1
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Deng Y, Wang JX, Ghosh B, Lu Y. Enzymatic CO 2 reduction catalyzed by natural and artificial Metalloenzymes. J Inorg Biochem 2024; 259:112669. [PMID: 39059175 DOI: 10.1016/j.jinorgbio.2024.112669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The continuously increasing level of atmospheric CO2 in the atmosphere has led to global warming. Converting CO2 into other carbon compounds could mitigate its atmospheric levels and produce valuable products, as CO2 also serves as a plentiful and inexpensive carbon feedstock. However, the inert nature of CO2 poses a major challenge for its reduction. To meet the challenge, nature has evolved metalloenzymes using transition metal ions like Fe, Ni, Mo, and W, as well as electron-transfer partners for their functions. Mimicking these enzymes, artificial metalloenzymes (ArMs) have been designed using alternative protein scaffolds and various metallocofactors like Ni, Co, Re, Rh, and FeS clusters. Both the catalytic efficiency and the scope of CO2-reduction product of these ArMs have been improved over the past decade. This review first focuses on the natural metalloenzymes that directly reduce CO2 by discussing their structures and active sites, as well as the proposed reaction mechanisms. It then introduces the common strategies for electrochemical, photochemical, or photoelectrochemical utilization of these native enzymes for CO2 reduction and highlights the most recent advancements from the past five years. We also summarize principles of protein design for bio-inspired ArMs, comparing them with native enzymatic systems and outlining challenges and opportunities in enzymatic CO2 reduction.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Jing-Xiang Wang
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Barshali Ghosh
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America.
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2
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Toropov NA, Houghton MC, Yu D, Vollmer F. Thermo-Optoplasmonic Single-Molecule Sensing on Optical Microcavities. ACS NANO 2024; 18:17534-17546. [PMID: 38924515 PMCID: PMC11238588 DOI: 10.1021/acsnano.4c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Whispering-gallery-mode (WGM) resonators are powerful instruments for single-molecule sensing in biological and biochemical investigations. WGM sensors leveraged by plasmonic nanostructures, known as optoplasmonic sensors, provide sensitivity down to single atomic ions. In this article, we describe that the response of optoplasmonic sensors upon the attachment of single protein molecules strongly depends on the intensity of WGM. At low intensity, protein binding causes red shifts of WGM resonance wavelengths, known as the reactive sensing mechanism. By contrast, blue shifts are obtained at high intensities, which we explain as thermo-optoplasmonic (TOP) sensing, where molecules transform absorbed WGM radiation into heat. To support our conclusions, we experimentally investigated seven molecules and complexes; we observed blue shifts for dye molecules, amino acids, and anomalous absorption of enzymes in the near-infrared spectral region. As an example of an application, we propose a physical model of TOP sensing that can be used for the development of single-molecule absorption spectrometers.
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Affiliation(s)
- Nikita A Toropov
- Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QD, U.K
- Optoelectronics Research Centre, University of Southampton, Southampton SO17 1BJ, U.K
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao, Shandong 266000, China
| | - Matthew C Houghton
- Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QD, U.K
- Department of Life Sciences, University of Bath, Bath BA2 7AX, U.K
| | - Deshui Yu
- National Time Service Center, Chinese Academy of Sciences, Xi'an 710600, China
| | - Frank Vollmer
- Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QD, U.K
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3
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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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4
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Tyson K, Tangtartharakul CB, Zeug M, Findling N, Haddy A, Hvastkovs E, Choe JY, Kim JE, Offenbacher AR. Electrochemical and Structural Study of the Buried Tryptophan in Azurin: Effects of Hydration and Polarity on the Redox Potential of W48. J Phys Chem B 2023; 127:133-143. [PMID: 36542812 PMCID: PMC9841983 DOI: 10.1021/acs.jpcb.2c06677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/16/2022] [Indexed: 12/24/2022]
Abstract
Tryptophan serves as an important redox-active amino acid in mediating electron transfer and mitigating oxidative damage in proteins. We previously showed a difference in electrochemical potentials for two tryptophan residues in azurin with distinct hydrogen-bonding environments. Here, we test whether reducing the side chain bulk at position Phe110 to Leu, Ser, or Ala impacts the electrochemical potentials (E°) for tryptophan at position 48. X-ray diffraction confirmed the influx of crystallographically resolved water molecules for both the F110A and F110L tyrosine free azurin mutants. The local environments of W48 in all azurin mutants were further evaluated by UV resonance Raman (UVRR) spectroscopy to probe the impact of mutations on hydrogen bonding and polarity. A correlation between the frequency of the ω17 mode─considered a vibrational marker for hydrogen bonding─and E° is proposed. However, the trend is opposite to the expectation from a previous study on small molecules. Density functional theory calculations suggest that the ω17 mode reflects hydrogen bonding as well as local polarity. Further, the UVRR data reveal different intensity/frequency shifts of the ω9/ω10 vibrational modes that characterize the local H-bonding environments of tryptophan. The cumulative data support that the presence of water increases E° and reveal properties of the protein microenvironment surrounding tryptophan.
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Affiliation(s)
- Kristin Tyson
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Chanin B. Tangtartharakul
- Department
of Chemistry and Biochemistry, University
of California at San Diego, La Jolla, California 92093, United States
| | - Matthias Zeug
- Department
of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville North Carolina, 27858, United States
| | - Nathan Findling
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Alice Haddy
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Eli Hvastkovs
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Jun-yong Choe
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
- Department
of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville North Carolina, 27858, United States
| | - Judy E. Kim
- Department
of Chemistry and Biochemistry, University
of California at San Diego, La Jolla, California 92093, United States
| | - Adam R. Offenbacher
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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5
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Pastore AJ, Montoya A, Kamat M, Basso KB, Italia JS, Chatterjee A, Drosou M, Pantazis DA, Angerhofer A. Selective incorporation of 5-hydroxytryptophan blocks long range electron transfer in oxalate decarboxylase. Protein Sci 2023; 32:e4537. [PMID: 36482787 PMCID: PMC9801070 DOI: 10.1002/pro.4537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Oxalate decarboxylase from Bacillus subtilis is a binuclear Mn-dependent acid stress response enzyme that converts the mono-anion of oxalic acid into formate and carbon dioxide in a redox neutral unimolecular disproportionation reaction. A π-stacked tryptophan dimer, W96 and W274, at the interface between two monomer subunits facilitates long-range electron transfer between the two Mn ions and plays an important role in the catalytic mechanism. Substitution of W96 with the unnatural amino acid 5-hydroxytryptophan leads to a persistent EPR signal which can be traced back to the neutral radical of 5-hydroxytryptophan with its hydroxyl proton removed. 5-Hydroxytryptophan acts as a hole sink preventing the formation of Mn(III) at the N-terminal active site and strongly suppresses enzymatic activity. The lower boundary of the standard reduction potential for the active site Mn(II)/Mn(III) couple can therefore be estimated as 740 mV against the normal hydrogen electrode at pH 4, the pH of maximum catalytic efficiency. Our results support the catalytic importance of long-range electron transfer in oxalate decarboxylase while at the same time highlighting the utility of unnatural amino acid incorporation and specifically the use of 5-hydroxytryptophan as an energetic sink for hole hopping to probe electron transfer in redox proteins.
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Affiliation(s)
| | - Alvaro Montoya
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Manasi Kamat
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Kari B. Basso
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - James S. Italia
- Department of ChemistryBoston CollegeChestnut HillMassachusettsUSA
| | | | - Maria Drosou
- Max‐Planck‐Institut für KohlenforschungMülheim an der RuhrGermany
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6
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Rivera JJ, Trinh C, Kim JE. Photoinduced Electron Transfer from the Tryptophan Triplet State in Zn-Azurin. ACS PHYSICAL CHEMISTRY AU 2022; 3:63-73. [PMID: 36718260 PMCID: PMC9881450 DOI: 10.1021/acsphyschemau.2c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
Tryptophan is one of few residues that participates in biological electron transfer reactions. Upon substitution of the native Cu2+ center with Zn2+ in the blue-copper protein azurin, a long-lived tryptophan neutral radical can be photogenerated. We report the following quantum yield values for Zn-substituted azurin in the presence of the electron acceptor Cu(II)-azurin: formation of the tryptophan neutral radical (Φrad), electron transfer (ΦET), fluorescence (Φfluo), and phosphorescence (Φphos), as well as the efficiency of proton transfer of the cation radical (ΦPT). Increasing the concentration of the electron acceptor increased Φrad and ΦET values and decreased Φphos without affecting Φfluo. At all concentrations of the acceptor, the value of ΦPT was nearly unity. These observations indicate that the phosphorescent triplet state is the parent state of electron transfer and that nearly all electron transfer events lead to proton loss. Similar results regarding the parent state were obtained with a different electron acceptor, [Co(NH3)5Cl]2+; however, Stern-Volmer graphs revealed that [Co(NH3)5Cl]2+ was a more effective phosphorescence quencher (K SV = 230 000 M-1) compared to Cu(II)-azurin (K SV = 88 000 M-1). Competition experiments in the presence of both [Co(NH3)5Cl]2+ and Cu(II)-azurin suggested that [Co(NH3)5Cl]2+ is the preferred electron acceptor. Implications of these results in terms of quenching mechanisms are discussed.
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7
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Highly sensitive and selective detection of tryptophan by antipyrine based fluorimetric sensor. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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López-Peña I, Lee CT, Rivera JJ, Kim JE. Role of the Triplet State and Protein Dynamics in the Formation and Stability of the Tryptophan Radical in an Apoazurin Mutant. J Phys Chem B 2022; 126:6751-6761. [PMID: 35977067 PMCID: PMC9483921 DOI: 10.1021/acs.jpcb.2c02441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The protein, azurin,
has enabled the study of the tryptophan radical.
Upon UV excitation of tyrosine-deficient apoazurin and in the presence
of a Co(III) electron acceptor, the neutral radical (W48•)
is formed. The lifetime of W48• in apoazurin is 41 s, which
is shorter than the lifetime of several hours in Zn-substituted azurin.
Molecular dynamics simulations revealed enhanced fluctuations of apoazurin
which likely destabilize W48•. The photophysics of W48 was
investigated to probe the precursor state for ET. The phosphorescence
intensity was eliminated in the presence of an electron acceptor while
the fluorescence was unchanged; this quenching of the phosphorescence
is attributed to ET. The kinetics associated with W48• were
examined with a model that incorporates intersystem crossing, ET,
deprotonation, and decay of the cation radical. The estimated rate
constants for ET (6 × 106 s–1) and
deprotonation (3 × 105 s–1) are
in agreement with a photoinduced mechanism where W48• is derived
from the triplet state. The triplet as the precursor state for ET
was supported by photolysis of apoazurin with 280 nm in the absence
and presence of triplet-absorbing 405 nm light. Absorption bands from
the neutral radical were observed only in the presence of blue light.
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Affiliation(s)
- Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Christopher T Lee
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Joel J Rivera
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
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9
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Fedoretz-Maxwell BP, Shin CH, MacNeil GA, Worrall LJ, Park R, Strynadka NCJ, Walsby CJ, Warren JJ. The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins. Inorg Chem 2022; 61:5563-5571. [DOI: 10.1021/acs.inorgchem.2c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brooklyn P. Fedoretz-Maxwell
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Catherine H. Shin
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Gregory A. MacNeil
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rachel Park
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles J. Walsby
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J. Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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10
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Brink A, Jacobs FJF, Helliwell JR. Trends in coordination of rhenium organometallic complexes in the Protein Data Bank. IUCRJ 2022; 9:180-193. [PMID: 35371500 PMCID: PMC8895017 DOI: 10.1107/s2052252522000665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Radiopharmaceutical development has similar overall characteristics to any biomedical drug development requiring a compound's stability, aqueous solubility and selectivity to a specific disease site. However, organometallic complexes containing 188/186Re or 99mTc involve a d-block transition-metal radioactive isotope and therefore bring additional factors such as metal oxidation states, isotope purity and half life into play. This topical review is focused on the development of radiopharmaceuticals containing the radioisotopes of rhenium and technetium and, therefore, on the occurrence of these organometallic complexes in protein structures in the Worldwide Protein Data Bank (wwPDB). The purpose of incorporating the group 7 transition metals of rhenium/technetium in the protein and the reasons for study by protein crystallography are described, as certain PDB studies were not aimed at drug development. Technetium is used as a medical diagnostic agent and involves the 99mTc isotope which decays to release gamma radiation, thereby employed for its use in gamma imaging. Due to the periodic relationship among group 7 transition metals, the coordination chemistry of rhenium is similar (but not identical) to that of technetium. The types of reactions the potential model radiopharmaceutical would prefer to partake in, and by extension knowing which proteins and biomolecules the compound would react with in vivo, are needed. Crystallography studies, both small molecule and macromolecular, are a key aspect in understanding chemical coordination. Analyses of bonding modes, coordination to particular residues and crystallization conditions are presented. In our Forward look as a concluding summary of this topical review, the question we ask is: what is the best way for this field to progress?
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Affiliation(s)
- Alice Brink
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Francois J. F. Jacobs
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
| | - John R. Helliwell
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
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11
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Gültekin A, Ünüvar A, Karanfil G, Yilmaz I, Say R. Development of molecularly ımprınted polymer based quartz crystal mıcrobalance nanosensor for the determınatıon of tryptophan. Supramol Chem 2020. [DOI: 10.1080/10610278.2020.1746313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Aytaç Gültekin
- Faculty of Engineering, Department of Energy Systems Engineering, Karamanoğlu Mehmetbey University, Karaman, Turkey
| | | | - Gamze Karanfil
- Faculty of Engineering, Department of Energy Systems Engineering, Karamanoğlu Mehmetbey University, Karaman, Turkey
| | - Ibrahim Yilmaz
- Department of Chemistry, Kamil Özdağ Science Faculty, Karamanoğlu Mehmetbey University, Karaman, Turkey
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12
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Tyson KJ, Davis AN, Norris JL, Bartolotti LJ, Hvastkovs EG, Offenbacher AR. Impact of Local Electrostatics on the Redox Properties of Tryptophan Radicals in Azurin: Implications for Redox-Active Tryptophans in Proton-Coupled Electron Transfer. J Phys Chem Lett 2020; 11:2408-2413. [PMID: 32134666 DOI: 10.1021/acs.jpclett.0c00614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tyrosine and tryptophan play critical roles in facilitating proton-coupled electron transfer (PCET) processes essential to life. The local protein environment is anticipated to modulate the thermodynamics of amino acid radicals to achieve controlled, unidirectional PCET. Herein, square-wave voltammetry was employed to investigate the electrostatic effects on the redox properties of tryptophan in two variants of the protein azurin. Each variant contains a single redox-active tryptophan, W48 or W108, in a unique and buried protein environment. These tryptophan residues exhibit reversible square-wave voltammograms. A Pourbaix plot, representing the reduction potentials versus pH, is presented for the non-H-bonded W48, which has potentials comparable to those of tryptophan in solution. The reduction potentials of W108 are seen to be increased by more than 100 mV across the same pH range. Molecular dynamics shows that, despite its buried indole ring, the N-H of W108 hydrogen bonds with a water cluster, while W48 is completely excluded from interactions with water or polar groups. These redox properties provide insight into the role of the protein in tuning the reactivity of tryptophan radicals, a requirement for controlled biological PCET.
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Affiliation(s)
- Kristin J Tyson
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Amanda N Davis
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Jessica L Norris
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Libero J Bartolotti
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Eli G Hvastkovs
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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13
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Rivera JJ, Liang JH, Shimamura GR, Shafaat HS, Kim JE. Raman and Quantum Yield Studies of Trp48- d5 in Azurin: Closed-Shell and Neutral Radical Species. J Phys Chem B 2019; 123:6430-6443. [PMID: 31313925 DOI: 10.1021/acs.jpcb.9b04655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isotopologues are valuable vibrational probes that shift features in a vibrational spectrum while preserving the electronic structure of the molecule. We report the vibrational and electronic spectra of perdeuterated tryptophan in solution (l-Trp-d5), as Trp48-d5 in azurin, and as the photogenerated neutral tryptophan radical, Trp48-d5•, in azurin. The UV resonance Raman bands of the perdeuterated closed-shell tryptophan in solution and in azurin are lower in frequency relative to the protiated counterpart. The observed decrease in frequencies of l-Trp-d5 bands relative to l-Trp-h5 enables the analysis of vibrational markers of other amino acids, e.g., phenylalanine, that overlap with some modes of l-Trp-h5. The Raman intensities vary between l-Trp-d5 and l-Trp-h5; these differences likely reflect modifications in normal mode composition upon perdeuteration. Analysis of the W3, W6, and W17 modes suggests that the W3 mode retains its utility as a conformational marker; however, the H-bond markers W6 and W17 appear to be less sensitive upon perdeuteration. The neutral tryptophan radical, Trp48-d5•, was generated in azurin with a slightly lower radical quantum yield than for Trp48-h5•. The visible resonance Raman spectrum of Trp48-d5• is different from that of Trp48-h5•, especially in terms of relative intensities, and all assignable peaks decreased in frequency upon perdeuteration. The absorption and emission spectra of the perdeuterated closed-shell and radical species exhibited hypsochromic shifts of less than 1 nm relative to the protiated species. The data presented here indicate that l-Trp-d5 is a valuable probe of vibrational structure, with minimal modification of photoreactivity and photophysics compared to l-Trp-h5.
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Affiliation(s)
- Joel J Rivera
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Justine H Liang
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Gregory R Shimamura
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , California 92093-0021 , United States
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14
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Konkankit CC, Marker SC, Knopf KM, Wilson JJ. Anticancer activity of complexes of the third row transition metals, rhenium, osmium, and iridium. Dalton Trans 2018; 47:9934-9974. [DOI: 10.1039/c8dt01858h] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A summary of recent developments on the anticancer activity of complexes of rhenium, osmium, and iridium is described.
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Affiliation(s)
| | - Sierra C. Marker
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| | - Kevin M. Knopf
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| | - Justin J. Wilson
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
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15
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Knopf KM, Murphy BL, MacMillan SN, Baskin JM, Barr MP, Boros E, Wilson JJ. In Vitro Anticancer Activity and in Vivo Biodistribution of Rhenium(I) Tricarbonyl Aqua Complexes. J Am Chem Soc 2017; 139:14302-14314. [PMID: 28948792 PMCID: PMC8091166 DOI: 10.1021/jacs.7b08640] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Seven rhenium(I) complexes of the general formula fac-[Re(CO)3(NN)(OH2)]+ where NN = 2,2'-bipyridine (8), 4,4'-dimethyl-2,2'-bipyridine (9), 4,4'-dimethoxy-2,2'-bipyridine (10), dimethyl 2,2'-bipyridine-4,4'-dicarboxylate (11), 1,10-phenanthroline (12), 2,9-dimethyl-1,10-phenanthroline (13), or 4,7-diphenyl-1,10-phenanthroline (14), were synthesized and characterized by 1H NMR spectroscopy, IR spectroscopy, mass spectrometry, and X-ray crystallography. With the exception of 11, all complexes exhibited 50% growth inhibitory concentration (IC50) values that were less than 20 μM in HeLa cells, indicating that these compounds represent a new potential class of anticancer agents. Complexes 9, 10, and 13 were as effective in cisplatin-resistant cells as wild-type cells, signifying that they circumvent cisplatin resistance. The mechanism of action of the most potent complex, 13, was explored further by leveraging its intrinsic luminescence properties to determine its intracellular localization. These studies indicated that 13 induces cytoplasmic vacuolization that is lysosomal in nature. Additional in vitro assays indicated that 13 induces cell death without causing an increase in intracellular reactive oxygen species or depolarization of the mitochondrial membrane potential. Further studies revealed that the mode of cell death does not fall into one of the canonical categories such as apoptosis, necrosis, paraptosis, and autophagy, suggesting that a novel mode of action may be operative for this class of rhenium compounds. The in vivo biodistribution and metabolism of complex 13 and its 99mTc analogue 13* were also evaluated in naı̈ve mice. Complexes 13 and 13* exhibited comparable biodistribution profiles with both hepatic and renal excretion. High-performance liquid chromatography inductively coupled plasma mass-spectrometry (HPLC-ICP-MS) analysis of mouse blood plasma and urine postadministration showed considerable metabolic stability of 13, rendering this potent complex suitable for in vivo applications. These studies have shown the biological properties of this class of compounds and demonstrated their potential as promising theranostic anticancer agents that can circumvent cisplatin resistance.
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Affiliation(s)
- Kevin M. Knopf
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brendan L. Murphy
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Samantha N. MacMillan
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M. Baskin
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell & Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Martin P. Barr
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James’s Hospital and Trinity College Dublin, Dublin, Ireland
| | - Eszter Boros
- A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, 149 13 Street, Suite 2301, Charlestown, MA 02129, USA
| | - Justin J. Wilson
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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16
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Juszczak LJ, Eisenberg AS. The Color of Cation-π Interactions: Subtleties of Amine-Tryptophan Interaction Energetics Allow for Radical-like Visible Absorbance and Fluorescence. J Am Chem Soc 2017; 139:8302-8311. [PMID: 28537725 DOI: 10.1021/jacs.7b03442] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Several peptides and a protein with an inter- or intramolecular cation-π interaction between tryptophan (Trp) and an amine cation are shown to absorb and fluoresce in the visible region of the spectrum. Titration of indole with sodium hydroxide or ammonium hydroxide yields an increasing visible fluorescence as well. Visible absorption and multipeaked fluorescence excitation spectra correlate with experimental absorption spectra and the vibrational modes of calculated absorption spectra for the neutral Trp radical. The radical character of the cation-indole interaction is predicted to stem from the electrostatic dislocation of indole highest occupied molecular orbital (HOMO) charge density toward the cation with a subsequent electronic transition from the HOMO-2 to the HOMO. Because this is a vertical transition, fluorescence is possible. Hydrogen bonding at the indole amine most likely stabilizes the radical-like state. These results provide new spectroscopic tools for the investigation of cation-π interactions in numerous biological systems, among them, proteins and their myriad ligands, and show that one, or at most, two, point mutations with natural amino acids are all that is required to impart visible fluorescence to proteins.
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Affiliation(s)
- Laura J Juszczak
- Chemistry Department, Brooklyn College, The City University of New York , New York, New York 11210, United States.,PhD programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York , New York, New York 10016, United States
| | - Azaria S Eisenberg
- Chemistry Department, Brooklyn College, The City University of New York , New York, New York 11210, United States
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17
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Darjee SM, Bhatt KD, Panchal US, Jain VK. Scrupulous recognition of biologically important acids by fluorescent “turn off-on” mechanism of thaicalix reduced silver nanoparticles. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2016.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Darjee SM, Bhatt KD, Panchal US, Jain VK. WITHDRAWN: Scrupulous recongnisation of biologically important acids by Fluorescent “turn off-on” mechanism of thaicalix reduced silver nanoparticles. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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19
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Dongare P, Maji S, Hammarström L. Direct Evidence of a Tryptophan Analogue Radical Formed in a Concerted Electron−Proton Transfer Reaction in Water. J Am Chem Soc 2016; 138:2194-9. [DOI: 10.1021/jacs.5b08294] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prateek Dongare
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
| | - Somnath Maji
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
| | - Leif Hammarström
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
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20
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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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21
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Sakurai M, Nakamura S. Unrestricted density functional theory based on the fragment molecular orbital method for the ground and excited state calculations of large systems. J Chem Phys 2014; 140:144101. [DOI: 10.1063/1.4870261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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22
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23
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Nakata H, Fedorov DG, Nagata T, Yokojima S, Ogata K, Kitaura K, Nakamura S. Unrestricted Hartree-Fock based on the fragment molecular orbital method: Energy and its analytic gradient. J Chem Phys 2012; 137:044110. [DOI: 10.1063/1.4737860] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Bernini C, Pogni R, Basosi R, Sinicropi A. The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: Insights from quantum mechanical/molecular mechanics simulations. Proteins 2012; 80:1476-83. [DOI: 10.1002/prot.24046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/18/2012] [Accepted: 01/25/2012] [Indexed: 01/21/2023]
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25
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Stoll S, Shafaat HS, Krzystek J, Ozarowski A, Tauber MJ, Kim JE, Britt RD. Hydrogen bonding of tryptophan radicals revealed by EPR at 700 GHz. J Am Chem Soc 2011; 133:18098-101. [PMID: 22007694 PMCID: PMC3251908 DOI: 10.1021/ja208462t] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Redox-active tryptophans are important in biological electron transfer and redox biochemistry. Proteins can tune the electron transfer kinetics and redox potentials of tryptophan via control of the protonation state and the hydrogen-bond strength. We examine the local environment of two neutral tryptophan radicals (Trp108 on the solvent-exposed surface and Trp48 buried in the hydrophobic core) in two azurin variants. Ultrahigh-field EPR spectroscopy at 700 GHz and 25 T allowed complete resolution of all of the principal components of the g tensors of the two radicals and revealed significant differences in the g tensor anisotropies. The spectra together with (2)H ENDOR spectra and supporting DFT calculations show that the g tensor anisotropy is directly diagnostic of the presence or absence as well as the strength of a hydrogen bond to the indole nitrogen. The approach is a powerful one for identifying and characterizing hydrogen bonds that are critical in the regulation of tryptophan-assisted electron transfer and tryptophan-mediated redox chemistry in proteins.
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Affiliation(s)
- Stefan Stoll
- Department of Chemistry, University of California Davis, Davis California 95616, United States
| | - Hannah S. Shafaat
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093, United States
| | - J. Krzystek
- National High Magnetic Field Laboratory, Florida State University, Tallahassee Florida 32310, United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, Tallahassee Florida 32310, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093, United States
| | - R. David Britt
- Department of Chemistry, University of California Davis, Davis California 95616, United States
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26
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Bellina B, Compagnon I, Houver S, Maître P, Allouche AR, Antoine R, Dugourd P. Spectroscopic Signatures of Peptides Containing Tryptophan Radical Cations. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Bellina B, Compagnon I, Houver S, Maître P, Allouche AR, Antoine R, Dugourd P. Spectroscopic Signatures of Peptides Containing Tryptophan Radical Cations. Angew Chem Int Ed Engl 2011; 50:11430-2. [DOI: 10.1002/anie.201104783] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Indexed: 11/06/2022]
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28
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Antoine R, Dugourd P. Visible and ultraviolet spectroscopy of gas phase protein ions. Phys Chem Chem Phys 2011; 13:16494-509. [PMID: 21811728 DOI: 10.1039/c1cp21531k] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.
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29
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Blanco-Rodríguez AM, Di Bilio AJ, Shih C, Museth AK, Clark IP, Towrie M, Cannizzo A, Sudhamsu J, Crane BR, Sýkora J, Winkler JR, Gray HB, Záliš S, Vlček A. Phototriggering electron flow through Re(I)-modified Pseudomonas aeruginosa azurins. Chemistry 2011; 17:5350-61. [PMID: 21469225 DOI: 10.1002/chem.201002162] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 12/12/2010] [Indexed: 11/07/2022]
Abstract
The [Re(I)(CO)(3)(4,7-dimethyl-1,10-phenanthroline)(histidine-124)(tryptophan-122)] complex, denoted [Re(I)(dmp)(W122)], of Pseudomonas aeruginosa azurin behaves as a single photoactive unit that triggers very fast electron transfer (ET) from a distant (2 nm) Cu(I) center in the protein. Analysis of time-resolved (ps-μs) IR spectroscopic and kinetics data collected on [Re(I)(dmp)(W122)AzM] (in which M=Zn(II), Cu(II), Cu(I); Az=azurin) and position-122 tyrosine (Y), phenylalanine (F), and lysine (K) mutants, together with excited-state DFT/time-dependent (TD)DFT calculations and X-ray structural characterization, reveal the character, energetics, and dynamics of the relevant electronic states of the [Re(I)(dmp)(W122)] unit and a cascade of photoinduced ET and relaxation steps in the corresponding Re-azurins. Optical population of [Re(I)(imidazole-H124)(CO)(3)]→dmp (1)CT states (CT=charge transfer) is followed by around 110 fs intersystem crossing and about 600 ps structural relaxation to a (3)CT state. The IR spectrum indicates a mixed Re(I)(CO)(3),A→dmp/π→π(*)(dmp) character for aromatic amino acids A122 (A=W, Y, F) and Re(I)(CO)(3)→dmp metal-ligand charge transfer (MLCT) for [Re(I)(dmp)(K122)AzCu(II)]. In a few ns, the (3)CT state of [Re(I)(dmp)(W122)AzM] establishes an equilibrium with the [Re(I)(dmp(.-))(W122(.+))AzM] charge-separated state, (3)CS, whereas the (3)CT state of the other Y, F, and K122 proteins decays to the ground state. In addition to this main pathway, (3)CS is populated by fs- and ps-W(indole)→Re(II) ET from (1)CT and the initially "hot" (3)CT states, respectively. The (3)CS state undergoes a tens-of-ns dmp(.-)→W122(.+) ET recombination leading to the ground state or, in the case of the Cu(I) azurin, a competitively fast (≈30 ns over 1.12 nm) Cu(I)→W(.+) ET, to give [Re(I)(dmp(.-))(W122)AzCu(II)]. The overall photoinduced Cu(I)→Re(dmp) ET through [Re(I)(dmp)(W122)AzCu(I)] occurs over a 2 nm distance in <50 ns after excitation, with the intervening fast (3)CT-(3)CS equilibrium being the principal accelerating factor. No reaction was observed for the three Y, F, and K122 analogues. Although the presence of [Re(dmp)(W122)AzCu(II)] oligomers in solution was documented by mass spectrometry and phosphorescence anisotropy, the kinetics data do not indicate any significant interference from the intermolecular ET steps. The ground-state dmp-indole π-π interaction together with well-matched W/W(.+) and excited-state [Re(II)(CO)(3)(dmp(.-))]/[Re(I)(CO)(3)(dmp(.-))] potentials that result in very rapid electron interchange and (3)CT-(3)CS energetic proximity, are the main factors responsible for the unique ET behavior of [Re(I)(dmp)(W122)]-containing azurins.
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Affiliation(s)
- Ana María Blanco-Rodríguez
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK
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Sokolová L, Williamson H, Sýkora J, Hof M, Gray HB, Brutschy B, Vlcek A. Mass spectrometric characterization of oligomers in Pseudomonas aeruginosa azurin solutions. J Phys Chem B 2011; 115:4790-800. [PMID: 21452827 DOI: 10.1021/jp110460k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have employed laser-induced liquid bead ion desorption mass spectroscopy (LILBID MS) to study the solution behavior of Pseudomonas aeruginosa azurin as well as two mutants and corresponding Re-labeled derivatives containing a Re(CO)(3)(4,7-dimethyl-1,10-phenanthroline)(+) chromophore appended to a surface histidine. LILBID spectra show broad oligomer distributions whose particular patterns depend on the solution composition (pure H(2)O, 20-30 mM NaCl, 20 and 50 mM NaP(i) or NH(4)P(i) at pH = 7). The distribution maximum shifts to smaller oligomers upon decreasing the azurin concentration and increasing the buffer concentration. Oligomerization is less extensive for native azurin than its mutants. The oligomerization propensities of unlabeled and Re-labeled proteins are generally comparable, and only Re126 shows some preference for the dimer that persists even in highly diluted solutions. Peak shifts to higher masses and broadening in 20-50 mM NaP(i) confirm strong azurin association with buffer ions and solvation. We have found that LILBID MS reveals the solution behavior of weakly bound nonspecific protein oligomers, clearly distinguishing individual components of the oligomer distribution. Independently, average data on oligomerization and the dependence on solution composition were obtained by time-resolved anisotropy of the Re-label photoluminescence that confirmed relatively long rotation correlation times, 6-30 ns, depending on Re-azurin and solution composition. Labeling proteins with Re-chromophores that have long-lived phosphorescence extends the time scale of anisotropy measurements to hundreds of nanoseconds, thereby opening the way for investigations of large oligomers with long rotation times.
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Affiliation(s)
- Lucie Sokolová
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
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Zhang Q, Chen D, Lin J, Liao R, Tong W, Xu Z, Liu W. Characterization of NocL involved in thiopeptide nocathiacin I biosynthesis: a [4Fe-4S] cluster and the catalysis of a radical S-adenosylmethionine enzyme. J Biol Chem 2011; 286:21287-94. [PMID: 21454624 DOI: 10.1074/jbc.m111.224832] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The radical S-adenosylmethionine (AdoMet) enzyme superfamily is remarkable at catalyzing chemically diverse and complex reactions. We have previously shown that NosL, which is involved in forming the indole side ring of the thiopeptide nosiheptide, is a radical AdoMet enzyme that processes L-Trp to afford 3-methyl-2-indolic acid (MIA) via an unusual fragmentation-recombination mechanism. We now report the expansion of the MIA synthase family by characterization of NocL, which is involved in nocathiacin I biosynthesis. EPR and UV-visible absorbance spectroscopic analyses demonstrated the interaction between L-Trp and the [4Fe-4S] cluster of NocL, leading to the assumption of nonspecific interaction of [4Fe-4S] cluster with other nucleophiles via the unique Fe site. This notion is supported by the finding of the heterogeneity in the [4Fe-4S] cluster of NocL in the absence of AdoMet, which was revealed by the EPR study at very low temperature. Furthermore, a free radical was observed by EPR during the catalysis, which is in good agreement with the hypothesis of a glycyl radical intermediate. Combined with the mutational analysis, these studies provide new insights into the function of the [4Fe-4S] cluster of radical AdoMet enzymes as well as the mechanism of the radical-mediated complex carbon chain rearrangement catalyzed by MIA synthase.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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Dieng SD, Schelvis JPM. Analysis of measured and calculated Raman spectra of indole, 3-methylindole, and tryptophan on the basis of observed and predicted isotope shifts. J Phys Chem A 2011; 114:10897-905. [PMID: 20860352 DOI: 10.1021/jp107295p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aromatic amino acid tryptophan plays an important role in protein electron-transfer and in enzyme catalysis. Tryptophan is also used as a probe of its local protein environment and of dynamic changes in this environment. Raman spectroscopy of tryptophan has been an important tool to monitor tryptophan, its radicals, and its protein environment. The proper interpretation of the Raman spectra requires not only the correct assignment of Raman bands to vibrational normal modes but also the correct identification of the Raman bands in the spectrum. A significant amount of experimental and computational work has been devoted to this problem, but inconsistencies still persist. In this work, the Raman spectra of indole, 3-methylindole (3MI), tryptophan, and several of their isotopomers have been measured to determine the isotope shifts of the Raman bands. Density functional theory calculations with the B3LYP functional and the 6-311+G(d,p) basis set have been performed on indole, 3MI, 3-ethylindole (3EI), and several of their isotopomers to predict isotope shifts of the vibrational normal modes. Comparison of the observed and predicted isotope shifts results in a consistent assignment of Raman bands to vibrational normal modes that can be used for both assignment and identification of the Raman bands. For correct assignments, it is important to determine force field scaling factors for each molecule separately, and scaling factors of 0.9824, 0.9843, and 0.9857 are determined for indole, 3MI, and 3EI, respectively. It is also important to use more than one parameter to assign vibrational normal modes to Raman bands, for example, the inclusion of isotope shifts other than those obtained from H/D-exchange. Finally, the results indicate that the Fermi doublet of indole may consist of just two fundamentals, whereas one fundamental and one combination band are identified for the Fermi resonance that gives rise to the doublet in 3MI and tryptophan.
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Affiliation(s)
- Senghane D Dieng
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, USA
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Yang CM, Zhang J. Insights into intramolecular Trp and His side-chain orientation and stereospecific π interactions surrounding metal centers: an investigation using protein metal-site mimicry in solution. Chemistry 2011; 16:10854-65. [PMID: 20669189 DOI: 10.1002/chem.200903149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Metal-binding scaffolds incorporating a Trp/His-paired epitope are instrumental in giving novel insights into the physicochemical basis of functional and mechanistic versatility conferred by the Trp-His interplay at a metal site. Herein, by coupling biometal site mimicry and (1)H and (13)C NMR spectroscopy experiments, modular constructs EDTA-(L-Trp, L-His) (EWH; EDTA=ethylenediamino tetraacetic acid) and DTPA-(L-Trp, L-His) (DWH; DTPA=diethylenetriamino pentaacetic acid) were employed to dissect the static and transient physicochemical properties of hydrophobic/hydrophilic aromatic interactive modes surrounding biometal centers. The binding feature and identities of the stoichiometric metal-bound complexes in solution were investigated by using (1)H and (13)C NMR spectroscopy, which facilitated a cross-validation of the carboxylate, amide oxygen, and tertiary amino groups as the primary ligands and indole as the secondary ligand, with the imidazole (Im) N3 nitrogen being weakly bound to metals such as Ca(2+) owing to a multivalency effect. Surrounding the metal centers, the stereospecific orientation of aromatic rings in the diastereoisomerism is interpreted with the Ca(2+)-EWH complex. With respect to perturbed Trp side-chain rotamer heterogeneity, drastically restricted Trp side-chain flexibility and thus a dynamically constrained rotamer interconversion due to π interactions is evident from the site-selective (13)C NMR spectroscopic signal broadening of the Trp indolyl C3 atom. Furthermore, effects of Trp side-chain fluctuation on indole/Im orientation were the subject of a 2D NMR spectroscopy study by using the Ca(2+)-bound state; a C-H2(indolyl)/C-H5(Im(+)) connectivity observed in the NOESY spectra captured direct evidence that the N-H1 of the Ca(2+)-Im(+) unit interacted with the pyrrole ring of the indole unit in Ca(2+)-bound EWH but not in DWH, which is assignable to a moderately static, anomalous, T-shaped, interplanar π(+)-π stacking alignment. Nevertheless, a comparative (13)C NMR spectroscopy study of the two homologous scaffolds revealed that the overall response of the indole unit arises predominantly from global attractions between the indole ring and the entire positively charged first coordination sphere. The study thus demonstrates the coordination-sphere/geometry dependence of the Trp/His side-chain interplay, and established that π interactions allow (13)C NMR spectroscopy to offer a new window for investigating Trp rotamer heterogeneity near metal-binding centers.
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Affiliation(s)
- Chi Ming Yang
- Neurochemistry & Biophysical Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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Bernini C, Pogni R, Ruiz-Dueñas FJ, Martínez AT, Basosi R, Sinicropi A. EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level. Phys Chem Chem Phys 2011; 13:5078-98. [DOI: 10.1039/c0cp02151b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Ming Yang C. Biometal binding-site mimicry with modular, hetero-bifunctionally modified architecture encompassing a Trp/His motif: Insights into spatiotemporal noncovalent interactions from a comparative spectroscopic study. Dalton Trans 2011; 40:3008-27. [DOI: 10.1039/c0dt00237b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Affiliation(s)
- Jillian L. Dempsey
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125
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Shafaat HS, Leigh BS, Tauber MJ, Kim JE. Spectroscopic Comparison of Photogenerated Tryptophan Radicals in Azurin: Effects of Local Environment and Structure. J Am Chem Soc 2010; 132:9030-9. [DOI: 10.1021/ja101322g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hannah S. Shafaat
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
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Gregersen JA, Tureček F. Mass-spectrometric and computational study of tryptophan radicals (Trp + H)˙ produced by collisional electron transfer to protonated tryptophan in the gas phase. Phys Chem Chem Phys 2010; 12:13434-47. [DOI: 10.1039/c0cp00597e] [Citation(s) in RCA: 16] [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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39
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Yang L, Qin S, Su X, Yang F, You J, Hu C, Xie R, Lan J. 1,1′-Binaphthyl-based imidazolium chemosensors for highly selective recognition of tryptophan in aqueous solutions. Org Biomol Chem 2010; 8:339-48. [DOI: 10.1039/b908540h] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Partyka DV, Deligonul N, Washington MP, Gray TG. fac-Tricarbonyl Rhenium(I) Azadipyrromethene Complexes. Organometallics 2009. [DOI: 10.1021/om900552e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Nihal Deligonul
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | | | - Thomas G. Gray
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
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41
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Spectroscopic evidence for an engineered, catalytically active Trp radical that creates the unique reactivity of lignin peroxidase. Proc Natl Acad Sci U S A 2009; 106:16084-9. [PMID: 19805263 DOI: 10.1073/pnas.0904535106] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The surface oxidation site (Trp-171) in lignin peroxidase (LiP) required for the reaction with veratryl alcohol a high-redox-potential (1.4 V) substrate, was engineered into Coprinus cinereus peroxidase (CiP) by introducing a Trp residue into a heme peroxidase that has similar protein fold but lacks this activity. To create the catalytic activity toward veratryl alcohol in CiP, it was necessary to reproduce the Trp site and its negatively charged microenvironment by means of a triple mutation. The resulting D179W+R258E+R272D variant was characterized by multifrequency EPR spectroscopy. The spectra unequivocally showed that a new Trp radical [g values of g(x) = 2.0035(5), g(y) = 2.0027(5), and g(z) = 2.0022(1)] was formed after the [Fe(IV)=O Por(*+)] intermediate, as a result of intramolecular electron transfer between Trp-179 and the porphyrin. Also, the EPR characterization crucially showed that [Fe(IV)=O Trp-179(*)] was the reactive intermediate with veratryl alcohol. Accordingly, our work shows that it is necessary to take into account the physicochemical properties of the radical, fine-tuned by the microenvironment, as well as those of the preceding [Fe(IV)=O Por(*+)] intermediate to engineer a catalytically competent Trp site for a given substrate. Manipulation of the microenvironment of the Trp-171 site in LiP allowed the detection by EPR spectroscopy of the Trp-171(*), for which direct evidence has been missing so far. Our work also highlights the role of Trp residues as tunable redox-active cofactors for enzyme catalysis in the context of peroxidases with a unique reactivity toward recalcitrant substrates that require oxidation potentials not realized at the heme site.
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Blanco-Rodríguez AM, Busby M, Ronayne K, Towrie M, Grădinaru C, Sudhamsu J, Sýkora J, Hof M, Záliš S, Di Bilio AJ, Crane BR, Gray HB, Vlček A. Relaxation Dynamics of Pseudomonas aeruginosa ReI(CO)3(α-diimine)(HisX)+ (X = 83, 107, 109, 124, 126)CuII Azurins. J Am Chem Soc 2009; 131:11788-800. [DOI: 10.1021/ja902744s] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana María Blanco-Rodríguez
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Michael Busby
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Kate Ronayne
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Michael Towrie
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Cristian Grădinaru
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Jawahar Sudhamsu
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Jan Sýkora
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Martin Hof
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Stanislav Záliš
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Angel J. Di Bilio
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Brian R. Crane
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Harry B. Gray
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Antonín Vlček
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
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Stoll S, Gunn A, Brynda M, Sughrue W, Kohler AC, Ozarowski A, Fisher AJ, Lagarias JC, Britt RD. Structure of the biliverdin radical intermediate in phycocyanobilin:ferredoxin oxidoreductase identified by high-field EPR and DFT. J Am Chem Soc 2009; 131:1986-95. [PMID: 19159240 DOI: 10.1021/ja808573f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyanobacterial enzyme phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the two-step four-electron reduction of biliverdin IXalpha to phycocyanobilin, the precursor of biliprotein chromophores found in phycobilisomes. It is known that catalysis proceeds via paramagnetic radical intermediates, but the structure of these intermediates and the transfer pathways for the four protons involved are not known. In this study, high-field electron paramagnetic resonance (EPR) spectroscopy of frozen solutions and single crystals of the one-electron reduced protein-substrate complex of two PcyA mutants D105N from the cyanobacteria Synechocystis sp. PCC6803 and Nostoc sp. PCC7120 are examined. Detailed analysis of Synechocystis D105N mutant spectra at 130 and 406 GHz reveals a biliverdin radical with a very narrow g tensor with principal values 2.00359(5), 2.00341(5), and 2.00218(5). Using density-functional theory (DFT) computations to explore the possible protonation states of the biliverdin radical, it is shown that this g tensor is consistent with a biliverdin radical where the carbonyl oxygen atoms on both the A and the D pyrrole rings are protonated. This experimentally confirms the reaction mechanism recently proposed (Tu, et al. Biochemistry 2007, 46, 1484).
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Affiliation(s)
- Stefan Stoll
- Department of Chemistry, University of California Davis, 1 Shields Avenue, Davis, California 95616, USA
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44
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Shafaat HS, Leigh BS, Tauber MJ, Kim JE. Resonance Raman Characterization of a Stable Tryptophan Radical in an Azurin Mutant. J Phys Chem B 2008; 113:382-8. [PMID: 19072535 DOI: 10.1021/jp809329a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hannah S. Shafaat
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Brian S. Leigh
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Michael J. Tauber
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Judy E. Kim
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
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45
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Joly L, Antoine R, Allouche AR, Dugourd P. Formation and Spectroscopy of a Tryptophan Radical Containing Peptide in the Gas Phase. J Am Chem Soc 2008; 130:13832-3. [PMID: 18817390 DOI: 10.1021/ja804508d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laure Joly
- Université de Lyon, CNRS, UMR 5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Rodolphe Antoine
- Université de Lyon, CNRS, UMR 5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Abdul-Rahman Allouche
- Université de Lyon, CNRS, UMR 5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Philippe Dugourd
- Université de Lyon, CNRS, UMR 5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
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46
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Fielding AJ, Singh R, Boscolo B, Loewen PC, Ghibaudi EM, Ivancich A. Intramolecular electron transfer versus substrate oxidation in lactoperoxidase: investigation of radical intermediates by stopped-flow absorption spectrophotometry and (9-285 GHz) electron paramagnetic resonance spectroscopy. Biochemistry 2008; 47:9781-92. [PMID: 18712881 DOI: 10.1021/bi801032k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have combined the information obtained from rapid-scan electronic absorption spectrophotometry and multifrequency (9-295 GHz) electron paramagnetic resonance (EPR) spectroscopy to unequivocally determine the electronic nature of the intermediates in milk lactoperoxidase as a function of pH and to monitor their reactivity with organic substrates selected by their different accessibilities to the heme site. The aim was to address the question of the putative catalytic role of the protein-based radicals. This experimental approach allowed us to discriminate between the protein-based radical intermediates and [Fe(IV)=O] species, as well as to directly detect the oxidation products by EPR. The advantageous resolution of the g anisotropy of the Tyr (*) EPR spectrum at high fields showed that the tyrosine of the [Fe(IV)=O Tyr (*)] intermediate has an electropositive and pH-dependent microenvironment [g(x) value of 2.0077(0) at pH >or= 8.0 and 2.0066(2) at 4.0 <or= pH <or= 7.5] possibly related to the radical stability and function. Two types of organic molecules (small aromatic vs bulkier substrates) allowed us to distinguish different mechanisms for substrate oxidation. [Fe(IV)=O Por (*+)] is the oxidizing species of benzohydroxamic acid, o-dianisidine, and o-anisidine via a heme-edge reaction and of mitoxantrone via a long-range electron transfer (favored at pH 8) not involving the tyrosyl radical, the formation of which competed with the substrate oxidation at pH 5. In contrast, the very efficient reaction with ABTS at pH 5 is consistent with [Fe(IV)=O Tyr (*)] being the oxidizing species. Accordingly, the identification of the ABTS binding site by X-ray crystallography may be a valuable tool in rational drug design.
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Affiliation(s)
- Alistair J Fielding
- CNRS, URA 2096. CEA, IBITEC, Laboratoire de Hyperfréquences, Métalloprotéines et Systèmes de Spin, F-91191 Gif-sur-Yvette, France
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47
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Connor HD, Sturgeon BE, Mottley C, Sipe HJ, Mason RP. L-tryptophan radical cation electron spin resonance studies: connecting solution-derived hyperfine coupling constants with protein spectral interpretations. J Am Chem Soc 2008; 130:6381-7. [PMID: 18433127 DOI: 10.1021/ja0780277] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fast-flow electron spin resonance (ESR) spectroscopy has been used to detect a free radical formed from the reaction of l-tryptophan with Ce (4+) in an acidic aqueous environment. Computer simulations of the ESR spectra from l-tryptophan and several isotopically modified forms strongly support the conclusion that the l-tryptophan radical cation has been detected by ESR for the first time. The hyperfine coupling constants (HFCs) determined from the well-resolved isotropic ESR spectra support experimental and computational efforts to understand l-tryptophan's role in protein catalysis of oxidation-reduction processes. l-Tryptophan HFCs facilitated the simulation of fast-flow ESR spectra of free radicals from two related compounds, tryptamine and 3-methylindole. Analysis of these three compounds' beta-methylene hydrogen HFC data along with equivalent l-tyrosine data has led to a new computational method that can distinguish between these two amino acid free radicals in proteins without dependence on isotope labeling, electron-nuclear double resonance, or high-field ESR. This approach also produces geometric parameters (dihedral angles for the beta-methylene hydrogens) that should facilitate protein site assignment of observed l-tryptophan radicals as has been done for l-tyrosine radicals.
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Affiliation(s)
- Henry D Connor
- Laboratory of Pharmacology and Chemistry, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709, USA
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48
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Gradinaru C, Crane BR. Comparison of intra- vs intermolecular long-range electron transfer in crystals of ruthenium-modified azurin. J Phys Chem B 2007; 110:20073-6. [PMID: 17034174 DOI: 10.1021/jp0644309] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective metal-ion incorporation and ligand substitution are employed to control whether electrons tunnel over intra- or intermolecular separations in crystals of P. aeruginosa azurin modified with Ru-polypyridine complexes. Cu(1+)-to-Ru3+ electron transfer (ET) across a specific protein-protein interface in the crystal lattice has a time constant 5-10 times longer than ET between the same donor and acceptor within a single protein (tauET = 5 vs 0.5-1.0 micros). Slower intermolecular ET agrees well with a longer distance between redox centers across the inter-protein (18.9 A) compared to the intra-protein separation (17.0 A) and indicates that the closest donor/acceptor pair dominates crystal ET. Lowering the crystal pH accelerates inter-protein ET (tauET = 1.0 micros) but not intra-protein ET. Faster inter-protein ET likely results from a pH-induced peptide bond flip that perturbs hydrogen bonding in the path between Ru and Cu centers on adjacent molecules.
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Machczynski MC, Kuhl KP, McGuirl MA. Modulation of the electrochemical behavior of tyrosyl radicals by the electrode surface. Anal Biochem 2007; 362:89-97. [PMID: 17254538 DOI: 10.1016/j.ab.2006.11.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 11/22/2006] [Accepted: 11/30/2006] [Indexed: 11/20/2022]
Abstract
The ability to adsorb proteins and enzymes on electrode surfaces enhances opportunities for studying enzyme activity and redox-based catalysis. Proteins may be bound in a chosen orientation on surfaces so that specific sites within them may be preferentially studied, but to date no systematic study of a redox moiety from solvent to electrode surface to the protein milieu has been performed. We report the redox and ionization behavior of tyrosine-cysteine, using the cysteine residue to form covalent linkages with Au and self-assembled-monolayer (SAM)-modified Au surfaces and using the tyrosine for redox activity. In addition, the same redox fragment incorporated into a protein bound to a SAM is examined. We find that directly binding the dipeptide to Au causes the greatest change in properties, while binding it to the SAM causes a slight perturbation in redox potential and a significant perturbation in pK(a). When azurin with a surface-exposed tyrosine is bound to a SAM-modified electrode, the redox potential and pK(a) of the tyrosine are nearly unperturbed from the values found for the dipeptide free in solution. Finally, quantification of the voltammetric signal indicates that tyrosine oxidation in the protein triggers the additional oxidation of another nearby amino acid.
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Affiliation(s)
- Michael C Machczynski
- Division of Biological Sciences and Biomolecular Structure and Dynamics Program, The University of Montana, Missoula, MT 59812, USA
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50
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Organometallic Chemistry of Polypyridine Ligands II. ADVANCES IN HETEROCYCLIC CHEMISTRY 2007. [DOI: 10.1016/s0065-2725(06)94002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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