101
|
Song QH, Tang WJ, Ji XB, Wang HB, Guo QX. Do photolyases need to provide considerable activation energy for the splitting of cyclobutane pyrimidine dimer radical anions? Chemistry 2007; 13:7762-70. [PMID: 17568458 DOI: 10.1002/chem.200700251] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
cis-syn Cyclobutane pyrimidine dimers, major UV-induced DNA lesions, are efficiently repaired by DNA photolyases. The key step of the repair reaction is a light-driven electron transfer from the FADH(-) cofactor to the dimer; the resulting radical anion splits spontaneously. Whether the splitting reaction requires considerable activation energy is still under dispute. Recent reports show that the splitting reaction of a dimer radical anion has a significant activation barrier (0.45 eV), and so photolyases have to provide considerable energy. However, these results contradict observations that cis-syn dimer radical anions split into monomers at -196 degrees C, and that the full process of DNA photoreactivation was fast (1.5-2 ns). To investigate the activation energies of dimer radical anions, three model compounds 1-3 were prepared. These include a covalently linked cyclobutane thymine dimer and a tryptophan residue (1) or a flavin unit (3), and the covalently linked uracil dimer and tryptophan (2). Their properties of photosensitised splitting of the dimer units by tryptophan or flavin unit were investigated over a large temperature range, -196 to 70 degrees C. The activation energies were obtained from the temperature dependency of splitting reactions for 1 and 2, 1.9 kJ mol(-1) and 0.9 kJ mol(-1) for the thymine and uracil dimer radical anions, respectively. These values are much lower than that obtained for E. coli photolyase (0.45 eV), and are surmountable at -196 degrees C. The activation energies provide support for previous observations that repair efficiencies for uracil dimers are higher than thymine dimers, both in enzymatic and model systems. The mechanisms of highly efficient enzymatic DNA repair are discussed.
Collapse
Affiliation(s)
- Qin-Hua Song
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, Anhui, P. R. China.
| | | | | | | | | |
Collapse
|
102
|
Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | | |
Collapse
|
103
|
Wiertz FGM, Richter OMH, Ludwig B, de Vries S. Kinetic Resolution of a Tryptophan-radical Intermediate in the Reaction Cycle of Paracoccus denitrificans Cytochrome c Oxidase. J Biol Chem 2007; 282:31580-91. [PMID: 17761680 DOI: 10.1074/jbc.m705520200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic mechanism, electron transfer coupled to proton pumping, of heme-copper oxidases is not yet fully understood. Microsecond freeze-hyperquenching single turnover experiments were carried out with fully reduced cytochrome aa(3) reacting with O(2) between 83 micros and 6 ms. Trapped intermediates were analyzed by low temperature UV-visible, X-band, and Q-band EPR spectroscopy, enabling determination of the oxidation-reduction kinetics of Cu(A), heme a, heme a(3), and of a recently detected tryptophan radical (Wiertz, F. G. M., Richter, O. M. H., Cherepanov, A. V., MacMillan, F., Ludwig, B., and de Vries, S. (2004) FEBS Lett. 575, 127-130). Cu(B) and heme a(3) were EPR silent during all stages of the reaction. Cu(A) and heme a are in electronic equilibrium acting as a redox pair. The reduction potential of Cu(A) is 4.5 mV lower than that of heme a. Both redox groups are oxidized in two phases with apparent half-lives of 57 micros and 1.2 ms together donating a single electron to the binuclear center in each phase. The formation of the heme a(3) oxoferryl species P(R) (maxima at 430 nm and 606 nm) was completed in approximately 130 micros, similar to the first oxidation phase of Cu(A) and heme a. The intermediate F (absorbance maximum at 571 nm) is formed from P(R) and decays to a hitherto undetected intermediate named F(W)(*). F(W)(*) harbors a tryptophan radical, identified by Q-band EPR spectroscopy as the tryptophan neutral radical of the strictly conserved Trp-272 (Trp-272(*)). The Trp-272(*) populates to 4-5% due to its relatively low rate of formation (t((1/2)) = 1.2 ms) and rapid rate of breakdown (t((1/2)) = 60 micros), which represents electron transfer from Cu(A)/heme a to Trp-272(*). The formation of the Trp-272(*) constitutes the major rate-determining step of the catalytic cycle. Our findings show that Trp-272 is a redox-active residue and is in this respect on an equal par to the metallocenters of the cytochrome c oxidase. Trp-272 is the direct reductant either to the heme a(3) oxoferryl species or to Cu (2+)(B). The potential role of Trp-272 in proton pumping is discussed.
Collapse
Affiliation(s)
- Frank G M Wiertz
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
| | | | | | | |
Collapse
|
104
|
Das A, Hecht MH. Peroxidase activity of de novo heme proteins immobilized on electrodes. J Inorg Biochem 2007; 101:1820-6. [PMID: 17765314 PMCID: PMC2080791 DOI: 10.1016/j.jinorgbio.2007.07.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 07/12/2007] [Accepted: 07/13/2007] [Indexed: 10/23/2022]
Abstract
De novo proteins from designed combinatorial libraries were bound to heme terminated gold electrodes. The novel heme proteins were shown to possess peroxidase activity, and this activity was compared to that of horseradish peroxidase and bovine serum albumin when immobilized in a similar fashion. The various designed proteins from the libraries displayed distinctly different levels of peroxidase activity, thereby demonstrating that the sequence and structure of a designed protein can exert a substantial effect on the peroxidase activity of immobilized heme.
Collapse
|
105
|
Bogani F, McConnell E, Joshi L, Chang Y, Ghirlanda G. A designed glycoprotein analogue of Gc-MAF exhibits native-like phagocytic activity. J Am Chem Soc 2007; 128:7142-3. [PMID: 16734450 DOI: 10.1021/ja0604212] [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: 11/29/2022]
Abstract
Rational protein design has been successfully used to create mimics of natural proteins that retain native activity. In the present work, de novo protein engineering is explored to develop a mini-protein analogue of Gc-MAF, a glycoprotein involved in the immune system activation that has shown anticancer activity in mice. Gc-MAF is derived in vivo from vitamin D binding protein (VDBP) via enzymatic processing of its glycosaccharide to leave a single GalNAc residue located on an exposed loop. We used molecular modeling tools in conjunction with structural analysis to splice the glycosylated loop onto a stable three-helix bundle (alpha3W, PDB entry 1LQ7). The resulting 69-residue model peptide, MM1, has been successfully synthesized by solid-phase synthesis both in the aglycosylated and the glycosylated (GalNAc-MM1) form. Circular dichroism spectroscopy confirmed the expected alpha-helical secondary structure. The thermodynamic stability as evaluated from chemical and thermal denaturation is comparable with that of the scaffold protein, alpha3W, indicating that the insertion of the exogenous loop of Gc-MAF did not significantly perturb the overall structure. GalNAc-MM1 retains the macrophage stimulation activity of natural Gc-MAF; in vitro tests show an identical enhancement of Fc-receptor-mediated phagocytosis in primary macrophages. GalNAc-MM1 provides a framework for the development of mutants with increased activity that could be used in place of Gc-MAF as an immunomodulatory agent in therapy.
Collapse
Affiliation(s)
- Federica Bogani
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | | | | | | | | |
Collapse
|
106
|
Ishikita H. Influence of the protein environment on the redox potentials of flavodoxins from Clostridium beijerinckii. J Biol Chem 2007; 282:25240-6. [PMID: 17602164 DOI: 10.1074/jbc.m702788200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flavin mononucleotide (FMN) quinones in flavodoxin have two characteristic redox potentials, namely, Em(FMNH./FMNH-) for the one-electron reduction of the protonated FMN (E1) and Em(FMN/FMNH.) for the proton-coupled one-electron reduction (E2). These redox potentials in native and mutant flavodoxins obtained from Clostridium beijerinckii were calculated by considering the protonation states of all titratable sites as well as the energy contributed at the pKa value of FMN during protonation at the N5 nitrogen (pKa(N5)). E1 is sensitive to the subtle differences in the protein environments in the proximity of FMN. The protein dielectric volume that prevents the solvation of charged FMN quinones is responsible for the downshift of 130-160 mV of the E1 values with respect to that in an aqueous solution. The influence of the negatively charged 5'-phosphate group of FMN quinone on E1 could result in a maximum shift of 90 mV. A dramatic difference of 130 mV in the calculated E2 values of FMN quinone of the native and G57T mutant flavodoxins is due to the difference in the pKa(N5) values. This is due to the difference in the influence exerted by the carbonyl group of the protein backbone at residue 57.
Collapse
Affiliation(s)
- Hiroshi Ishikita
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
| |
Collapse
|
107
|
Renger G. Oxidative photosynthetic water splitting: energetics, kinetics and mechanism. PHOTOSYNTHESIS RESEARCH 2007; 92:407-25. [PMID: 17647091 DOI: 10.1007/s11120-007-9185-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 04/19/2007] [Indexed: 05/16/2023]
Abstract
This minireview is an attempt to summarize our current knowledge on oxidative water splitting in photosynthesis. Based on the extended Kok model (Kok, Forbush, McGloin (1970) Photochem Photobiol 11:457-476) as a framework, the energetics and kinetics of two different types of reactions comprising the overall process are discussed: (i) P680+* reduction by the redox active tyrosine YZ of polypeptide D1 and (ii) Yz (ox) induced oxidation of the four step sequence in the water oxidizing complex (WOC) leading to the formation of molecular oxygen. The mode of coupling between electron transport (ET) and proton transfer (PT) is of key mechanistic relevance for the redox turnover of YZ and the reactions within the WOC. The peculiar energetics of the oxidation steps in the WOC assure that redox state S1 is thermodynamically most stable. This is a general feature in all oxygen evolving photosynthetic organisms and assumed to be of physiological relevance. The reaction coordinate of oxidative water splitting is discussed on the basis of the available information about the Gibbs energy differences between the individual redox states Si+1 and Si and the data reported for the activation energies of the individual oxidation steps in the WOC. Finally, an attempt is made to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O-O bond and on the active role of the protein in tuning the local proton activity that depends on time and redox state Si. The O-O linkage is assumed to take place at the level of a complexed peroxide.
Collapse
Affiliation(s)
- Gernot Renger
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium für Biophysikalische Chemie, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
| |
Collapse
|
108
|
Berry BW, Elvekrog MM, Tommos C. Environmental modulation of protein cation-pi interactions. J Am Chem Soc 2007; 129:5308-9. [PMID: 17417844 DOI: 10.1021/ja068957a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bruce W Berry
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | |
Collapse
|
109
|
Abstract
The electrochemistry of 2,6-dimethylbenzoquinone (DMBQ) has been characterized for three different systems: DMBQ freely solvated in aqueous buffer; DMBQ bound to a neutral, blocked cysteine (N-acetyl-L-cysteine methyl ester) and the resulting DMBQ-bCys compound solvated in aqueous buffer; and DMBQ bound to a small model protein denoted alpha(3)C. The goal of this study is to detect and characterize differences in the redox properties of the protein-ligated DMBQ relative to the solvated quinones. The alpha(3)C protein used here is a tryptophan-32 to cysteine-32 variant of the structurally defined alpha(3)W de novo protein (Dai et al. J. Am. Chem. Soc. 2002, 124, 10952-10953). The properties of alpha(3)C were recently described (Hay et al. Biochemistry 2005, 44, 11891-11902). DMBQ was covalently bound to bCys and alpha(3)C through a sulfur substitution reaction with the cysteine thiol. In contrast to the solvated DMBQ and DMBQ-bCys compounds, diffusion controlled electrochemistry of DMBQ-alpha(3)C showed well-behaved and fully reversible n = 2 oxidation/reduction with a peak separation of approximately 30 mV between pH 5 and 9. DMBQ-alpha(3)C could also be immobilized on a gold electrode modified with a self-assembled monolayer of 3-mercaptopropionoic acid, allowing the measurement, by cyclic voltammetry, of an apparent rate of electron transfer of 22 s(-1). The (cysteine) sulfur substitution significantly lowers one of the hydroquinone pKA's from 10.4 in DMBQ to 6.8 in DMBQ-bCys. This pKA is slightly elevated in DMBQ-alpha(3)C to 7.0 and the E1/2 at pH 7.0 is raised by 110 mV from +190 mV in DMBQ-bCys to +297 mV in DMBQ-alpha(3)C.
Collapse
Affiliation(s)
- Sam Hay
- Department of Biochemistry & Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | | |
Collapse
|
110
|
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.
Collapse
Affiliation(s)
- Michael C Machczynski
- Division of Biological Sciences and Biomolecular Structure and Dynamics Program, The University of Montana, Missoula, MT 59812, USA
| | | | | |
Collapse
|
111
|
Renger G, Kühn P. Reaction pattern and mechanism of light induced oxidative water splitting in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1767:458-71. [PMID: 17428439 DOI: 10.1016/j.bbabio.2006.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 12/08/2006] [Accepted: 12/13/2006] [Indexed: 11/18/2022]
Abstract
This mini review is an attempt to briefly summarize our current knowledge on light driven oxidative water splitting in photosynthesis. The reaction leading to molecular oxygen and four protons via photosynthesis comprises thermodynamic and kinetic constraints that require a balanced fine tuning of the reaction coordinates. The mode of coupling between electron (ET) and proton transfer (PT) reactions is shown to be of key mechanistic relevance for the redox turnover of Y(Z) and the reactions within the WOC. The WOC is characterized by peculiar energetics of its oxidation steps in the WOC. In all oxygen evolving photosynthetic organisms the redox state S(1) is thermodynamically most stable and therefore this general feature is assumed to be of physiological relevance. Available information on the Gibbs energy differences between the individual redox states S(i+1) and S(i) and on the activation energies of their oxidative transitions are used to construct a general reaction coordinate of oxidative water splitting in photosystem II (PS II). Finally, an attempt is presented to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O-O bond and the active role of the protein environment in tuning the local proton activity that depends on time and redox state S(i). The O-O linkage is assumed to take place within a multistate equilibrium at the redox level of S(3), comprising both redox isomerism and proton tautomerism. It is proposed that one state, S(3)(P), attains an electronic configuration and nuclear geometry that corresponds with a hydrogen bonded peroxide which acts as the entatic state for the generation of complexed molecular oxygen through S(3)(P) oxidation by Y(Z)(ox).
Collapse
Affiliation(s)
- Gernot Renger
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium für Biophysikalische Chemie, Strasse des 17.Juni 135, D-10623 Berlin, Germany.
| | | |
Collapse
|
112
|
Li WW, Hellwig P, Ritter M, Haehnel W. De Novo Design, Synthesis, and Characterization of Quinoproteins. Chemistry 2006; 12:7236-45. [PMID: 16819733 DOI: 10.1002/chem.200501212] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quinones and quinoproteins are essential redox components and enzymes in biological systems. Here, we report the de novo design, synthesis, and properties of model four-alpha-helix bundle quinoproteins. The proteins were designed and constructed from three different helices with 21 or 22 amino acid residues by chemoselective ligation to a cyclic decapeptide template. A free cysteine unit is placed at the hydrophobic core of the protein for binding of ubiquinone-0 and menaquinone-0 through a thioether bond. The quinoproteins with molecular weights of 11-12 kDa were characterized by electrospray ionization mass spectrometry, UV/Vis spectroscopy, size-exclusion chromatography, circular dichroism measurements, (1)H NMR spectroscopy, cyclic voltammetry, and redox-induced FTIR difference spectroscopy. The midpoint redox potentials at pH 8 in aqueous solution E(m,8) of thioether conjugates with N-acetyl cysteine methyl ester were 89 mV and -63 mV and with a synthetic protein 229 mV and 249 mV versus standard hydrogen electrode (SHE) for ubiquinone-0 and menaquinone-0, respectively. Detailed redox-induced FTIR difference spectroscopic studies of the model compounds and quinoproteins show the special resonance features for C=O bands at 1656-1660 and 1655-1665 cm(-1) due to the sulfur substitution to ubiquinone-0 and menaquinone-0, respectively. The construction of model quinoproteins represents a significant step toward more complex artificial redox systems.
Collapse
Affiliation(s)
- Wen-Wu Li
- Institut für Biologie II/Biochemie, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
| | | | | | | |
Collapse
|
113
|
Elias B, Kirsch-De Mesmaeker A. Photo-reduction of polyazaaromatic Ru(II) complexes by biomolecules and possible applications. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2005.11.011] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
114
|
Dunetz JR, Sandstrom C, Young ER, Baker P, Van Name SA, Cathopolous T, Fairman R, de Paula JC, Akerfeldt KS. Self-assembling porphyrin-modified peptides. Org Lett 2006; 7:2559-61. [PMID: 15957890 DOI: 10.1021/ol050644h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] We report the synthesis and characterization of a novel supramolecular assembly that features long-range electronic coupling between porphyrins covalently attached to a designed peptide scaffold. The resulting construct self-assembles to form extended organized aggregates in which the porphyrins engage in exciton coupling.
Collapse
Affiliation(s)
- Joshua R Dunetz
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
115
|
Seyedsayamdost MR, Yee CS, Reece SY, Nocera DG, Stubbe J. pH Rate profiles of FnY356-R2s (n = 2, 3, 4) in Escherichia coli ribonucleotide reductase: evidence that Y356 is a redox-active amino acid along the radical propagation pathway. J Am Chem Soc 2006; 128:1562-8. [PMID: 16448127 DOI: 10.1021/ja055927j] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Escherichia coli ribonucleotide reductase (RNR), composed of two subunits (R1 and R2), catalyzes the conversion of nucleotides to deoxynucleotides. Substrate reduction requires that a tyrosyl radical (Y(122)*) in R2 generate a transient cysteinyl radical (C(439)*) in R1 through a pathway thought to involve amino acid radical intermediates [Y(122)* --> W(48) --> Y(356) within R2 to Y(731) --> Y(730) --> C(439) within R1]. To study this radical propagation process, we have synthesized R2 semisynthetically using intein technology and replaced Y(356) with a variety of fluorinated tyrosine analogues (2,3-F(2)Y, 3,5-F(2)Y, 2,3,5-F(3)Y, 2,3,6-F(3)Y, and F(4)Y) that have been described and characterized in the accompanying paper. These fluorinated tyrosine derivatives have potentials that vary from -50 to +270 mV relative to tyrosine over the accessible pH range for RNR and pK(a)s that range from 5.6 to 7.8. The pH rate profiles of deoxynucleotide production by these F(n)()Y(356)-R2s are reported. The results suggest that the rate-determining step can be changed from a physical step to the radical propagation step by altering the reduction potential of Y(356)* using these analogues. As the difference in potential of the F(n)()Y* relative to Y* becomes >80 mV, the activity of RNR becomes inhibited, and by 200 mV, RNR activity is no longer detectable. These studies support the model that Y(356) is a redox-active amino acid on the radical-propagation pathway. On the basis of our previous studies with 3-NO(2)Y(356)-R2, we assume that 2,3,5-F(3)Y(356), 2,3,6-F(3)Y(356), and F(4)Y(356)-R2s are all deprotonated at pH > 7.5. We show that they all efficiently initiate nucleotide reduction. If this assumption is correct, then a hydrogen-bonding pathway between W(48) and Y(356) of R2 and Y(731) of R1 does not play a central role in triggering radical initiation nor is hydrogen-atom transfer between these residues obligatory for radical propagation.
Collapse
Affiliation(s)
- Mohammad R Seyedsayamdost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
| | | | | | | | | |
Collapse
|
116
|
Abstract
Water oxidation at photosystem II Mn-cluster is mediated by the redox-active tyrosine Y(Z). We calculated the redox potential (E(m)) of Y(Z) and its symmetrical counterpart Y(D), by solving the linearized Poisson-Boltzmann equation. The calculated E(m)(Y( )/Y(-)) were +926 mV/+694 mV for Y(Z)/Y(D) with the Mn-cluster in S2 state. Together with the asymmetric position of the Mn-cluster relative to Y(Z/D), differences in H-bond network between Y(Z) (Y(Z)/D1-His(190)/D1-Asn(298)) and Y(D) (Y(D)/D2-His(189)/D2-Arg(294)/CP47-Glu(364)) are crucial for E(m)(Y(Z/D)). When D1-His(190) is protonated, corresponding to a thermally activated state, the calculated E(m)(Y(Z)) was +1216 mV, which is as high as the E(m) for P(D1/D2). We observed deprotonation at CP43-Arg(357) upon S-state transition, which may suggest its involvement in the proton exit pathway. E(m)(Y(D)) was affected by formation of P(D2)(+) (but not P(D1)(+)) and sensitive to the protonation state of D2-Arg(180). This points to an electrostatic link between Y(D) and P(D2).
Collapse
Affiliation(s)
- Hiroshi Ishikita
- Institute of Chemistry and Biochemistry, Free University of Berlin, Berlin, Germany
| | | |
Collapse
|
117
|
Seyedsayamdost MR, Reece SY, Nocera DG, Stubbe J. Mono-, Di-, Tri-, and Tetra-Substituted Fluorotyrosines: New Probes for Enzymes That Use Tyrosyl Radicals in Catalysis†. J Am Chem Soc 2006; 128:1569-79. [PMID: 16448128 DOI: 10.1021/ja055926r] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A set of N-acylated, carboxyamide fluorotyrosine (F(n)()Y) analogues [Ac-3-FY-NH(2), Ac-3,5-F(2)Y-NH(2), Ac-2,3-F(2)Y-NH(2), Ac-2,3,5-F(3)Y-NH(2), Ac-2,3,6-F(3)Y-NH(2) and Ac-2,3,5,6-F(4)Y-NH(2)] have been synthesized from their corresponding amino acids to interrogate the detailed reaction mechanism(s) accessible to F(n)()Y*s in small molecules and in proteins. These Ac-F(n)()Y-NH(2) derivatives span a pK(a) range from 5.6 to 8.4 and a reduction potential range of 320 mV in the pH region accessible to most proteins (6-9). DFT electronic-structure calculations capture the observed trends for both the reduction potentials and pK(a)s. Dipeptides of the methyl ester of 4-benzoyl-l-phenylalanyl-F(n)()Ys at pH 4 were examined with a nanosecond laser pulse and transient absorption spectroscopy to provide absorption spectra of F(n)()Y*s. The EPR spectrum of each F(n)()Y* has also been determined by UV photolysis of solutions at pH 11 and 77 K. The ability to vary systematically both pK(a) and radical reduction potential, together with the facility to monitor radical formation with distinct absorption and EPR features, establishes that F(n)()Ys will be useful in the study of biological charge-transport mechanisms involving tyrosine. To demonstrate the efficacy of the fluorotyrosine method in unraveling charge transport in complex biological systems, we report the global substitution of tyrosine by 3-fluorotyrosine (3-FY) in the R2 subunit of ribonucleotide reductase (RNR) and present the EPR spectrum along with its simulation of 3-FY122*. In the companion paper, we demonstrate the utility of F(n)()Ys in providing insight into the mechanism of tyrosine oxidation in biological systems by incorporating them site-specifically at position 356 in the R2 subunit of Escherichia coli RNR.
Collapse
Affiliation(s)
- Mohammad R Seyedsayamdost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
| | | | | | | |
Collapse
|
118
|
Pogni R, Baratto MC, Teutloff C, Giansanti S, Ruiz-Dueñas FJ, Choinowski T, Piontek K, Martínez AT, Lendzian F, Basosi R. A tryptophan neutral radical in the oxidized state of versatile peroxidase from Pleurotus eryngii: a combined multifrequency EPR and density functional theory study. J Biol Chem 2006; 281:9517-26. [PMID: 16443605 DOI: 10.1074/jbc.m510424200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Versatile peroxidases are heme enzymes that combine catalytic properties of lignin peroxidases and manganese peroxidases, being able to oxidize Mn(2+) as well as phenolic and non-phenolic aromatic compounds in the absence of mediators. The catalytic process (initiated by hydrogen peroxide) is the same as in classical peroxidases, with the involvement of 2 oxidizing equivalents and the formation of the so-called Compound I. This latter state contains an oxoferryl center and an organic cation radical that can be located on either the porphyrin ring or a protein residue. In this study, a radical intermediate in the reaction of versatile peroxidase from the ligninolytic fungus Pleurotus eryngii with H(2)O(2) has been characterized by multifrequency (9.4 and 94 GHz) EPR and assigned to a tryptophan residue. Comparison of experimental data and density functional theory theoretical results strongly suggests the assignment to a tryptophan neutral radical, excluding the assignment to a tryptophan cation radical or a histidine radical. Based on the experimentally determined side chain orientation and comparison with a high resolution crystal structure, the tryptophan neutral radical can be assigned to Trp(164) as the site involved in long-range electron transfer for aromatic substrate oxidation.
Collapse
Affiliation(s)
- Rebecca Pogni
- Department of Chemistry, University of Siena, 53100 Siena, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
119
|
Koder RL, Dutton PL. Intelligent design: the de novo engineering of proteins with specified functions. Dalton Trans 2006:3045-51. [PMID: 16786062 DOI: 10.1039/b514972j] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the principal successes of de novo protein design has been the creation of small, robust protein-cofactor complexes which can serve as simplified models, or maquettes, of more complicated multicofactor protein complexes commonly found in nature. Different maquettes, generated by us and others, recreate a variety of aspects, or functional elements, recognized as parts of natural enzyme function. The current challenge is to both expand the palette of functional elements and combine and/or integrate them in recreating familiar enzyme activities or generating novel catalysis in the simplest protein scaffolds.
Collapse
Affiliation(s)
- Ronald L Koder
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | |
Collapse
|
120
|
Hossain MA, Thomas F, Hamman S, Saint-Aman E, Boturyn D, Dumy P, Pierre JL. Cyclodecapeptides to mimic the radical site of tyrosyl-containing proteins. J Pept Sci 2006; 12:612-9. [PMID: 16770835 DOI: 10.1002/psc.769] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Tyrosyl radicals are involved in many biologically important processes. The development of model compounds to mimic radical enzyme active sites, such as galactose oxidase (GO), has widely contributed to an enhanced understanding of their spectral properties, structural attributes and even reactivity. An emerging approach towards the synthesis of such active site mimetics is the use of peptidic ligands. The potential of cyclodecapeptides to bear phenoxyl radicals has been evaluated through three compounds. LH(4) (2+) is a cyclodecapetide containing two histidine residues (mimicking His(496) and His(581) of GO) and two tyrosine residues (mimicking Tyr(495) and the Tyr(272)* radical of GO). L(tBu)H(4) (2+) and L(OMe)H(4) (2+) incorporate 2,4,6-protected phenols in place of each tyrosine in LH(4) (2+). The deprotonation constants of each peptide determined by potentiometric titrations showed that there are some interactions between the acido-basic residues. Cyclic voltammetric studies revealed that only the peptides incorporating 2,4,6-protected phenolates exhibit reversible redox couples and are thus precursors of radicals stable enough to persist in solution. These studies also showed L(OMe2-) to possess the lower oxidation potential, indicating that this peptide, in its radical form, is the most stabilized. The electrochemically generated radical species have been characterized by EPR spectroscopy.
Collapse
Affiliation(s)
- Mohammed Akhter Hossain
- Laboratoire de Chimie Biomimétique, LEDSS, UMR CNRS 5616, ICMG FR CNRS 2607, Université J. Fourier, BP 53, 38041, Grenoble Cedex 9, France
| | | | | | | | | | | | | |
Collapse
|
121
|
Jung C, Lendzian F, Schünemann V, Richter M, Böttger LH, Trautwein AX, Contzen J, Galander M, Ghosh DK, Barra AL. Multi-frequency EPR and Mössbauer spectroscopic studies on freeze-quenched reaction intermediates of nitric oxide synthase. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2005; 43 Spec no.:S84-95. [PMID: 16235218 DOI: 10.1002/mrc.1694] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is believed by analogy to chloroperoxidase (CPO) from Caldariomyces fumago that the electronic structure of the intermediate iron-oxo species in the catalytic cycle of nitric oxide synthase (NOS) corresponds to an iron(IV) porphyrin-pi -cation radical. Such species can also be produced by the reaction of ferric NOS with external oxidants within the shunt pathway. We present multi-frequency EPR (9.6, 94, 285 GHz) and Mössbauer spectroscopic studies on freeze-quenched intermediates of the oxygenase domain of nitric oxide synthase which has reacted with peroxy acetic acid within 8-200 ms. The intermediates of the oxygenase domain of both the cytokine inducible NOS (iNOSox) and the neuronal NOS (nNOSox) show an organic radical signal in the 9.6-GHz spectrum overlapping with the spectrum of an unknown species with g-values of 2.24, 2.23 and 1.96. Using 94- and 285-GHz EPR the organic radical signal is assigned to a tyrosine radical on the basis of g-values (i.e. Tyr*562 in nNOSox and Tyr*341 in iNOSox). Mössbauer spectroscopy of (57)Fe-labeled unreacted nNOSox shows a ferric low-spin heme-iron (delta = 0.38 mms(-1), deltaE(Q) = 2.58 mms(-1)). The reaction of nNOSox with peroxy acetic acid for 8 ms leads to the disappearance of the magnetic background characteristic for native nNOSox and a new species with delta = 0.27 mms(-1) and deltaE(Q) = 2.41 mms(-1) is detected at 4.2 K which does not resemble the parameters typical for a Fe(IV) center. It is proposed that this intermediate species corresponds to a ferric low-spin species which magnetically couples to an amino acid radical (presumably Trp*409).
Collapse
Affiliation(s)
- C Jung
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
122
|
Kang SA, Crane BR. Effects of interface mutations on association modes and electron-transfer rates between proteins. Proc Natl Acad Sci U S A 2005; 102:15465-70. [PMID: 16227441 PMCID: PMC1266099 DOI: 10.1073/pnas.0505176102] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Accepted: 09/08/2005] [Indexed: 11/18/2022] Open
Abstract
Although bonding networks determine electron-transfer (ET) rates within proteins, the mechanism by which structure and dynamics influence ET across protein interfaces is not well understood. Measurements of photochemically induced ET and subsequent charge recombination between Zn-porphyrin-substituted cytochrome c peroxidase and cytochrome c in single crystals correlate reactivity with defined structures for different association modes of the redox partners. Structures and ET rates in crystals are consistent with tryptophan oxidation mediating charge recombination reactions. Conservative mutations at the interface can drastically affect how the proteins orient and dispose redox centers. Whereas some configurations are ET inactive, the wild-type complex exhibits the fastest recombination rate. Other association modes generate ET rates that do not correlate with predictions based on cofactor separations or simple bonding pathways. Inhibition of photoinduced ET at <273 K indicates gating by small-amplitude dynamics, even within the crystal. Thus, different associations achieve states of similar reactivity, and within those states conformational fluctuations enable interprotein ET.
Collapse
Affiliation(s)
- Seong A Kang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | |
Collapse
|
123
|
Gindt YM, Schelvis JPM, Thoren KL, Huang TH. Substrate binding modulates the reduction potential of DNA photolyase. J Am Chem Soc 2005; 127:10472-3. [PMID: 16045318 DOI: 10.1021/ja051441r] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reduction potential of the (FADH-/FADH*) couple in DNA photolyase was measured, and the value was found to be significantly higher than the values estimated in the literature. In the absence of substrate, the enzyme has a reduction potential of 16 +/- 6 mV vs NHE. In the presence of excess substrate the reduction potential increases to 81 +/- 8 mV vs NHE. The increase in reduction potential has physiological relevance since it gives the catalytic state greater resistance to oxidation. This is the first measurement of a reduction potential for this class of DNA-repair enzymes and the larger family of blue-light photoreceptors.
Collapse
Affiliation(s)
- Yvonne M Gindt
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, USA.
| | | | | | | |
Collapse
|
124
|
Reece SY, Nocera DG. Direct Tyrosine Oxidation Using the MLCT Excited States of Rhenium Polypyridyl Complexes. J Am Chem Soc 2005; 127:9448-58. [PMID: 15984872 DOI: 10.1021/ja0510360] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rhenium(I) polypyridyl complexes have been designed for the intramolecular photogeneration of tyrosyl radical. Tyrosine (Y) and phenylalanine (F) have each been separately appended to a conventional Re(I)(bpy)(CO)(3)CN framework via an amide linkage to the bipyridine (bpy) ligand. Comparative time-resolved emission quenching and transient absorption spectra of Re(bpy-Y)(CO)(3)CN and Re(bpy-F)(CO)(3)CN show that Y is oxidized only upon its deprotonation at pH 12. In an effort to redirect electron transport so that it is more compatible with intramolecular Y oxidation, polypyridyl Re(I) complexes have been prepared with the amide bond functionality located on a pendant phosphine ligand. A [Re(phen)(PP-Bn)(CO)(2)](PF(6)) (PP = bis(diphenylphosphino)ethylene) complex has been synthesized and crystallographically characterized. Electrochemistry and phosphorescence measurements of this complex indicate a modest excited-state potential for tyrosine oxidation, similar to that for the (bpy)Re(I)(CO)(3)CN framework. The excited-state oxidation potential can be increased by introducing a monodentate phosphine to the Re(I)(NN)(CO)(3)(+) framework (NN = polypyridyl). In this case, Y is oxidized at all pHs when appended to the triphenylphosphine (P) of [Re(phen)(P-Y)(CO(3))](PF(6)). Analysis of the pH dependence of the rate constant for tyrosyl radical generation is consistent with a proton-coupled electron transfer (PCET) quenching mechanism.
Collapse
Affiliation(s)
- Steven Y Reece
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
| | | |
Collapse
|
125
|
Westerlund K, Berry BW, Privett HK, Tommos C. Exploring amino-acid radical chemistry: protein engineering and de novo design. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1707:103-16. [PMID: 15721609 DOI: 10.1016/j.bbabio.2004.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Accepted: 02/26/2004] [Indexed: 11/21/2022]
Abstract
Amino-acid radical enzymes are often highly complex structures containing multiple protein subunits and cofactors. These properties have in many cases hampered the detailed characterization of their amino-acid redox cofactors. To address this problem, a range of approaches has recently been developed in which a common strategy is to reduce the complexity of the radical-containing system. This work will be reviewed and it includes the light-induced generation of aromatic radicals in small-molecule and peptide systems. Natural redox proteins, including the blue copper protein azurin and a bacterial photosynthetic reaction center, have been engineered to introduce amino-acid radical chemistry. The redesign strategies to achieve this remarkable change in the properties of these proteins will be described. An additional approach to gain insights into the properties of amino-acid radicals is to synthesize de novo designed model proteins in which the redox chemistry of these species can be studied. Here we describe the design, synthesis and characteristics of monomeric three-helix bundle and four-helix bundle proteins designed to study the redox chemistry of tryptophan and tyrosine. This work demonstrates that de novo protein design combined with structural, electrochemical and quantum chemical analyses can provide detailed information on how the protein matrix tunes the thermodynamic properties of tryptophan.
Collapse
Affiliation(s)
- Kristina Westerlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | | | | |
Collapse
|
126
|
Reece SY, Stubbe J, Nocera DG. pH Dependence of charge transfer between tryptophan and tyrosine in dipeptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1706:232-8. [PMID: 15694351 DOI: 10.1016/j.bbabio.2004.11.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Revised: 11/11/2004] [Accepted: 11/15/2004] [Indexed: 11/20/2022]
Abstract
Time-resolved absorption spectroscopy has been employed to study the directionality and rate of charge transfer in W-Y and Ac-W-Y dipeptides as a function of pH. Excitation with 266-nm nanosecond laser pulses produces both W (or [WH](+), depending on pH) and Y. Between pH 6 and 10, W to was found to oxidize Y with k(X)=9.0x10(4) s(-1) and 1.8x10(4) s(-1) for the W-Y and Ac-W-Y dipeptide systems, respectively. The intramolecular charge transfer rate increases as the pH is lowered over the range 6>pH>2. For 10<pH<12, the rate of radical transport for the W-Y dipeptide decreases and becomes convoluted with other radical decay processes, the timescales of which have been identified in studies of control dipeptides Ac-F-Y and W-F. Further increases in pH prompt the reverse reaction to occur, W-Y-->W-Y(-) (Y(-), tyrosinate anion), with a rate constant of k(X)=1.2x10(5) s(-1). The dependence of charge transfer directionality between W and Y on pH is important to the enzymatic function of several model and natural biological systems as discussed here for ribonucleotide reductase.
Collapse
Affiliation(s)
- Steven Y Reece
- Department of Chemistry, 6-335, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | | | | |
Collapse
|
127
|
Sjödin M, Styring S, Wolpher H, Xu Y, Sun L, Hammarström L. Switching the Redox Mechanism: Models for Proton-Coupled Electron Transfer from Tyrosine and Tryptophan. J Am Chem Soc 2005; 127:3855-63. [PMID: 15771521 DOI: 10.1021/ja044395o] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coupling of electron and proton transfer is an important controlling factor in radical proteins, such as photosystem II, ribinucleotide reductase, cytochrome oxidases, and DNA photolyase. This was investigated in model complexes in which a tyrosine or tryptophan residue was oxidized by a laser-flash generated trisbipyridine-Ru(III) moiety in an intramolecular, proton-coupled electron transfer (PCET) reaction. The PCET was found to proceed in a competition between a stepwise reaction, in which electron transfer is followed by deprotonation of the amino acid radical (ETPT), and a concerted reaction, in which both the electron and proton are transferred in a single reaction step (CEP). Moreover, we found that we could analyze the kinetic data for PCET by Marcus' theory for electron transfer. By altering the solution pH, the strength of the Ru(III) oxidant, or the identity of the amino acid, we could induce a switch between the two mechanisms and obtain quantitative data for the parameters that control which one will dominate. The characteristic pH-dependence of the CEP rate (M. Sjodin et al. J. Am. Chem. Soc. 2000, 122, 3932) reflects the pH-dependence of the driving force caused by proton release to the bulk. For the pH-independent ETPT on the other hand, the driving force of the rate-determining ET step is pH-independent and smaller. On the other hand, temperature-dependent data showed that the reorganization energy was higher for CEP, while the pre-exponential factors showed no significant difference between the mechanisms. Thus, the opposing effect of the differences in driving force and reorganization energy determines which of the mechanisms will dominate. Our results show that a concerted mechanism is in general quite likely and provides a low-barrier reaction pathway for weakly exoergonic reactions. In addition, the kinetic isotope effect was much higher for CEP (kH/kD > 10) than for ETPT (kH/kD = 2), consistent with significant changes along the proton reaction coordinate in the rate-determining step of CEP.
Collapse
Affiliation(s)
- Martin Sjödin
- Department of Physical Chemistry, BMC, Uppsala University, PO Box 579, SE-751 23 Uppsala, Sweden
| | | | | | | | | | | |
Collapse
|
128
|
Chang MCY, Yee CS, Nocera DG, Stubbe J. Site-Specific Replacement of a Conserved Tyrosine in Ribonucleotide Reductase with an Aniline Amino Acid: A Mechanistic Probe for a Redox-Active Tyrosine. J Am Chem Soc 2004; 126:16702-3. [PMID: 15612690 DOI: 10.1021/ja044124d] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An aniline-based amino acid provides a powerful mechanistic probe for redox-active tyrosines, affording a general method for elucidating the sequence of proton and electron transfer events during side-chain oxidation in biological systems. Intein technology allows Y356 to be site-specifically replaced with p-aminophenylalanine (PheNH2) on the R2 subunit of the class I ribonucleotide reductase. Analysis of the pH rate profile of Y356PheNH2-R2 strongly suggests that the mechanism of long-distance intrasubunit radical transfer through position 356 proceeds with electron transfer prior to proton transfer. In addition, we propose that radical transfer through position 356 only becomes rate-limiting upon raising the reduction potential of the residue at that location and is not affected by protonation state of either the ground state or oxidized amino acid.
Collapse
Affiliation(s)
- Michelle C Y Chang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | | | | |
Collapse
|
129
|
Buddha MR, Tao T, Parry RJ, Crane BR. Regioselective Nitration of Tryptophan by a Complex between Bacterial Nitric-oxide Synthase and Tryptophanyl-tRNA Synthetase. J Biol Chem 2004; 279:49567-70. [PMID: 15466862 DOI: 10.1074/jbc.c400418200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial nitric-oxide synthase proteins (NOSs) from certain Streptomyces strains have been shown to participate in biosynthetic nitration of tryptophanyl moieties in vivo (Kers, J. A., Wach, M. J., Krasnoff, S. B., Cameron, K. D., Widom, J., Bukhaid, R. A., Gibson, D. M., and Crane, B. R., and Loria, R. (2004) Nature 429, 79-82). We report that the complex between Deinococcus radiodurans NOS (deiNOS) and an unusual tryptophanyl-tRNA synthetase (TrpRS II) catalyzes the regioselective nitration of tryptophan (Trp) at the 4-position. Unlike non-enzymatic Trp nitration, and similar reactions catalyzed by globins and peroxidases, deiNOS only produces the otherwise unfavorable 4-nitro-Trp isomer. Although deiNOS alone will catalyze 4-nitro-Trp production, yields are significantly enhanced by TrpRS II and ATP. 4-Nitro-Trp formation exhibits saturation behavior with Trp (but not tyrosine) and is completely inhibited by the addition of the mammalian NOS cofactor (6R)-5,6,7,8-tetrahydro-l-biopterin (H(4)B). Trp stimulates deiNOS oxidation of substrate l-arginine (Arg) to the same degree as H(4)B. These observations are consistent with a mechanism where Trp or a derivative thereof binds in the NOS pterin site, participates in Arg oxidation, and becomes nitrated at the 4-position.
Collapse
Affiliation(s)
- Madhavan R Buddha
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | | | | | | |
Collapse
|
130
|
Peterson RW, Anbalagan K, Tommos C, Wand AJ. Forced folding and structural analysis of metastable proteins. J Am Chem Soc 2004; 126:9498-9. [PMID: 15291527 DOI: 10.1021/ja047900q] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A significant fraction of the proteins encoded by the human and other genomes appears to be significantly unfolded in vitro. This will undoubtedly hamper attempts to characterize their structure by classical crystallographic or solution NMR methods. Here we show that encapsulation of a metastable protein within the restricted volume a reverse micelle can be used to force fold the protein and allow its characterization by modern methods of NMR spectroscopy. This may have significant utility in the context of structural proteomics. In addition, variation of the inner volume of the reverse micelle can be used to probe the character of the manifold of unfolded states.
Collapse
Affiliation(s)
- Ronald W Peterson
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | | | |
Collapse
|
131
|
Kapetanaki SM, Ramsey M, Gindt YM, Schelvis JPM. Substrate electric dipole moment exerts a pH-dependent effect on electron transfer in Escherichia coli photolyase. J Am Chem Soc 2004; 126:6214-5. [PMID: 15149202 DOI: 10.1021/ja049226i] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transient absorption spectroscopy is used to demonstrate that the electric dipole moment of the substrate cyclobutane thymine dimer affects the charge recombination reaction between fully reduced flavin adenine dinucleotide (FADH-) and the neutral radical tryptophan 306 (Trp306*) in Escherichia coli DNA photolyase. At pH 7.4, the charge recombination is slowed by a factor of 1.75 in the presence of substrate, but not at pH 5.4. Photolyase does bind substrate at pH 5.4, and it seems that this pH effect originates from the conversion of FADH- to FADH2 at lower pH. The free-energy changes calculated from the electric field parameters and from the change in electron transfer rate are in good agreement and support the idea that the substrate electric dipole is responsible for the observed change in electron transfer rate. It is expected that the substrate electric field will also modify the physiologically important from excited 1FADH- to the substrate in the DNA repair reaction.
Collapse
Affiliation(s)
- Sofia M Kapetanaki
- Department of Chemistry, New York University, New York, New York 10003, USA
| | | | | | | |
Collapse
|
132
|
Miller JE, Di Bilio AJ, Wehbi WA, Green MT, Museth AK, Richards JR, Winkler JR, Gray HB. Electron tunneling in rhenium-modified Pseudomonas aeruginosa azurins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:59-63. [PMID: 15100017 DOI: 10.1016/j.bbabio.2003.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2003] [Revised: 06/26/2003] [Accepted: 06/26/2003] [Indexed: 10/26/2022]
Abstract
Laser flash-quench methods have been used to generate tyrosine and tryptophan radicals in structurally characterized rhenium-modified Pseudomonas aeruginosa azurins. Cu(I) to "Re(II)" electron tunneling in Re(H107) azurin occurs in the microsecond range. This reaction is much faster than that studied previously for Cu(I) to Ru(III) tunneling in Ru(H107) azurin, suggesting that a multistep ("hopping") mechanism might be involved. Although a Y108 radical can be generated by flash-quenching a Re(H107)M(II) (M=Cu, Zn) protein, the evidence suggests that it is not an active intermediate in the enhanced Cu(I) oxidation. Rather, the likely explanation is rapid conversion of Re(II)(H107) to deprotonated Re(I)(H107 radical), followed by electron tunneling from Cu(I) to the hole in the imidazole ligand.
Collapse
Affiliation(s)
- Jeremiah E Miller
- Beckman Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | | | | | | | | | | | | | | |
Collapse
|
133
|
Byrdin M, Sartor V, Eker APM, Vos MH, Aubert C, Brettel K, Mathis P. Intraprotein electron transfer and proton dynamics during photoactivation of DNA photolyase from E. coli: review and new insights from an "inverse" deuterium isotope effect. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:64-70. [PMID: 15100018 DOI: 10.1016/j.bbabio.2003.07.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2003] [Revised: 07/29/2003] [Accepted: 07/29/2003] [Indexed: 10/26/2022]
Abstract
We review our work on electron transfer and proton dynamics during photoactivation in DNA photolyase from E. coli and discuss a recent theoretical study on this issue. In addition, we present unpublished data on the charge recombination between the fully reduced FADH(-) and the neutral (deprotonated) radical of the solvent exposed tryptophan W306. We found a pronounced acceleration with decreasing pH and an inverse deuterium isotope effect (k(H)/k(D)=0.35 at pL 6.5) and interpret it in a model of a fast protonation equilibrium for the W306 radical. Due to this fast equilibrium, two parallel recombination channels contribute differently at different pH values: one where reprotonation of the W306 radical is followed by electron transfer from FADH(-) (electron transfer time constant tau(et) in the order of 10-50 micros), and one where electron transfer from FADH(-) (tau(et)=25 ms) is followed by reprotonation of the W306 anion.
Collapse
Affiliation(s)
- Martin Byrdin
- Service de Bioénergétique, CEA, and URA 2096 CNRS, CEA Saclay, Bat. 532, F-91191 Gif-sur-Yvette Cedex, France.
| | | | | | | | | | | | | |
Collapse
|
134
|
Pan J, Byrdin M, Aubert C, Eker APM, Brettel K, Vos MH. Excited-State Properties of Flavin Radicals in Flavoproteins: Femtosecond Spectroscopy of DNA Photolyase, Glucose Oxidase, and Flavodoxin. J Phys Chem B 2004. [DOI: 10.1021/jp037837b] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jie Pan
- Laboratory for Optical Biosciences, INSERM U451, CNRS UMR 7645, Ecole Polytechnique-ENSTA, 91128 Palaiseau Cedex, France, Service de Bioénergétique, CEA, and URA 2096 CNRS, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France, Laboratoire de Bioénergétique et Ingénierie des ProtéinesCNRS, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Martin Byrdin
- Laboratory for Optical Biosciences, INSERM U451, CNRS UMR 7645, Ecole Polytechnique-ENSTA, 91128 Palaiseau Cedex, France, Service de Bioénergétique, CEA, and URA 2096 CNRS, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France, Laboratoire de Bioénergétique et Ingénierie des ProtéinesCNRS, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Corinne Aubert
- Laboratory for Optical Biosciences, INSERM U451, CNRS UMR 7645, Ecole Polytechnique-ENSTA, 91128 Palaiseau Cedex, France, Service de Bioénergétique, CEA, and URA 2096 CNRS, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France, Laboratoire de Bioénergétique et Ingénierie des ProtéinesCNRS, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - André P. M. Eker
- Laboratory for Optical Biosciences, INSERM U451, CNRS UMR 7645, Ecole Polytechnique-ENSTA, 91128 Palaiseau Cedex, France, Service de Bioénergétique, CEA, and URA 2096 CNRS, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France, Laboratoire de Bioénergétique et Ingénierie des ProtéinesCNRS, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Klaus Brettel
- Laboratory for Optical Biosciences, INSERM U451, CNRS UMR 7645, Ecole Polytechnique-ENSTA, 91128 Palaiseau Cedex, France, Service de Bioénergétique, CEA, and URA 2096 CNRS, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France, Laboratoire de Bioénergétique et Ingénierie des ProtéinesCNRS, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Marten H. Vos
- Laboratory for Optical Biosciences, INSERM U451, CNRS UMR 7645, Ecole Polytechnique-ENSTA, 91128 Palaiseau Cedex, France, Service de Bioénergétique, CEA, and URA 2096 CNRS, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France, Laboratoire de Bioénergétique et Ingénierie des ProtéinesCNRS, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| |
Collapse
|
135
|
Immoos CE, Di Bilio AJ, Cohen MS, Van der Veer W, Gray HB, Farmer PJ. Electron-Transfer Chemistry of Ru−Linker−(Heme)-Modified Myoglobin: Rapid Intraprotein Reduction of a Photogenerated Porphyrin Cation Radical. Inorg Chem 2004; 43:3593-6. [PMID: 15180412 DOI: 10.1021/ic049741h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the synthesis and characterization of RuC7, a complex in which a heme is covalently attached to a [Ru(bpy)(3)](2+) complex through a -(CH(2))(7)- linker. Insertion of RuC7 into horse heart apomyoglobin gives RuC7Mb, a Ru(heme)-protein conjugate in which [Ru(bpy)(3)](2+) emission is highly quenched. The rate of photoinduced electron transfer (ET) from the resting (Ru(2+)/Fe(3+)) to the transient (Ru(3+)/Fe(2+)) state of RuC7Mb is >10(8) s(-1); the back ET rate (to regenerate Ru(2+)/Fe(3+)) is 1.4 x 10(7) s(-1). Irreversible oxidative quenching by [Co(NH(3))(5)Cl](2+) generates Ru(3+)/Fe(3+): the Ru(3+) complex then oxidizes the porphyrin to a cation radical (P*+); in a subsequent step, P*+ oxidizes both Fe(3+) (to give Fe(IV)=O) and an amino acid residue. The rate of intramolecular reduction of P*+ is 9.8 x 10(3) s(-1); the rate of ferryl formation is 2.9 x 10(3) s(-1). Strong EPR signals attributable to tyrosine and tryptophan radicals were recorded after RuC7MbM(3+) (M = Fe, Mn) was flash-quenched/frozen.
Collapse
Affiliation(s)
- Chad E Immoos
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | | | | | | | | | | |
Collapse
|
136
|
Chang MCY, Yee CS, Stubbe J, Nocera DG. Turning on ribonucleotide reductase by light-initiated amino acid radical generation. Proc Natl Acad Sci U S A 2004; 101:6882-7. [PMID: 15123822 PMCID: PMC406436 DOI: 10.1073/pnas.0401718101] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms, providing the monomeric precursors required for DNA replication and repair. The class I RNRs are composed of two subunits; the R1 subunit contains the active site for nucleotide reduction and allosteric effector binding sites, whereas the R2 subunit houses the essential diirontyrosyl (Y.) radical cofactor. A major unresolved issue is the mechanism by which the tyrosyl radical on R2 (Y122, Escherichia coli numbering) reversibly generates the transient thiyl radical (S.) on R1 that initiates nucleotide reduction. This intersubunit radical initiation is postulated to occur through a defined pathway involving conserved aromatic amino acids (R2: Y122, W48, Y356; R1: Y731, Y730) over a long distance of 35 A. A 20-mer peptide identical to the C-terminal tail of R2 (356-375) and containing Y356 is a competitive inhibitor with respect to R2, and it effectively blocks nucleotide reduction. We now report that a 21-mer peptide, in which a tryptophan has been incorporated at the N terminus of the 20th mer, can replace the R2 subunit and initiate nucleotide reduction by photoinitiated radical generation. The deoxynucleotide generated depends on the presence of allosteric effector and is pathway-dependent. Replacement of Y731 of R2 with phenylalanine prevents deoxynucleotide formation. These results provide direct evidence for the chemical competence of aromatic amino acid radicals and the importance of Y356 in R2 in the radical initiation process of the class I RNRs.
Collapse
Affiliation(s)
- Michelle C Y Chang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | | | | | | |
Collapse
|
137
|
Hoganson CW, Tommos C. The function and characteristics of tyrosyl radical cofactors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:116-22. [PMID: 15100023 DOI: 10.1016/j.bbabio.2003.10.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2003] [Accepted: 10/31/2003] [Indexed: 11/18/2022]
Abstract
Amino-acid radicals are involved in the catalytic cycles of a number of enzymes. The main focus of this mini-review is to discuss the function and properties of tyrosyl radical cofactors. We start by briefly summarizing the experimental studies that led to the detection and identification of the two redox-active tyrosines, denoted Y(Z) and Y(D), found in the water-oxidizing photosystem II (PSII) enzyme. More recent work that shows that the histidine-cross-linked tyrosine located in the active site of cytochrome c oxidase forms a radical during the catalytic oxygen-oxygen bond-cleavage process is also described. Advanced spectroscopic and structural studies have been performed to investigate the spin-density distribution, the protonation state and the hydrogen bonding of redox-active tyrosines. These studies have shown that the radical spin-density distribution is highly insensitive to the environment and that it is typical of a deprotonated species. In contrast, the hydrogen bonding and the nature of the proton acceptor or network of acceptors vary substantially in different systems. This is important for the function of the tyrosyl radical, as will be emphasized in a detailed discussion on the proposed function of Y(Z) as a proton coupled electron-transfer cofactor in photosynthetic water oxidation. Amino-acid radical enzymes are typically large complexes containing multiple subunits, chromophores and redox cofactors. The structural and mechanistic complexity of these systems has hampered the detailed characterization of their radical cofactors. In the final section of this mini-review, we will describe a project aimed at investigating how the protein controls the thermodynamic and kinetic redox properties of aromatic residues by using de novo protein design. Two model proteins of different size have been constructed. The smaller protein is a 67-residue three-helix bundle containing either a single buried tryptophan or tyrosine residue. The high-resolution NMR structure of the tryptophan-containing protein, denoted alpha(3)W, shows that the aromatic side chain is involved in a pi-cation interaction with a nearby lysine. The effects of this interaction on the tryptophan reduction potential were investigated by electrochemical and quantum mechanical methods. The calculations predict that the pi-cation interaction increases the potential, which is consistent with the electrochemical characterization of alpha(3)W. A larger 117-residue four-helix bundle, alpha(4)W, has more recently been constructed to complement the work on the three-helix-bundles and expand the family of model radical proteins.
Collapse
Affiliation(s)
- Curtis W Hoganson
- Department of Chemistry, Ursinus College, Collegeville, PA 19426, USA
| | | |
Collapse
|
138
|
Huang SS, Koder RL, Lewis M, Wand AJ, Dutton PL. The HP-1 maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange. Proc Natl Acad Sci U S A 2004; 101:5536-41. [PMID: 15056758 PMCID: PMC397418 DOI: 10.1073/pnas.0306676101] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synthetic heme-binding four-alpha-helix bundles show promise as working model systems, maquettes, for understanding heme cofactor-protein assembly and function in oxidoreductases. Despite successful inclusion of several key functional elements of natural proteins into a family of heme protein maquettes, the lack of 3D structures, due principally to conformational heterogeneity, has prevented them from achieving their full potential. We report here the design and synthesis of HP-1, a disulfide-bridged two-alpha-helix peptide that self-assembles to form an antiparallel twofold symmetric diheme four-alpha-helix bundle protein with a stable conformation on the NMR time-scale. The HP-1 design strategy began with the x-ray crystal structure of the apomaquette L31M, an apomaquette derived from the structurally heterogeneous tetraheme-binding H10H24 prototype. L31M was functionally redesigned to accommodate two hemes ligated to histidines and to retain the strong coupling of heme oxidation-reduction to glutamate acid-base transitions and proton exchange that was characterized in molten globule predecessors. Heme insertion was modeled with angular constraints statistically derived from natural proteins, and the pattern of hydrophobic and hydrophilic residues on each helix was then altered to account for this large structural reorganization. The transition to structured holomaquette involved the alteration of 6 of 31 residues in each of the four identical helices and, unlike our earlier efforts, required no design intermediates. Oxidation-reduction of both hemes displays an unusually low midpoint potential (-248 mV vs. normal hydrogen electrode at pH 9.0), which is strongly coupled to proton binding, as designed.
Collapse
Affiliation(s)
- Steve S Huang
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | |
Collapse
|
139
|
Miller JE, Grădinaru C, Crane BR, Di Bilio AJ, Wehbi WA, Un S, Winkler JR, Gray HB. Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment. J Am Chem Soc 2004; 125:14220-1. [PMID: 14624538 DOI: 10.1021/ja037203i] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Near-UV irradiation of structurally characterized [Re(I)(CO)3(1,10-phenanthroline)(Q107H)](W48F/Y72F/H83Q/Y108W)AzM(II) [Az = Pseudomonas aeruginosa azurin, M = Cu, Zn]/[Co(NH3)5Cl]Cl2 produces a tryptophan radical (W108*) with unprecedented kinetic stability. After rapid formation (k = 2.8 x 106 s-1), the radical persists for more than 5 h at room temperature in the folded ReAzM(II) structure. The absorption spectrum of ReAz(W108*)M(II) exhibits maxima at 512 and 536 nm. Oxidation of K4[Mo(CN)8] by ReAz(W108*)Zn(II) places the W108*/W108 reduction potential in the protein above 0.8 V vs NHE.
Collapse
Affiliation(s)
- Jeremiah E Miller
- Beckman Institute, California Institute of Technology, CA 91125, USA
| | | | | | | | | | | | | | | |
Collapse
|
140
|
Milligan JR, Aguilera JA, Ly A, Tran NQ, Hoang O, Ward JF. Repair of oxidative DNA damage by amino acids. Nucleic Acids Res 2003; 31:6258-63. [PMID: 14576314 PMCID: PMC275458 DOI: 10.1093/nar/gkg816] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Guanyl radicals, the product of the removal of a single electron from guanine, are produced in DNA by the direct effect of ionizing radiation. We have produced guanyl radicals in DNA by using the single electron oxidizing agent (SCN)2-, itself derived from the indirect effect of ionizing radiation via thiocyanate scavenging of OH. We have examined the reactivity of guanyl radicals in plasmid DNA with the six most easily oxidized amino acids cysteine, cystine, histidine, methionine, tryptophan and tyrosine and also simple ester and amide derivatives of them. Cystine and histidine derivatives are unreactive. Cysteine, methionine, tyrosine and particularly tryptophan derivatives react to repair guanyl radicals in plasmid DNA with rate constants in the region of approximately 10(5), 10(5), 10(6) and 10(7) dm3 mol(-1) s(-1), respectively. The implication is that amino acid residues in DNA binding proteins such as histones might be able to repair by an electron transfer reaction the DNA damage produced by the direct effect of ionizing radiation or by other oxidative insults.
Collapse
Affiliation(s)
- J R Milligan
- Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610, USA.
| | | | | | | | | | | |
Collapse
|
141
|
Ellerby HM, Lee S, Ellerby LM, Chen S, Kiyota T, del Rio G, Sugihara G, Sun Y, Bredesen DE, Arap W, Pasqualini R. An artificially designed pore-forming protein with anti-tumor effects. J Biol Chem 2003; 278:35311-6. [PMID: 12750379 DOI: 10.1074/jbc.m300474200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein engineering is an emerging area that has expanded our understanding of protein folding and laid the groundwork for the creation of unprecedented structures with unique functions. We previously designed the first native-like pore-forming protein, small globular protein (SGP). We show here that this artificially engineered protein has membrane-disrupting properties and anti-tumor activity in several cancer animal models. We propose and validate a mechanism for the selectivity of SGP toward cell membranes in tumors. SGP is the prototype for a new class of artificial proteins designed for therapeutic applications.
Collapse
Affiliation(s)
- H Michael Ellerby
- Program on Cancer and Aging, The Buck Institute, Novato, California 94945, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
142
|
Yee CS, Chang MCY, Ge J, Nocera DG, Stubbe J. 2,3-difluorotyrosine at position 356 of ribonucleotide reductase R2: a probe of long-range proton-coupled electron transfer. J Am Chem Soc 2003; 125:10506-7. [PMID: 12940718 DOI: 10.1021/ja036242r] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli class I ribonucleotide reductase catalyzes the conversion of ribonucleotides to deoxyribonucleotides and consists of two subunits: R1 and R2. R1 possesses the active site, while R2 harbors the essential diferric-tyrosyl radical (Y*) cofactor. The Y* on R2 is proposed to generate a transient thiyl radical on R1, 35 A distant, through amino acid radical intermediates. To study the putative long-range proton-coupled electron transfer (PCET), R2 (375 residues) was prepared semisynthetically using intein technology. Y356, a putative intermediate in the pathway, was replaced with 2,3-difluorotyrosine (F2Y, pKa = 7.8). pH rate profiles (pH 6.5-9.0) of wild-type and F2Y-R2 were very similar. Thus, a proton can be lost from the putative PCET pathway without affecting nucleotide reduction. The current model involving H* transfer is thus unlikely.
Collapse
Affiliation(s)
- Cyril S Yee
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | | | | | | |
Collapse
|
143
|
Stubbe J, Nocera DG, Yee CS, Chang MCY. Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer? Chem Rev 2003; 103:2167-201. [PMID: 12797828 DOI: 10.1021/cr020421u] [Citation(s) in RCA: 666] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA.
| | | | | | | |
Collapse
|
144
|
Tommos C. Electron, proton and hydrogen-atom transfers in photosynthetic water oxidation. Philos Trans R Soc Lond B Biol Sci 2002; 357:1383-94; discussion 1394, 1419-20. [PMID: 12437877 PMCID: PMC1693038 DOI: 10.1098/rstb.2002.1135] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
When photosynthetic organisms developed so that they could use water as an electron source to reduce carbon dioxide, the stage was set for efficient proliferation. Algae and plants spread globally and provided the foundation for our atmosphere and for O(2)-based chemistry in biological systems. Light-driven water oxidation is catalysed by photosystem II, the active site of which contains a redox-active tyrosine denoted Y(Z), a tetramanganese cluster, calcium and chloride. In 1995, Gerald Babcock and co-workers presented the hypothesis that photosynthetic water oxidation occurs as a metallo-radical catalysed process. In this model, the oxidized tyrosine radical is generated by coupled proton/electron transfer and re-reduced by abstracting hydrogen atoms from substrate water or hydroxide-ligated to the manganese cluster. The proposed function of Y(Z) requires proton transfer from the tyrosine site upon oxidation. The oxidation mechanism of Y(Z) in an inhibited and O(2)-evolving photosystem II is discussed. Domino-deprotonation from Y(Z) to the bulk solution is shown to be consistent with a variety of data obtained on metal-depleted samples. Experimental data that suggest that the oxidation of Y(Z) in O(2)-evolving samples is coupled to proton transfer in a hydrogen-bonding network are described. Finally, a dielectric-dependent model for the proton release that is associated with the catalytic cycle of photosystem II is discussed.
Collapse
Affiliation(s)
- Cecilia Tommos
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
| |
Collapse
|
145
|
Schünemann V, Jung C, Terner J, Trautwein AX, Weiss R. Spectroscopic studies of peroxyacetic acid reaction intermediates of cytochrome P450cam and chloroperoxidase. J Inorg Biochem 2002; 91:586-96. [PMID: 12237224 DOI: 10.1016/s0162-0134(02)00476-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is generally assumed that the putative compound I (cpd I) in cytochrome P450 should contain the same electron and spin distribution as is observed for cpd I of peroxidases and catalases and many synthetic cpd I analogues. In these systems one oxidation equivalent resides on the Fe(IV)=O unit (d(4), S=1) and one is located on the porphyrin (S'=1/2), constituting a magnetically coupled ferryl iron-oxo porphyrin pi-cation radical system. However, this laboratory has recently reported detection of a ferryl iron (S=1) and a tyrosyl radical (S'=1/2), via Mössbauer and EPR studies of 8 ms-reaction intermediates of substrate-free P450cam from Pseudomonas putida, prepared by a freeze-quench method using peroxyacetic acid as the oxidizing agent [Schünemann et al., FEBS Lett. 479 (2000) 149]. In the present study we show that under the same reaction conditions, but in the presence of the substrate camphor, only trace amounts of the tyrosine radical are formed and no Fe(IV) is detectable. We conclude that camphor restricts the access of the heme pocket by peroxyacetic acid. This conclusion is supported by the additional finding that binding of camphor and metyrapone inhibit heme bleaching at room temperature and longer reaction times, forming only trace amounts of 5-hydroxy-camphor, the hydroxylation product of camphor, during peroxyacetic acid oxidation. As a control we performed freeze-quench experiments with chloroperoxidase from Caldariomyces fumago using peroxyacetic acid under the identical conditions used for the substrate-free P450cam oxidations. We were able to confirm earlier findings [Rutter et al., Biochemistry 23 (1984) 6809], that an antiferromagnetically coupled Fe(IV)=O porphyrin pi-cation radical system is formed. We conclude that CPO and P450 behave differently when reacting with peracids during an 8-ms reaction time. In P450cam the formation of Fe(IV) is accompanied by the formation of a tyrosine radical, whereas in CPO Fe(IV) formation is accompanied by the formation of a porphyrin radical.
Collapse
Affiliation(s)
- V Schünemann
- Institute of Physics, Medical University Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany.
| | | | | | | | | |
Collapse
|
146
|
Dai QH, Tommos C, Fuentes EJ, Blomberg MRA, Dutton PL, Wand AJ. Structure of a de novo designed protein model of radical enzymes. J Am Chem Soc 2002; 124:10952-3. [PMID: 12224922 DOI: 10.1021/ja0264201] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of side chains as catalytic cofactors for protein mediated redox chemistry raises significant mechanistic issues as to how these amino acids are activated toward radical chemistry in a controlled manner. De novo protein design has been used to examine the structural basis for the creation and maintenance of a tryptophanyl radical in a three-helix bundle protein maquette. Here we report the detailed structural analysis of the protein by multidimensional NMR methods. An interesting feature of the structure is an apparent pi-cation interaction involving the sole tryptophan and a lysine side chain. Hybrid density functional calculations support the notion that this interaction raises the reduction potential of the W degrees /WH redox pair and helps explain the redox characteristics of the protein. This model protein system therefore provides a powerful model for exploring the structural basis for controlled radical chemistry in protein.
Collapse
Affiliation(s)
- Qing-Hong Dai
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | | | | | | | |
Collapse
|
147
|
Fang Y, Liu L, Feng Y, Li XS, Guo QX. Effects of Hydrogen Bonding to Amines on the Phenol/Phenoxyl Radical Oxidation. J Phys Chem A 2002. [DOI: 10.1021/jp014425z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ying Fang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Lei Liu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Yong Feng
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Xiao-Song Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Qing-Xiang Guo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, P. R. China
| |
Collapse
|
148
|
Popović DM, Zmirić A, Zarić SD, Knapp EW. Energetics of radical transfer in DNA photolyase. J Am Chem Soc 2002; 124:3775-82. [PMID: 11929268 DOI: 10.1021/ja016249d] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Charge separation and radical transfer in DNA photolyase from Escherichia coli is investigated by computing electrostatic free energies from a solution of the Poisson-Boltzmann equation. For the initial charge separation 450 meV are available. According to recent experiments [Aubert et al. Nature 2000, 405, 586-590] the flavin receives an electron from the proximal tryptophan W382, which consequently forms a cationic radical WH(*)(+)382. The radical state is subsequently transferred along the triad W382-W359-W306 of conserved tryptophans. The radical transfer to the intermediate tryptophan W359 is nearly isoenergetic (58 meV uphill); the radical transfer from the intermediate W359 to the distal W306 is 200 meV downhill in energy, funneling and stabilizing the radical state at W306. The resulting cationic radical WH(*)(+)306 is further stabilized by deprotonation, yielding the neutral radical W(*)306, which is 214 meV below WH(*)(+)306. The time scale of the charge recombination process yielding back the resting enzyme with FADH(*) is governed by reprotonation of W306, with a calculated lifetime of 1.2 ms that correlates well with the measured lifetime of 17 ms. In photolyase from Anacystis nidulans the radical state is partially transferred to a tyrosine [Aubert et al. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 5423-5427]. In photolyase from Escherichia coli, there is a tyrosine (Y464) close to the distal tryptophan W306 that could play this role. We show that this tyrosine cannot be involved in radical transfer, because the electron transfer from tyrosine to W306 is much too endergonic (750 meV) and a direct hydrogen transfer is likely too slow. Coupling of specific charge states of the tryptophan triad with protonation patterns of titratable residues of photolyase is small.
Collapse
Affiliation(s)
- Dragan M Popović
- Department of Biology, Chemistry, and Pharmacy, Institute of Chemistry, Free University of Berlin, Takustrasse 6, D-14195 Berlin, Germany
| | | | | | | |
Collapse
|
149
|
Affiliation(s)
- R P Pesavento
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | |
Collapse
|
150
|
Affiliation(s)
- L Baltzer
- Department of Chemistry, Linköping University, 581 83 Linköping, Sweden.
| | | | | |
Collapse
|