.
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22
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Davidson VL. Protein-derived cofactors. Expanding the scope of post-translational modifications. Biochemistry 2007; 46:5283-92. [PMID: 17439161 DOI: 10.1021/bi700468t] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent advances in enzymology, structural biology, and protein chemistry have extended the scope of the field of cofactor-dependent enzyme catalysis. It has been documented that catalytic and redox-active prosthetic groups may be derived from post-translational modification of amino acid residues of proteins. These protein-derived cofactors typically arise from the oxygenation of aromatic residues, covalent cross-linking of amino acid residues, or cyclization or cleavage of internal amino acid residues. In some cases, the post-translation modification is a self-processing event, whereas in others, another processing enzyme is required. The characterization of protein-derived cofactors and their mechanisms of biogenesis introduce a new dimension to our current views about protein evolution and protein structure-function relationships.
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Affiliation(s)
- Victor L Davidson
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA.
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23
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Manzanares D, Rodriguez-Capote K, Liu S, Haines T, Ramos Y, Zhao L, Doherty-Kirby A, Lajoie G, Possmayer F. Modification of Tryptophan and Methionine Residues Is Implicated in the Oxidative Inactivation of Surfactant Protein B. Biochemistry 2007; 46:5604-15. [PMID: 17425286 DOI: 10.1021/bi062304p] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exposing BLES (bovine lipid extract surfactant), a clinical surfactant, to reactive oxygen species (ROS) alters surfactant protein B (SP-B), as indicated by Coomassie Blue staining, silver staining, and Western analysis. Hypochlorous acid (HOCl) treatment leads to elevated maximum surface tension (gammamax) and a deterioration in minimum gamma (gammamin) during surface area cycling. Fenton reaction resulted in immediate increases in gammamin and gammamax. Intrinsic fluorescence measurements indicated Fenton, but not HOCl, induced conversion of Trp9 of SP-B to hydroxyTrp (OHTrp), N-formylkynurenine (NFKyn), and kynurenine (Kyn). Electrospray ionization mass spectrometry (ESI-MS) revealed molecular weight alterations consistent with oxidation of Met (HOCl, Fenton) and Trp (Fenton) residues. Oxidative alterations to Met29 and Met65 (HOCl, Fenton) and to Trp9 (OHTrp with HOCL and NFKyn plus Kyn with Fenton) were confirmed by matrix-assisted laser desorption mass spectrometry (MALDI-MS) studies on SP-B tryptic fragments. Some Met oxidation was observed with control SP-B. When taken together with captive bubble tensiometer measurements, these studies suggest that Met oxidation of SP-B by HOCl or Fenton interferes with phospholipid respreading during compression-expansion of surfactant films, while Fenton oxidation, which produces more extensive Met oxidation and disruption of the indole ring of Trp9, further abrogated the ability of such films to attain low surface tensions during compression. These studies provide insight into the manner by which ROS generated during acute lung injury and the acute respiratory distress syndrome act to inhibit not only endogenous surfactant but also therapeutic surfactants administered to counteract these conditions.
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Affiliation(s)
- Dahis Manzanares
- Department of Obstetrics and Gynaecology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada N6A 5C1
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