1
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Specific metallo-protein interactions and antimicrobial activity in Histatin-5, an intrinsically disordered salivary peptide. Sci Rep 2019; 9:17303. [PMID: 31754129 PMCID: PMC6872563 DOI: 10.1038/s41598-019-52676-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
Histatin-5 (Hst-5) is an antimicrobial, salivary protein that is involved in the host defense system. Hst-5 has been proposed to bind functionally relevant zinc and copper but presents challenges in structural studies due to its disordered conformation in aqueous solution. Here, we used circular dichroism (CD) and UV resonance Raman (UVRR) spectroscopy to define metallo-Hst-5 interactions in aqueous solution. A zinc-containing Hst-5 sample exhibits shifted Raman bands, relative to bands observed in the absence of zinc. Based on comparison to model compounds and to a family of designed, zinc-binding beta hairpins, the alterations in the Hst-5 UVRR spectrum are attributed to zinc coordination by imidazole side chains. Zinc addition also shifted a tyrosine aromatic ring UVRR band through an electrostatic interaction. Copper addition did not have these effects. A sequence variant, H18A/H19A, was employed; this mutant has less potent antifungal activity, when compared to Hst-5. Zinc addition had only a small effect on the thermal stability of this mutant. Interestingly, both zinc and copper addition shifted histidine UVRR bands in a manner diagnostic for metal coordination. Results obtained with a K13E/R22G mutant were similar to those obtained with wildtype. These experiments show that H18 and H19 contribute to a zinc binding site. In the H18A/H19A mutant the specificity of the copper/zinc binding sites is lost. The experiments implicate specific zinc binding to be important in the antimicrobial activity of Hst-5.
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2
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McCaslin TG, Pagba CV, Hwang H, Gumbart JC, Chi SH, Perry JW, Barry BA. Tyrosine, cysteine, and proton coupled electron transfer in a ribonucleotide reductase-inspired beta hairpin maquette. Chem Commun (Camb) 2019; 55:9399-9402. [PMID: 31322154 DOI: 10.1039/c9cc04067f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tyrosine residues act as intermediates in proton coupled electron transfer reactions (PCET) in proteins. For example, in ribonucleotide reductase (RNR), a tyrosyl radical oxidizes an active site cysteine via a 35 Å pathway that contains multiple aromatic groups. When singlet tyrosine is oxidized, the radical becomes a strong acid, and proton transfer reactions, which are coupled with the redox reaction, may be used to control reaction rate. Here, we characterize a tyrosine-containing beta hairpin, Peptide O, which has a cross-strand, noncovalent interaction between its single tyrosine, Y5, and a cysteine (C14). Circular dichroism provides evidence for a thermostable beta-turn. EPR spectroscopy shows that Peptide O forms a neutral tyrosyl radical after UV photolysis at 160 K. Molecular dynamics simulations support a phenolic/SH interaction in the tyrosine singlet and radical states. Differential pulse voltammetry exhibits pH dependence consistent with the formation of a neutral tyrosyl radical and a pKa change in two other residues. A redox-coupled decrease in cysteine pKa from 9 (singlet) to 6.9 (radical) is assigned. At pD 11, picosecond transient absorption spectroscopy after UV photolysis monitors tyrosyl radical recombination via electron transfer (ET). The ET rate in Peptide O is indistinguishable from the ET rates observed in peptides containing a histidine and a cyclohexylalanine (Cha) at position 14. However, at pD 9, the tyrosyl radical decays via PCET, and the decay rate is slowed, when compared to the histidine 14 variant. Notably, the decay rate is accelerated, when compared to the Cha 14 variant. We conclude that redox coupling between tyrosine and cysteine can act as a PCET control mechanism in proteins.
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Affiliation(s)
- Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA and School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - San-Hui Chi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and Center of Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph W Perry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and Center of Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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McCaslin TG, Pagba CV, Chi SH, Hwang HJ, Gumbart JC, Perry JW, Olivieri C, Porcelli F, Veglia G, Guo Z, McDaniel M, Barry BA. Structure and Function of Tryptophan-Tyrosine Dyads in Biomimetic β Hairpins. J Phys Chem B 2019; 123:2780-2791. [PMID: 30888824 PMCID: PMC6463897 DOI: 10.1021/acs.jpcb.8b12452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Tyrosine–tryptophan (YW) dyads
are ubiquitous
structural motifs in enzymes and play roles in proton-coupled electron
transfer (PCET) and, possibly, protection from oxidative stress. Here,
we describe the function of YW dyads in de novo designed 18-mer, β
hairpins. In Peptide M, a YW dyad is formed between W14 and Y5. A
UV hypochromic effect and an excitonic Cotton signal are observed,
in addition to singlet, excited state (W*) and fluorescence emission
spectral shifts. In a second Peptide, Peptide MW, a Y5–W13
dyad is formed diagonally across the strand and distorts the backbone.
On a picosecond timescale, the W* excited-state decay kinetics are
similar in all peptides but are accelerated relative to amino acids
in solution. In Peptide MW, the W* spectrum is consistent with increased
conformational flexibility. In Peptide M and MW, the electron paramagnetic
resonance spectra obtained after UV photolysis are characteristic
of tyrosine and tryptophan radicals at 160 K. Notably, at pH 9, the
radical photolysis yield is decreased in Peptide M and MW, compared
to that in a tyrosine and tryptophan mixture. This protective effect
is not observed at pH 11 and is not observed in peptides containing
a tryptophan–histidine dyad or tryptophan alone. The YW dyad
protective effect is attributed to an increase in the radical recombination
rate. This increase in rate can be facilitated by hydrogen-bonding
interactions, which lower the barrier for the PCET reaction at pH
9. These results suggest that the YW dyad structural motif promotes
radical quenching under conditions of reactive oxygen stress.
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Affiliation(s)
| | | | | | | | | | | | | | - Fernando Porcelli
- Department for Innovation in Biological, Agro-Food and Forest Systems , University of Tuscia , 01100 Viterbo , Italy
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4
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Calcium, conformational selection, and redox-active tyrosine YZ in the photosynthetic oxygen-evolving cluster. Proc Natl Acad Sci U S A 2018; 115:5658-5663. [PMID: 29752381 DOI: 10.1073/pnas.1800758115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Photosystem II (PSII), YZ (Tyr161D1) participates in radical transfer between the chlorophyll donor and the Mn4CaO5 cluster. Under flashing illumination, the metal cluster cycles among five Sn states, and oxygen is evolved from water. The essential YZ is transiently oxidized and reduced on each flash in a proton-coupled electron transfer (PCET) reaction. Calcium is required for function. Of reconstituted divalent ions, only strontium restores oxygen evolution. YZ is predicted to hydrogen bond to calcium-bound water and to His190D1 in PSII structures. Here, we report a vibrational spectroscopic study of YZ radical and singlet in the presence of the metal cluster. The S2 state is trapped by illumination at 190 K; flash illumination then generates the S2YZ radical. Using reaction-induced FTIR spectroscopy and divalent ion depletion/substitution, we identify calcium-sensitive tyrosyl radical and tyrosine singlet bands in the S2 state. In calcium-containing PSII, two CO stretching bands are detected at 1,503 and 1,478 cm-1 These bands are assigned to two different radical conformers in calcium-containing PSII. At pH 6.0, the 1,503-cm-1 band shifts to 1,507 cm-1 in strontium-containing PSII, and the band is reduced in intensity in calcium-depleted PSII. These effects are consistent with a hydrogen-bonding interaction between the calcium site and one conformer of radical YZ. Analysis of the amide I region indicates that calcium selects for a PCET reaction in a subset of the YZ conformers, which are trapped in the S2 state. These results support the interpretation that YZ undergoes a redox-coupled conformational change, which is calcium dependent.
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5
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Najafpour MM, Madadkhani S, Akbarian S, Zand Z, Hołyńska M, Kompany-Zareh M, Tatsuya T, Singh JP, Chae KH, Allakhverdiev SI. Links between peptides and Mn oxide: nano-sized manganese oxide embedded in a peptide matrix. NEW J CHEM 2018. [DOI: 10.1039/c8nj02119h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a poly-peptide/Mn oxide nanocomposite as a model for the water-oxidizing catalyst in Photosystem II.
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
- Center of Climate Change and Global Warming
| | - Sepideh Madadkhani
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
| | - Somayyeh Akbarian
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
| | - Zahra Zand
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
| | - Małgorzata Hołyńska
- Fachbereich Chemie und Wissenschaftliches Zentrum für Materialwissenschaften (WZMW)
- Philipps-Universität Marburg
- Marburg D-35032
- Germany
| | - Mohsen Kompany-Zareh
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
- Center of Climate Change and Global Warming
| | - Tomo Tatsuya
- Department of Biology
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601
- Japan
| | - Jitendra Pal Singh
- Advanced Analysis Center
- Korea Institute of Science and Technology
- Seoul 02792
- Republic of Korea
| | - Keun Hwa Chae
- Advanced Analysis Center
- Korea Institute of Science and Technology
- Seoul 02792
- Republic of Korea
| | - Suleyman I. Allakhverdiev
- Controlled Photobiosynthesis Laboratory
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow 127276
- Russia
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6
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Geng J, Aioub M, El-Sayed MA, Barry BA. An Ultraviolet Resonance Raman Spectroscopic Study of Cisplatin and Transplatin Interactions with Genomic DNA. J Phys Chem B 2017; 121:8975-8983. [PMID: 28925698 DOI: 10.1021/acs.jpcb.7b08156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet resonance Raman (UVRR) spectroscopy is a label-free method to define biomacromolecular interactions with anticancer compounds. Using UVRR, we describe the binding interactions of two Pt(II) compounds, cisplatin (cis-diamminedichloroplatinum(II)) and its isomer, transplatin, with nucleotides and genomic DNA. Cisplatin binds to DNA and other cellular components and triggers apoptosis, whereas transplatin is clinically ineffective. Here, a 244 nm UVRR study shows that purine UVRR bands are altered in frequency and intensity when mononucleotides are treated with cisplatin. This result is consistent with previous suggestions that purine N7 provides the cisplatin-binding site. The addition of cisplatin to DNA also causes changes in the UVRR spectrum, consistent with binding of platinum to purine N7 and disruption of hydrogen-bonding interactions between base pairs. Equally important is that transplatin treatment of DNA generates similar UVRR spectral changes, when compared to cisplatin-treated samples. Kinetic analysis, performed by monitoring decreases of the 1492 cm-1 band, reveals biphasic kinetics and is consistent with a two-step binding mechanism for both platinum compounds. For cisplatin-DNA, the rate constants (6.8 × 10-5 and 6.5 × 10-6 s-1) are assigned to the formation of monofunctional adducts and to bifunctional, intrastrand cross-linking, respectively. In transplatin-DNA, there is a 3.4-fold decrease in the rate constant of the slow phase, compared with the cisplatin samples. This change is attributed to generation of interstrand, rather than intrastrand, adducts. This longer reaction time may result in increased competition in the cellular environment and account, at least in part, for the lower pharmacological efficacy of transplatin.
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Affiliation(s)
- Jiafeng Geng
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Mena Aioub
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Mostafa A El-Sayed
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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7
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Bila WC, Mariano RMDS, Silva VR, Dos Santos MESM, Lamounier JA, Ferriolli E, Galdino AS. Applications of deuterium oxide in human health. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2017; 53:327-343. [PMID: 28165769 DOI: 10.1080/10256016.2017.1281806] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
The main aim goal of this review was to gather information about recent publications related to deuterium oxide (D2O), and its use as a scientific tool related to human health. Searches were made in electronic databases Pubmed, Scielo, Lilacs, Medline and Cochrane. Moreover, the following patent databases were consulted: EPO (Espacenet patent search), USPTO (United States Patent and Trademark Office) and Google Patents, which cover researches worldwide related to innovations using D2O.
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Affiliation(s)
- Wendell Costa Bila
- a Graduate Programme in Health Sciences , Federal University of São João Del Rei-West Centre Campus , Divinópolis , Brazil
| | - Reysla Maria da Silveira Mariano
- b Graduate Programme in Biochemistry and Molecular Biology , Federal University of São João del Rei , Divinópolis , Brazil
- c Graduate Program in Biotechnology , Federal University of São João del Rei , Divinópolis , Brazil
| | - Valmin Ramos Silva
- d Faculty of Medicine, School of Sciences of Santa Casa de Misericórdia of Vitória , Nossa Senhora da Glória Children's Hospital , Vitória , Brazil
| | | | - Joel Alves Lamounier
- a Graduate Programme in Health Sciences , Federal University of São João Del Rei-West Centre Campus , Divinópolis , Brazil
| | - Eduardo Ferriolli
- e Ribeirão Preto Medical School , University of São Paulo , Ribeirão Preto , Brazil
| | - Alexsandro Sobreira Galdino
- b Graduate Programme in Biochemistry and Molecular Biology , Federal University of São João del Rei , Divinópolis , Brazil
- c Graduate Program in Biotechnology , Federal University of São João del Rei , Divinópolis , Brazil
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8
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Joy S, Sureshbabu VV, Periyasamy G. DFT Studies on the Terminal Dependent Reversible Switching of Selenoxo Peptides Induced by Cationization. ChemistrySelect 2017. [DOI: 10.1002/slct.201700480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sherin Joy
- Department of ChemistryBangalore University Bangalore-560001
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9
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Hwang H, McCaslin TG, Hazel A, Pagba CV, Nevin CM, Pavlova A, Barry BA, Gumbart JC. Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation. J Phys Chem B 2017; 121:3536-3545. [DOI: 10.1021/acs.jpcb.6b09481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Hyea Hwang
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Tyler G. McCaslin
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anthony Hazel
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Cynthia V. Pagba
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Christina M. Nevin
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Bridgette A. Barry
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School
of Materials Science and Engineering, ‡School of Chemistry and Biochemistry, §Petit Institute for
Bioengineering and Biosciences, and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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10
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Pagba CV, McCaslin TG, Chi SH, Perry JW, Barry BA. Proton-Coupled Electron Transfer and a Tyrosine-Histidine Pair in a Photosystem II-Inspired β-Hairpin Maquette: Kinetics on the Picosecond Time Scale. J Phys Chem B 2016; 120:1259-72. [PMID: 26886811 DOI: 10.1021/acs.jpcb.6b00560] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem II (PSII) and ribonucleotide reductase employ oxidation and reduction of the tyrosine aromatic ring in radical transport pathways. Tyrosine-based reactions involve either proton-coupled electron transfer (PCET) or electron transfer (ET) alone, depending on the pH and the pKa of tyrosine's phenolic oxygen. In PSII, a subset of the PCET reactions are mediated by a tyrosine-histidine redox-driven proton relay, YD-His189. Peptide A is a PSII-inspired β-hairpin, which contains a single tyrosine (Y5) and histidine (H14). Previous electrochemical characterization indicated that Peptide A conducts a net PCET reaction between Y5 and H14, which have a cross-strand π-π interaction. The kinetic impact of H14 has not yet been explored. Here, we address this question through time-resolved absorption spectroscopy and 280-nm photolysis, which generates a neutral tyrosyl radical. The formation and decay of the neutral tyrosyl radical at 410 nm were monitored in Peptide A and its variant, Peptide C, in which H14 is replaced by cyclohexylalanine (Cha14). Significantly, both electron transfer (ET, pL 11, L = lyonium) and PCET (pL 9) were accelerated in Peptide A and C, compared to model tyrosinate or tyrosine at the same pL. Increased electronic coupling, mediated by the peptide backbone, can account for this rate acceleration. Deuterium exchange gave no significant solvent isotope effect in the peptides. At pL 9, but not at pL 11, the reaction rate decreased when H14 was mutated to Cha14. This decrease in rate is attributed to an increase in reorganization energy in the Cha14 mutant. The Y5-H14 mechanism in Peptide A is reminiscent of proton- and electron-transfer events involving YD-H189 in PSII. These results document a mechanism by which proton donors and acceptors can regulate the rate of PCET reactions.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - San-Hui Chi
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Joseph W Perry
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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11
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Pagba CV, McCaslin TG, Veglia G, Porcelli F, Yohannan J, Guo Z, McDaniel M, Barry BA. A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette. Nat Commun 2015; 6:10010. [PMID: 26627888 PMCID: PMC4686667 DOI: 10.1038/ncomms10010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/23/2015] [Indexed: 01/29/2023] Open
Abstract
In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit. The conserved W48 β2 is ∼10 Å from Y122OH; mutations at W48 inactivate RNR. Here, we design a beta hairpin peptide, which contains such an interacting tyrosine–tryptophan dyad. The NMR structure of the peptide establishes that there is no direct hydrogen bond between the phenol and the indole rings. However, electronic coupling between the tyrosine and tryptophan occurs in the peptide. In addition, downshifted ultraviolet resonance Raman (UVRR) frequencies are observed for the radical state, reproducing spectral downshifts observed for β2. The frequency downshifts of the ring and CO bands are consistent with charge transfer from YO· to W or another residue. Such a charge transfer mechanism implies a role for the β2 Y-W dyad in electron transfer. Tyrosine-tryptophan dyads are known to mediate electron transfer reactions in a range of different proteins. Here, the authors study a beta hairpin peptide, probing the tyrosine-tryptophan interaction and showing no hydrogen bonding but rather charge transfer between the tyrosyl radical and tryptophan'.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Fernando Porcelli
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo 01100, Italy
| | - Jiby Yohannan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zhanjun Guo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Miranda McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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12
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Abstract
An enormous variety of biological redox reactions are accompanied by changes in proton content at enzyme active sites, in their associated cofactors, in substrates and/or products, and between protein interfaces. Understanding this breadth of reactivity is an ongoing chemical challenge. A great many workers have developed and investigated biomimetic model complexes to build new ways of thinking about the mechanistic underpinnings of such complex biological proton-coupled electron transfer (PCET) reactions. Of particular importance are those model reactions that involve transfer of one proton (H(+)) and one electron (e(-)), which is equivalent to transfer of a hydrogen atom (H(•)). In this Current Topic, we review key concepts in PCET reactivity and describe important advances in biomimetic PCET chemistry, with a special emphasis on research that has enhanced efforts to understand biological PCET reactions.
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Affiliation(s)
- Jeffrey J. Warren
- Simon Fraser University, Department of Chemistry, 8888 University Drive, Burnaby BC, Canada V5A 1S6
| | - James M. Mayer
- Yale University, Department of Chemistry, P.O. Box 208107, 225 Prospect Street, New Haven, CT 06520-8107
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13
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Barry BA. Reaction dynamics and proton coupled electron transfer: studies of tyrosine-based charge transfer in natural and biomimetic systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:46-54. [PMID: 25260243 DOI: 10.1016/j.bbabio.2014.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/27/2014] [Accepted: 09/10/2014] [Indexed: 11/25/2022]
Abstract
In bioenergetic reactions, electrons are transferred long distances via a hopping mechanism. In photosynthesis and DNA synthesis, the aromatic amino acid residue, tyrosine, functions as an intermediate that is transiently oxidized and reduced during long distance electron transfer. At physiological pH values, oxidation of tyrosine is associated with a deprotonation of the phenolic oxygen, giving rise to a proton coupled electron transfer (PCET) reaction. Tyrosine-based PCET reactions are important in photosystem II, which carries out the light-induced oxidation of water, and in ribonucleotide reductase, which reduces ribonucleotides to form deoxynucleotides. Photosystem II contains two redox-active tyrosines, YD (Y160 in the D2 polypeptide) and YZ (Y161 in the D1 polypeptide). YD forms a light-induced stable radical, while YZ functions as an essential charge relay, oxidizing the catalytic Mn₄CaO₅ cluster on each of four photo-oxidation reactions. In Escherichia coli class 1a RNR, the β2 subunit contains the radical initiator, Y122O•, which is reversibly reduced and oxidized in long range electron transfer with the α2 subunit. In the isolated E. coli β2 subunit, Y122O• is a stable radical, but Y122O• is activated for rapid PCET in an α2β2 substrate/effector complex. Recent results concerning the structure and function of YD, YZ, and Y122 are reviewed here. Comparison is made to recent results derived from bioengineered proteins and biomimetic compounds, in which tyrosine-based charge transfer mechanisms have been investigated. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Offenbacher AR, Pagba CV, Polander BC, Brahmachari U, Barry BA. First site-specific incorporation of a noncanonical amino acid into the photosynthetic oxygen-evolving complex. ACS Chem Biol 2014; 9:891-6. [PMID: 24437616 DOI: 10.1021/cb400880u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In photosystem II (PSII), water is oxidized at the oxygen-evolving complex. This process occurs through a light-induced cycle that produces oxygen and protons. While coupled proton and electron transfer reactions play an important role in PSII and other proteins, direct detection of internal proton transfer reactions is challenging. Here, we demonstrate that the unnatural amino acid, 7-azatryptophan (7AW), has unique, pH-sensitive vibrational frequencies, which are sensitive markers of proton transfer. The intrinsically disordered, PSII subunit, PsbO, which contains a single W residue (Trp241), was engineered to contain 7AW at position 241. Fluorescence shows that 7AW-241 is buried in a hydrophobic environment. Reconstitution of 7AW(241)PsbO to PSII had no significant impact on oxygen evolution activity or flash-dependent protein dynamics. We conclude that directed substitution of 7AW into other structural domains is likely to provide a nonperturbative spectroscopic probe, which can be used to define internal proton pathways in PsbO.
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Affiliation(s)
- Adam R. Offenbacher
- Department of Chemistry and
Biochemistry and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| | - Cynthia V. Pagba
- Department of Chemistry and
Biochemistry and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| | - Brandon C. Polander
- Department of Chemistry and
Biochemistry and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| | - Udita Brahmachari
- Department of Chemistry and
Biochemistry and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| | - Bridgette A. Barry
- Department of Chemistry and
Biochemistry and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
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MORISAKU T, ARAI S, YUI H. Dehydration-induced Initial Conformational Change of Hydrated Proteins Detected by the Changes in Vibrational Circular Dichroism Activity. ANAL SCI 2014; 30:961-9. [DOI: 10.2116/analsci.30.961] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Toshinori MORISAKU
- Graduate School of Chemical Science and Technology, Tokyo University of Science
| | - Sho ARAI
- Graduate School of Chemical Science and Technology, Tokyo University of Science
| | - Hiroharu YUI
- Graduate School of Chemical Science and Technology, Tokyo University of Science
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Offenbacher AR, Burns LA, Sherrill CD, Barry BA. Redox-linked conformational control of proton-coupled electron transfer: Y122 in the ribonucleotide reductase β2 subunit. J Phys Chem B 2013; 117:8457-68. [PMID: 23822111 DOI: 10.1021/jp404757r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in β2. Although Y122O(•) is extremely stable in free β2, Y122O(•) is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli β2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.
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Affiliation(s)
- Adam R Offenbacher
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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