151
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Borg OA, Eriksson LA, Durbeej B. Electron-Transfer Induced Repair of 6-4 Photoproducts in DNA: A Computational Study. J Phys Chem A 2007; 111:2351-61. [PMID: 17388321 DOI: 10.1021/jp0676383] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C-O bond followed by cleavage of the C-C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C-N and C-C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.
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Zhang RB, Gao FX, Eriksson LA. Radical-Induced Damage in 3‘dTMP Insights into a Mechanism for DNA Strand Cleavage. J Chem Theory Comput 2007; 3:803-10. [DOI: 10.1021/ct6003593] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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153
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Larsson A, Eriksson LA, Andersson PL, Ivarson P, Olsson PE. Identification of the brominated flame retardant 1,2-dibromo-4-(1,2-dibromoethyl)cyclohexane as an androgen agonist. J Med Chem 2007; 49:7366-72. [PMID: 17149866 DOI: 10.1021/jm060713d] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To investigate androgen receptor (AR) activation by exogenous compounds, we used a combination of experimental analysis and theoretical modeling to compare a set of brominated flame retardants (BFRs) to dihydrotestosterone (DHT) with regard to ligand docking, AR binding, and AR activation in human hepatocellular liver carcinoma cells, as well as interacting energy analysis. Modeling of receptor docking was found to be a useful first step in predicting the potential to translocate to the ligand pocket of the receptor, and the computed interaction energy was found to correlate with the observed binding affinity. Flexible alignment studies of the BFR compounds demonstrated that 1,2-dibromo-4-(1,2-dibromoethyl)cyclohexane (BCH) closely overlap DHT. Combining the theoretical modeling with in vitro ligand-binding and receptor-activation assays, we show that BCH binds to and activates the human AR. The remaining BFRs did not successfully interact with the ligand pocket, were not able to replace a synthetic androgen from the receptor, and failed to activate the receptor.
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154
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Zhang RB, Eriksson LA. The role of nucleobase carboradical and carbanion on DNA lesions: a theoretical study. J Phys Chem B 2007; 110:23583-9. [PMID: 17107214 DOI: 10.1021/jp063605b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA base release induced by H and OH radical addition to thymine and their corresponding electron adducts is studied at the DFT B3LYP/6-31+G(d,p) level in gas phase and in solution. H atom transfer after radical formation from C2' on the sugar to the C6 site on the base is shown to be prohibited for the radical species. Their corresponding electron adducts, albeit minor events in cellular systems, show excellent capabilities to proton transfer from C2' on the sugar to the C6 site on the base. The barriers for subsequent N-glycosidic bond dissociation range from 0.1 to 1.6 kcal mol(-1) at the B3LYP level and around 5 kcal mol(-1) using the BB1K functional, implying that these reactions can serve as a source to abasic sites. Analysis of bond dissociation energies show that all the reactions are exothermic, which is consistent with the changes in N-glycosidic bond lengths during the proton-transfer reactions. Bulk solvation plays a reverse influence on proton transfer and the bond rupture reactions. Molecular orbitals, NPA charges, and electron affinities are calculated to shed further light on the properties leading up to the intramolecular reactions.
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155
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Schyman P, Zhang RB, Eriksson LA, Laaksonen A. Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical. Phys Chem Chem Phys 2007; 9:5975-9. [DOI: 10.1039/b711083a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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156
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Matxain JM, Ristilä M, Strid A, Eriksson LA. Theoretical Study of the Antioxidant Properties of Pyridoxine. J Phys Chem A 2006; 110:13068-72. [PMID: 17134167 DOI: 10.1021/jp065115p] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of utmost importance in the living cell. The antioxidative properties of pyridoxine (vitamin B6) have recently been discovered. In this study, we have analyzed the reactivity of pyridoxine toward the ROS (.-)OH, (.-)OOH, and (.-)O(2)- at the density functional theory level (functionals B3LYP and MPW1B95). Two reaction types have been studied as follows: addition to the aromatic ring atoms and hydrogen/proton abstraction. Our results show that (.-)OH is the most reactive species, while (.-)OOH displays low reactivity and (.-)O2(-) does not react at all with pyridoxine. The most exergonic reactions are those where (.-)H is removed from the CH(2)OH groups or the ring-bound OH group and range from -33 to -39 kcal/mol. The most exergonic addition reactions occur by attacking the carbon atoms bonded to nitrogen but with an energy gain of only 6 kcal/mol.
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157
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Matxain JM, Eriksson LA, Mercero JM, Ugalde JM, Spano E, Hamad S, Catlow CRA. Electronic excitation energies of Zn(i)S(i) nanoparticles. NANOTECHNOLOGY 2006; 17:4100-4105. [PMID: 21727544 DOI: 10.1088/0957-4484/17/16/018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The excitation energies of small ZnS nanoclusters characterized in previous studies have been calculated using TDDFT. The relativistic pseudopotentials of Stevens et al have been used, including Zn 4s(2) electrons and S 3s(2) and 3p(4) electrons as valence electrons. Results obtained with these pseudopotentials are compared to those obtained considering also Zn 3s(2)3p(6)3d(10) electrons in the valence part, and demonstrated to be consistent. The results show that spheroid-like bubble structures have absorption energies in the range of 5-5.3 eV for small sizes, which decreases to 5 eV with increasing particle size.
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158
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Ristilä M, Matxain JM, Strid A, Eriksson LA. pH-Dependent Electronic and Spectroscopic Properties of Pyridoxine (Vitamin B6). J Phys Chem B 2006; 110:16774-80. [PMID: 16913817 DOI: 10.1021/jp062800n] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The key electronic and spectroscopic properties of vitamin B(6) (pyridoxine) and some of its main charged and protonated/deprotonated species are explored using hybrid density functional theory (DFT) methods including polarized solvation models. It is found that the dominant species at low pH is the N(1)-protonated form and, at high pH, the O(3)(')-deprotonated compound. Computed and experimental UV-spectra for these species (experimental spectra recorded at pH 1.7 and 11.1, respectively) show a very close resemblance. At pH 4.3, the protonated species dominates, but with onset of the zwitterionic oxo form which is also the dominant species at neutral pH. The computational studies furthermore show that neither a polarized continuum model of the polar aqueous solvent or explicit hydrogen bonding through additional water molecules are sufficient to describe accurately the spectrum at physiological pH. Instead, Na(+) and Cl(-) counterions were required to give a blue-shift of approximately 0.15 eV.
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159
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Abstract
Molecular dynamics simulations have been performed to explore the distribution and translocation of a set of furocoumarins (psoralen derivatives) inside saturated and partially unsaturated lipid membranes. Within the simulations, strong accumulation of the photodynamic drugs is observed near the polar headgroup region, although the populations also extend out into the membrane/water interface as well as to the membrane center. The computed transverse (Dz) diffusion coefficients are in the range 0.01-0.03 x 10(-5) cm2 s(-1)-significantly slower than those reported for small molecules like water, ethane, and ammonia-and are related to the low mobility inside the polar headgroup region. Trimethylpsoralen (TMP) has a very low free energy barrier to transversion, only approximately 10 kJ/mol, whereas 5- and 8-methoxy psoralens (5-MOP, 8-MOP) have the largest barriers of the compounds studied-between 25 and 40 kJ/mol. Upper bounds to the permeation coefficients, obtained by integrating the resistance profiles across the bilayers, range from 5.2 x 10(-8) cm s(-1) for TMP to 4.1 x 10(-12) cm s(-1) for 5-MOP. The current simulations explain the high level of furocoumarin-lipid membrane complexes found in experimental studies of albino Wistar rats exposed to topical application of 8-MOP, and points to the possibility of membrane photodamage as a viable mechanism in psoralen ultraviolet-A treatment.
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160
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Li XY, Eriksson LA. Photoreaction of skin-sensitizing trimethyl psoralen with lipid membrane models. Photochem Photobiol 2006; 81:1153-60. [PMID: 15882092 DOI: 10.1562/2005-03-21-ra-467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The concerted photoreaction between trimethyl psoralen (TMP) and isomeric model compounds of oleic acid methyl ester (OAME) and eadilic acid methyl ester (EAME) are explored using density functional theory. The S(1) surfaces all reveal large barriers (25-31 kcal/mol) to reach the decay channels, whereas the S(2) surfaces differ considerably between the furan and pyrone side adducts. For the pyrone side adducts, a small barrier to reach the intersection between the S(1) and S(2) states is found, followed by a small second barrier on the S(1) surface to the low-lying decay channel. For the furan-side adducts, no such intersection between S(1) and S(2) is seen, which thus prevents these products from being formed in high yields. The photoinduced cycloaddition is more favorable between OAME and the pyrone side double bond of TMP than for any of the other systems, which agrees with the experimental findings that this is formed in the highest yield. The computed UV absorption spectra of TMP and the TMP(pyrone)-OAME cycloadduct agree well with the experimental spectra.
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161
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Mercero JM, Formoso E, Matxain JM, Eriksson LA, Ugalde JM. Sandwich Complexes Based on the “All-Metal” Al42− Aromatic Ring. Chemistry 2006; 12:4495-502. [PMID: 16683278 DOI: 10.1002/chem.200600106] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on novel sandwichlike structures [Al(4)MAl(4)](q-) (q=0-2 and M=Ti, V, Cr, Zr, Nb, Mo, Hf, Ta and W) based on the recently synthesized all-metal aromatic Al(4)(2-) square ring. The sandwichlike structures have two aromatic tetraaluminum square rings which trap a transition-metal cation from either the first, second, or third row. The stability of the anionic sandwichlike complexes towards electron detachment is discussed, and addition of alkali cations is found to stabilize the 2- charged complexes, preventing spontaneous electron detachment. Once the sandwichlike complexes are formed, the Al(4)(2-) square properties remain nearly unchanged; this fact strongly supports the hypothesis that in these complexes the Al(4)(2-) square rings remain aromatic.
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162
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Durbeej B, Eriksson LA. Protein-bound chromophores astaxanthin and phytochromobilin: excited state quantum chemical studies. Phys Chem Chem Phys 2006; 8:4053-71. [PMID: 17028694 DOI: 10.1039/b605682b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an overview of excited state quantum chemical calculations aimed at elucidating controversial issues regarding the photochemistry of the protein-bound chromophores astaxanthin and phytochromobilin. In particular, we show how the application of time-dependent density functional theory and other single-reference quantum chemical excited state methods have contributed to shed new light on the origin of the >0.5 eV bathochromic shift of the electronic absorption by the carotenoid astaxanthin in the protein macromolecular complex crustacyanin, and the mechanism for C15-Z,syn --> C15-E,anti isomerization of the tetrapyrrole phytochromobilin that underlies the photoactivation of the plant photoreceptor phytochrome. Within the approximation that exciton coupling is neglected, the calculations on astaxanthin provide support for the notion that the bathochromic shift, which is responsible for the slate-blue coloration of lobster shell, is due to polarization rather than a conformational change of the chromophore in the protein-bound state. Furthermore, the polarization is attributed to a hydrogen-bonded protonated histidine residue. The calculations on phytochromobilin, in turn, suggest that a stepwise C15-Z,syn --> C15-E,syn (photochemical), C15-E,syn --> C15-E,anti (thermal) mechanism is much more favorable than a concerted, fully photochemical mechanism, and that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form. Accordingly, the calculations indirectly support the view that the photoactivation of phytochrome does not involve a proton transfer from the chromophore to the surrounding protein.
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163
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Cerqueira NMFSA, Fernandes PA, Eriksson LA, Ramos MJ. Dehydration of ribonucleotides catalyzed by ribonucleotide reductase: the role of the enzyme. Biophys J 2005; 90:2109-19. [PMID: 16361339 PMCID: PMC1386789 DOI: 10.1529/biophysj.104.054627] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This article focuses on the second step of the catalytic mechanism for the reduction of ribonucleotides catalyzed by the enzyme Ribonucleotide Reductase (RNR). This step corresponds to the protonation/elimination of the substrate's C-2' hydroxyl group. Protonation is accomplished by the neighbor Cys-225, leading to the formation of one water molecule. This is a very relevant step since most of the known inhibitors of this enzyme, which are already used in the fight against certain forms of cancer, are 2'-substituted substrate analogs. Even though some theoretical studies have been performed in the past, they have modeled the enzyme with minimal gas-phase models, basically represented by a part of the side chain of the relevant amino acids, disconnected from the protein backbone. This procedure resulted in a limited accuracy in the position and/or orientation of the participating residues, which can result in erroneous energetics and even mistakes in the choice of the correct mechanism for this step. To overcome these limitations we have used a very large model, including a whole R1 model with 733 residues plus the substrate and 10 A thick shell of water molecules, instead of the minimal gas-phase models used in previous works. The ONIOM method was employed to deal with such a large system. This model can efficiently account for the restrained mobility of the reactive residues, as well as the long-range enzyme-substrate interactions. The results gave additional information about this step, which previous small models could not provide, allowing a much clearer evaluation of the role of the enzyme. The interaction energy between the enzyme and the substrate along the reaction coordinate and the substrate steric strain energy have been obtained. The conclusion was that the barrier obtained with the present model was very similar to the one previously determined with minimal gas-phase models. Therefore, the role of the enzyme in this step was concluded to be mainly entropic, rather than energetic, by placing the substrate and the two reactive residues in a position that allows for the highly favorable concerted trimolecular reaction, and to protect the enzyme radical from the solvent.
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164
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Durbeej B, Borg OA, Eriksson LA. Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.09.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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165
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Durbeej B, Eriksson LA. Photodegradation of Substituted Stilbene Compounds: What Colors Aging Paper Yellow? J Phys Chem A 2005; 109:5677-82. [PMID: 16833900 DOI: 10.1021/jp050873l] [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: 11/29/2022]
Abstract
Photodegradation of lignin is one of the major postprocessing problems in paper production, as this renders yellowing of the paper and reduced paper quality. In this study, we have explored the photochemical properties of substituted stilbene derivatives believed to be key chromophores in the photodegradation of lignin derived from cinnamyl alcohol. In particular, the present work focuses on the computation of UV/vis electronic absorption spectra for different methoxylated stilbenes and their proposed photodegradation products. All calculations were performed using the time-dependent formalism of density functional theory (TD-DFT) and the B3LYP hybrid functional. It is concluded that the methodology employed is capable of reproducing not only the overall spectra, but also subtle features owing to the effects of different substitution patterns. For the strongly absorbing first excited singlet state (HOMO --> LUMO excitation) of the methoxylated stilbenes, the calculated transition energies are, albeit somewhat fortuitously, in excellent agreement with experimental data. The light-induced yellowing indirectly caused by the presence of stilbenes can be rationalized in terms of the absorption spectra of the resulting photodegraded o-quinones, for which distinct transitions in the 420-500 nm region of the visible spectrum lacking prior to degradation are observed.
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166
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167
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Raber J, Zhu C, Eriksson LA. Theoretical Study of Cisplatin Binding to DNA: The Importance of Initial Complex Stabilization. J Phys Chem B 2005; 109:11006-15. [PMID: 16852341 DOI: 10.1021/jp050057d] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first and second substitution reactions between activated (hydrolyzed) cisplatin, Pt(NH3)2(H2O)2(2+), and purine bases guanine and adenine are explored using the B3LYP hybrid functional, IEF-PCM solvation models, and large basis sets. The computed free energy barrier for the first substitution is 19.5 kcal/mol for guanine (exptl value = 18.3 kcal/mol) and 24.0 kcal/mol for adenine. The observed predominance toward guanine in the first substitution is explained in terms of significantly larger stabilization energy for the initially formed complex, compared with adenine, in combination with favored kinetics, and represents a revised view of the proposed mechanism for cisplatin binding to DNA. For the second substitution, the computed barrier for Pt(NH3)2G2(2+) head-to-head formation is 22.5 kcal/mol, in very good agreement with experimental data for adduct closure (23.4 kcal/mol). Again, a higher stability in complexation with G over A is ascribed as the main contributing factor favoring G over A substitution. The calculations provide a first explanation for the predominance of 1,2-d(GpG) over 1,2-d(ApG) intrastrand didentate adducts, and the origin of the 5'-3' direction specificity of the 1,2-d(ApG) adducts.
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168
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Llano J, Eriksson LA. Response to “Comment on ‘First principles electrochemistry: Electrons and protons reacting as independent ions’ ” [J. Chem. Phys. 122, 087103 (2005)]. J Chem Phys 2005. [DOI: 10.1063/1.1849164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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169
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Li X, Eriksson LA. Influence of C5-methylation of cytosine on the formation of cyclobutane pyrimidine dimers. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.11.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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170
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Cerqueira NMFSA, Fernandes PA, Eriksson LA, Ramos MJ. Ribonucleotide activation by enzyme ribonucleotide reductase: understanding the role of the enzyme. J Comput Chem 2004; 25:2031-7. [PMID: 15481089 DOI: 10.1002/jcc.20127] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This article focuses on the first step of the catalytic mechanism for the reduction of ribonucleotides catalyzed by the enzyme Ribonucleotide Reductase (RNR). This corresponds to the activation of the substrate. In this work a large model of the active site region involving 130 atoms was used instead of the minimal gas phase models used in previous works. The ONIOM method was employed to deal with such a large system. The results gave additional information, which previous small models could not provide, allowing a much clearer evaluation of the role of the enzyme in this step. Enzyme-substrate interaction energies, specific transition state stabilization, and substrate steric strain energies were obtained. It was concluded that the transition state is stabilized in 4.0 kcal/mol by specific enzyme-substrate interactions. However, this stabilization is cancelled by the cost in conformational energy for the enzyme to adopt the transition state geometry; the overall result is that the enzyme machinery does not lead to a rate enhancement in this step. It was also found that the substrate binds to the active site with almost no steric strain, emphasizing the complementarity and specificity of the RNR active site for nucleotide binding. The main role of the enzyme at the very beginning of the catalytic cycle was concluded to be to impose stereospecifity upon substrate activation and to protect the enzyme radical from the solvent, rather than to be an reaction rate enhancement.
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171
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Tejero I, González-Lafont A, Lluch JM, Eriksson LA. Photo-oxidation of lipids by singlet oxygen: a theoretical study. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.09.093] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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172
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Tejero I, Eriksson LA, González-Lafont À, Marquet J, Lluch JM. Hydrogen Abstraction by Soybean Lipoxygenase-1. Density Functional Theory Study on Active Site Models in Terms of Gibbs Free Energies. J Phys Chem B 2004. [DOI: 10.1021/jp040114n] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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173
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Lipfert J, Llano J, Eriksson LA. Radiation-Induced Damage in Serine PhosphateInsights into a Mechanism for Direct DNA Strand Breakage. J Phys Chem B 2004. [DOI: 10.1021/jp037499e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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174
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Llano J, Eriksson LA. Oxidation pathways of adenine and guanine in aqueous solution from first principles electrochemistry. Phys Chem Chem Phys 2004. [DOI: 10.1039/b410922h] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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175
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Llano J, Eriksson LA. First principles electrochemical study of redox events in DNA bases and chemical repair in aqueous solution. Phys Chem Chem Phys 2004. [DOI: 10.1039/b400507d] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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176
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Durbeej B, Anders Borg O, Eriksson LA. Phytochromobilin C15-Z,syn? C15-E,anti isomerization: concerted or stepwise? Phys Chem Chem Phys 2004. [DOI: 10.1039/b411005f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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177
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Durbeej B, Eriksson LA. On the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: why are thymines more reactive? Photochem Photobiol 2003; 78:159-67. [PMID: 12945584 DOI: 10.1562/0031-8655(2003)078<0159:otfocp>2.0.co;2] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The reaction pathways for thermal and photochemical formation of cyclobutane pyrimidine dimers in DNA are explored using density functional theory techniques. Although it is found that the thermal [2 + 2] cycloadditions of thymine + thymine (T + T --> T x T), cytosine + cytosine (C + C --> C x C) and cytosine + thymine (C + T --> C x T) all are similarly unfavorable in terms of energy barriers and reaction energies, the excited-state energy curves associated with the corresponding photochemical cycloadditions display differences that--in line with experimental findings--unanimously point to the predominance of T x T in UV-irradiated DNA. It is shown that the photocycloaddition of thymines is facilitated by the fact that the S1 state of the corresponding reactant complex lies comparatively high in energy. Moreover, at a nuclear configuration coinciding with the ground-state transition structure, the excited-state energy curve displays an absolute minimum only for the T + T system. Finally, the T + T system is also associated with the most favorable excited-state energy barriers and has the smallest S2-S0 energy gap at the ground-state transition structure.
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178
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Durbeej B, Eriksson LA. On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00800-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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179
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Lucas MDF, Fernandes PA, Eriksson LA, Ramos MJ. Pyruvate Formate Lyase: A New Perspective. J Phys Chem B 2003. [DOI: 10.1021/jp0223096] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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180
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Llano J, Raber J, Eriksson LA. Theoretical study of phototoxic reactions of psoralens. J Photochem Photobiol A Chem 2003. [DOI: 10.1016/s1010-6030(02)00351-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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181
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Llano J, Eriksson LA. First principles electrochemistry: Electrons and protons reacting as independent ions. J Chem Phys 2002. [DOI: 10.1063/1.1516786] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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182
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Durbeej B, Eriksson LA. Reaction mechanism of thymine dimer formation in DNA induced by UV light. J Photochem Photobiol A Chem 2002. [DOI: 10.1016/s1010-6030(02)00180-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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183
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Alvarez-Idaboy JR, Eriksson LA, Faengstroem T, Lunell S. Theoretical investigation of the ethene-ethene radical cation addition reaction. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100151a018] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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184
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Eriksson LA, Lunell S, Boyd RJ. Electronic structure calculations of hydrocarbon radical cations: a density functional study. J Am Chem Soc 2002. [DOI: 10.1021/ja00068a055] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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185
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Eriksson LA, Wang J, Boyd RJ, Lunell S. A comparative study of the hyperfine structures of neutral nitrogen oxides: DFT vs CISD results. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100054a014] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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186
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Martell JM, Boyd RJ, Eriksson LA. Hyperfine Structures of the Series C2HnF5-n, n = 0-5: A Density Functional Theory Study. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100002a027] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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187
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Eriksson LA, Lunell S. Ab initio study of vibrationally preferred deuteration sites in the cyclopropane-d2 radical cation. J Am Chem Soc 2002. [DOI: 10.1021/ja00038a013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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188
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Eriksson LA, Sjoeqvist L, Lunell S, Shiotani M, Usui M, Lund A. Effects of ionization in linear alkenes: a study of the radical cations of 1- and 2-pentene. J Am Chem Soc 2002. [DOI: 10.1021/ja00061a024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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189
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Alvarez-Idaboy JR, Eriksson LA, Lunell S. Theoretical study of reactions of the 1-butene radical cation in frozen halocarbon matrixes. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100151a019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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190
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Wang J, Eriksson LA, Boyd RJ, Shi Z, Johnson BG. Diazasilene (SiNN): a comparative study of electron density distributions derived from Hartree-Fock, second-order Moller-Plesset perturbation theory, and density functional methods. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100058a021] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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191
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Ban F, Lundqvist MJ, Boyd RJ, Eriksson LA. Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine. J Am Chem Soc 2002; 124:2753-61. [PMID: 11890827 DOI: 10.1021/ja011528m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-protein cross-linking is one of the many DNA lesions mediated by hydroxyl radicals, the most damaging among the reactive oxygen species in biological systems. Density functional theory methods are employed to investigate the complex reaction mechanisms of the formation of cytosine-tyrosine cross-links as observed in gamma-irradiated aqueous solutions of cytosine and tyrosine, as well as in gamma-irradiated nucleohistone. The majority of the radical addition mechanisms considered are found to have significant barriers and therefore to be thermodynamically unfavorable for the formation of the initial cross-linked product. Our calculated reaction potential energy surfaces suggest that a feasible complete mechanism consists of radical combination forming the initial cross-linked product, a hydrogen shuffle within the initial cross-linked product, and an acid-catalyzed dehydration reaction. Water and hydrogen-bonding interactions are suggested to play a key role in catalyzing the hydrogen-transfer step of the reaction.
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192
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Durbeej B, Eriksson LA. Thermodynamics of the Photoenzymic Repair Mechanism Studied by Density Functional Theory. J Am Chem Soc 2000. [DOI: 10.1021/ja000929j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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193
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Lassmann G, Eriksson LA, Lendzian F, Lubitz W. Structure of a Transient Neutral Histidine Radical in Solution: EPR Continuous-Flow Studies in a Ti3+/EDTA−Fenton System and Density Functional Calculations. J Phys Chem A 2000. [DOI: 10.1021/jp001437w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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194
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Close DM, Eriksson LA, Hole EO, Sagstuen E, Nelson WH. Experimental and Theoretical Investigation of the Mechanism of Radiation-Induced Radical Formation in Hydrogen-Bonded Cocrystals of 1-Methylcytosine and 5-Fluorouracil. J Phys Chem B 2000. [DOI: 10.1021/jp0018246] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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195
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Himo F, Eriksson LA, Maseras F, Siegbahn PEM. Catalytic Mechanism of Galactose Oxidase: A Theoretical Study. J Am Chem Soc 2000. [DOI: 10.1021/ja994527r] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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196
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Wetmore SD, Boyd RJ, Eriksson LA. Electron affinities and ionization potentials of nucleotide bases. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00391-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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197
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198
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Lundqvist MJ, Eriksson LA. Hydroxyl Radical Reactions with Phenol as a Model for Generation of Biologically Reactive Tyrosyl Radicals. J Phys Chem B 2000. [DOI: 10.1021/jp993011r] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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199
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Himo F, Babcock GT, Eriksson LA. Tyrosyl radical in galactose oxidase not strongly perturbed by cysteine cross-link. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)00906-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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200
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Wetmore SD, Boyd RJ, Eriksson LA, Laaksonen A. A combined quantum mechanics and molecular dynamics study of small Jahn–Teller distorted hydrocarbons: Another difficult test for density-functional theory. J Chem Phys 1999. [DOI: 10.1063/1.479141] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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