Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.     

G-tensors of the flavin adenine dinucleotide radicals in glucose oxidase: a comparative multifrequency electron paramagnetic resonance and electron-nuclear double resonance study

The flavin adenine dinucleotide (FAD) cofactor of Aspergillus niger glucose oxidase (GO) in its anionic (FAD*-) and neutral (FADH*) radical form was investigated by electron paramagnetic resonance (EPR) at high microwave frequencies (93.9 and 360 GHz) and correspondingly high magnetic fields and by pulsed electron-nuclear double resonance (ENDOR) spectroscopy at 9.7 GHz. Because of the high spectral resolution of the frozen-solution continuous-wave EPR spectrum recorded at 360 GHz, the anisotropy of the g-tensor of FAD*- could be fully resolved. By least-squares fittings of spectral simulations to experimental data, the principal values of g have been established with high precision: gX=2.00429(3), gY=2.00389(3), gZ=2.00216(3) (X, Y, and Z are the principal axes of g) yielding giso=2.00345(3). The gY-component of FAD*- from GO is moderately shifted upon deprotonation of FADH*, rendering the g-tensor of FAD*- slightly more axially symmetric as compared to that of FADH*. In contrast, significantly altered proton hyperfine couplings were observed by ENDOR upon transforming the neutral FADH* radical into the anionic FAD*- radical by pH titration of GO. That the g-principal values of both protonation forms remain largely identical demonstrates the robustness of g against local changes in the electron-spin density distribution of flavins. Thus, in flavins, the g-tensor reflects more global changes in the electronic structure and, therefore, appears to be ideally suited to identify chemically different flavin radicals.     

Electron magnetic resonance and density functional theory study of room temperature X-irradiated β-D-fructose single crystals

Stable free radical formation in fructose single crystals X-irradiated at room temperature was investigated using Q-band electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three main crystallographic planes allowed an unambiguous determination of 12 proton HFC tensors. From the EIE studies, these hyperfine interactions were assigned to six different radical species, labeled F1-F6. Two of the radicals (F1 and F2) were studied previously by Vanhaelewyn et al. [Vanhaelewyn, G. C. A. M.; Pauwels, E.; Callens, F. J.; Waroquier, M.; Sagstuen, E.; Matthys, P. J. Phys. Chem. A 2006, 110, 2147.] and Tarpan et al. [Tarpan, M. A.; Vrielinck, H.; De Cooman, H.; Callens, F. J. J. Phys. Chem. A 2009, 113, 7994.]. The other four radicals are reported here for the first time and periodic density functional theory (DFT) calculations were used to aid their structural identification. For the radical F3 a C3 carbon centered radical with a carbonyl group at the C4 position is proposed. The close similarity in HFC tensors suggests that F4 and F5 originate from the same type of radical stabilized in two slightly different conformations. For these radicals a C2 carbon centered radical model with a carbonyl group situated at the C3 position is proposed. A rather exotic C2 centered radical model is proposed for F6.     

Catalytic Amine Oxidation under Ambient Aerobic Conditions: Mimicry of Monoamine Oxidase B

The flavoenzyme monoamine oxidase (MAO) regulates mammalian behavioral patterns by modulating neurotransmitters such as adrenaline and serotonin. The mechanistic basis which underpins this enzyme is far from agreed upon. Reported herein is that the combination of a synthetic flavin and alloxan generates a catalyst system which facilitates biomimetic amine oxidation. Mechanistic and electron paramagnetic (EPR) spectroscopic data supports the conclusion that the reaction proceeds through a radical manifold. This data provides the first example of a biorelevant synthetic model for monoamine oxidase B activity.     

Engineering the properties of D-amino acid oxidases by a rational and a directed evolution approach

D-amino acid oxidase (DAAO) is a FAD-containing flavoprotein that dehydrogenates the D-isomer of amino acids to the corresponding imino acids, coupled with the reduction of FAD. The cofactor then reoxidizes on molecular oxygen and the imino acid hydrolyzes spontaneously to the alpha-keto acid and ammonia. In vitro DAAO displays broad substrate specificity, acting on several neutral and basic D-amino acids: the most efficient substrates are amino acids with hydrophobic side chains. D-aspartic acid and D-glutamic acid are not substrates for DAAO. Through the years, it has been the subject of a number of structural, functional and kinetic investigations. The most recent advances are represented by site-directed mutagenesis studies and resolution of the 3D-structure of the enzymes from pig, human and yeast. The two approaches have given us a deeper understanding of the structure-function relationships and promoted a number of investigations aimed at the modulating the protein properties. By a rational and/or a directed evolution approach, DAAO variants with altered substrate specificity (e.g., active on acidic or on all D-amino acids), increased stability (e.g., stable up to 60 degrees C), modified interaction with the flavin cofactor, and altered oligomeric state were produced. The aim of this paper is to provide an overview of the most recent research on the engineering of DAAOs to illustrate their new intriguing properties, which also have enabled us to pursue new biotechnological applications.     

Direct electron transfer in immobilized flavoenzyme chemically modified graphite electrodes

Direct electron transfer between covalently immobilized flavoenzymes and a cyanuric chloride-modified graphite electrode is observed via differential pulse voltammetry. L-Amino acid oxidase and xanthine oxidase display peaks arising from the reduction of flavin adenine dinucleotide. Peak current enhancements are observed for both covalently attached enzymes compared to their free and adsorbed state voltammograms. Studies concerning flavin removal and reconstitution indicate that xanthine oxidase contains multiple flavin chromophores which are nonequivalent.     

Radical quantum yields from formaldehyde photolysis in the 30,400-32,890 cm(-1) (304-329 nm) spectral region: detection of radical photoproducts using pulsed laser photolysis-pulsed laser induced fluorescence

The relative quantum yield for the production of radical products, H + HCO, from the UV photolysis of formaldehyde (HCHO) has been measured using a pulsed laser photolysis–pulsed laser induced fluorescence (PLP–PLIF) technique across the 30,400–32,890 cm(–1) (304–329 nm) spectral region of the ?(1)A2–X?(1)A1 electronic transition. The photolysis laser had a bandwidth of 0.09 cm(–1), which is slightly broader than the Doppler width of a rotational line of formaldehyde at 300 K (0.07 cm(–1)), and the yield spectrum shows detailed rotational structure. The H and HCO photofragments were monitored using LIF of the OH radical as a spectroscopic marker. The OH radicals were produced by rapid reaction of the H and HCO photofragments with NO2. This technique produced an “action” spectrum that at any photolysis wavelength is the product of the H + HCO radical quantum yield and HCHO absorption cross section at the photolysis wavelength and is a relative measurement. Using the HCHO absorption cross section previously obtained in this laboratory, the relative quantum yield was determined two different ways. One produced band specific yields, and the other produced yields averaged over each 100 cm(–1). Yields were normalized to a value of 0.69 at 31,750 cm(–1) based on the current recommendation of Sander et al. (Sander, S. P.; Abbatt, J.; Barker, J. R.; Burkholder, J. B.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Moortgat, G. K.; et al. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 17; Jet Propulsion Laboratory: Pasadena, CA, USA, 2011). The resulting radical quantum yields agree well with previous experimental studies and the current JPL recommendation but show greater wavelength dependent structure. A significant decrease in the quantum yield was observed for the 5(0)(1) + 1(0)(1)4(0)(1) combination band centered at 31,125 cm(–1). This band has a low absorption cross section and has little impact on the calculated atmospheric photodissociation rate but is a further indication of the complexity of HCHO photodissociation dynamics.     

Unambiguous determination of the g-matrix orientation in a neutral flavin radical by pulsed electron-nuclear double resonance at 94 GHz

The recent observation of photoinduced radical pairs comprising a flavin radical and an oxidized amino acid residue in various blue-light-sensitive proteins has highlighted the need to gain a more complete understanding of the electronic structure of flavin radicals. In particular, precise knowledge of the anisotropy of the Zeeman interaction quantified by the g-tensor is necessary for attaining an unambiguous identification of flavin radicals by electron paramagnetic resonance (EPR). In a recent study of a protein-bound neutral flavin radical, we have determined the principal values of the g-tensor using high-frequency/high magnetic field EPR performed at 360 GHz/12.8 T. However, in those experiments, the orientation of the principal axes of g could not be unambiguously established with respect to the molecular frame of the isoalloxazine moiety. In this contribution we resolve this ambiguity by pulsed electron-nuclear double resonance (ENDOR) at 95 GHz/3.5 T (W-band). At such high values of the microwave frequency and the magnetic field, the g anisotropy provides improved spectral resolution compared to an ENDOR experiment performed at conventional 9.5 GHz/0.35 mT (X-band). This enables one to utilize Zeeman magnetoselection to obtain single-crystal-like data from disordered samples in frozen solution. Experiments exploiting this orientation selection have allowed us to use the hyperfine coupling of the methyl protons at C(8alpha) of the isoalloxazine ring to determine the angle between the molecular frame and the principal axes of g. Quite surprisingly, the g-tensor in FADH* is not oriented as one would have expected for a 1,3-semibenzoquinone radical. For the latter, the X-axis of g commonly bisects the smaller angle between the two axes along the C=O bonds. In FADH*, the large spin density on N(5) and C(4a) apparently contributes to a significant (44 degrees ) reorientation of the g-tensor axes.     

X- and W-band EPR and Q-band ENDOR studies of the flavin radical in the Na+ -translocating NADH:quinone oxidoreductase from Vibrio cholerae

Na(+)-NQR is the entry point for electrons into the respiratory chain of Vibrio cholerae. It oxidizes NADH, reduces ubiquinone, and uses the free energy of this redox reaction to translocate sodium across the cell membrane. The enzyme is a membrane complex of six subunits that accommodates a 2Fe-2S center and several flavins. Both the oxidized and reduced forms of Na(+)-NQR exhibit a radical EPR signal. Here, we present EPR and ENDOR data that demonstrate that, in both forms of the enzyme, the radical is a flavin semiquinone. In the oxidized enzyme, the radical is a neutral flavin, but in the reduced enzyme the radical is an anionic flavin, where N(5) is deprotonated. By combining results of ENDOR and multifrequency continuous wave EPR, we have made an essentially complete determination of the g-matrix and all major nitrogen and proton hyperfine matrices. From careful analysis of the W-band data, the full g-matrix of a flavin radical has been determined. For the neutral radical, the g-matrix has significant rhombic character, but this is significantly decreased in the anionic radical. The out-of-plane component of the g-matrix and the nitrogen hyperfine matrices are found to be noncoincident as a result of puckering of the pyrazine ring. Two possible assignments of the radical signals are considered. The neutral and anionic forms of the radical may each arise from a different flavin cofactor, one of which is converted from semiquinone to flavohydroquinone, while the other goes from flavoquinone to semiquinone, at almost exactly the same redox potential, during reduction of the enzyme. Alternatively, both forms of the radical signal may arise from a single, extremely stable, flavin semiquinone, which becomes deprotonated upon reduction of the enzyme.     

A comparative computational investigation on the proton and hydride transfer mechanisms of monoamine oxidase using model molecules

Monoamine oxidase (MAO) enzymes regulate the level of neurotransmitters by catalyzing the oxidation of various amine neurotransmitters, such as serotonin, dopamine and norepinephrine. Therefore, they are the important targets for drugs used in the treatment of depression, Parkinson, Alzeimer and other neurodegenerative disorders. Elucidation of MAO-catalyzed amine oxidation will provide new insights into the design of more effective drugs. Various amine oxidation mechanisms have been proposed for MAO so far, such as single electron transfer mechanism, polar nucleophilic mechanism and hydride mechanism. Since amine oxidation reaction of MAO takes place between cofactor flavin and the amine substrate, we focus on the small model structures mimicking flavin and amine substrates so that three model structures were employed. Reactants, transition states and products of the polar nucleophilic (proton transfer), the water-assisted proton transfer and the hydride transfer mechanisms were fully optimized employing various semi-empirical, ab initio and new generation density functional theory (DFT) methods. Activation energy barriers related to these mechanisms revealed that hydride transfer mechanism is more feasible.     

Analysis of monoamine oxidase enzymatic activity by reversed-phase high performance liquid chromatography and inhibition by beta-carboline alkaloids occurring in foods and plants

Monoamine oxidase (MAO) is a flavin adenine dinucleotide (FAD)-containing enzyme located at the outer membranes of mitochondria that catalyzes the oxidative deamination of biogenic and xenobiotic amines. We have used a chromatographic method to measure MAO-enzymatic activity by using kynuramine as a non-selective substrate with its MAO-oxidation product subsequently analyzed by RP-HPLC-DAD and HPLC-mass spectrometry (MS). This method was applied to study the kinetic parameters, inhibition and reaction products of MAO recombinant enzymes in presence of tetrahydro-beta-carboline and beta-carboline alkaloids occurring in foods, plants and mammals. Analysis by HPLC showed that tetrahydro-beta-carbolines or beta-carbolines were not modified by MAO. Several beta-carbolines such as tryptoline (1,2,3,4-tetrahydro-beta-carboline) and 1-methyltryptoline (1-methyl-1,2,3,4-tetrahydro-beta-carboline) were inhibitors of MAO-A; instead their corresponding 6-hydroxy-derivatives (6-hydroxytryptoline and 6-hydroxy-1-methyltryptoline) lacked this activity. Tetrahydro-beta-carboline-3-carboxylic acids were unable to inhibit MAO enzymes. In contrast, their oxidation products, i.e. the fully aromatic beta-carbolines (norharman and harman), acted as good inhibitors of MAO. Two tetrahydro-beta-carbolines (i.e. tryptoline and 1-methyltryptoline) occurring in foods were isolated by solid-phase extraction (SPE) and RP-HPLC from selected samples of sausages and the corresponding extracts exhibited good inhibition properties over MAO-A. These results suggest that beta-carbolines from foods, plants, and mammals may exert inhibitory actions on MAO enzymes.     

Structure of the charge separated state P865(+)Q(A)- in the photosynthetic reaction centers of Rhodobacter sphaeroides by quantum beat oscillations and high-field electron paramagnetic resonance: evidence for light-induced Q(A)- reorientation

The structure of the secondary radical pair, P865(+)Q(A)-, in fully deuterated and Zn-substituted reaction centers (RCs) of the purple bacterium Rhodobacter sphaeroides R-26 has been determined by high-time resolution and high-field electron paramagnetic resonance (EPR). A computer analysis of quantum beat oscillations, observed in a two-dimensional Q-band (34 GHz) EPR experiment, provides the orientation of the various magnetic tensors of P865(+)Q(A)- with respect to a magnetic reference frame. The orientation of the g-tensor of P865(+) in an external reference system is adapted from a single-crystal W-band (95 GHz) EPR study [Klette, R.; T?rring, J. T.; Plato, M.; M?bius, K.; B?nigk, B.; Lubitz, W. J. Phys. Chem. 1993, 97, 2015-2020]. Thus, we obtain the three-dimensional structure of the charge separated state P865(+)Q(A)- on a nanosecond time scale after light-induced charge separation. Comparison with crystallographic data reveals that the position of the quinone is essentially the same as that in the X-ray structure. However, the head group of Q(A)- has undergone a 60 degrees rotation in the ring plane relative to its orientation in the crystal structure. Analysis suggests that the two different QA conformations are functionally relevant states which control the electron-transfer kinetics from Q(A)- to the secondary quinone acceptor QB. It appears that the rate-limiting step of this reaction is a reorientation of Q(A)- in its binding pocket upon light-induced reduction. The new kinetic model accounts for striking observations by Kleinfeld et al. who reported that electron transfer from Q(A)- to QB proceeds in RCs cooled to cryogenic temperature under illumination but does not proceed in RCs cooled in the dark [Kleinfeld, D.; Okamura, M. Y.; Feher, G. Biochemistry 1984, 23, 5780-5786].     

Ring current effects in the active site of medium-chain Acyl-CoA dehydrogenase revealed by NMR spectroscopy

Medium-chain acyl-CoA dehydrogenase (MCAD) catalyzes the flavin-dependent oxidation of fatty acyl-CoAs to the corresponding trans-2-enoyl-CoAs. The interaction of hexadienoyl-CoA (HD-CoA), a product analogue, with recombinant pig MCAD (pMCAD) has been studied using (13)C NMR and (1)H-(13)C HSQC spectroscopy. Upon binding to oxidized pMCAD, the chemical shifts of the C1, C2, and C3 HD carbons are shifted upfield by 12.8, 2.1, and 13.8 ppm, respectively. In addition, the (1)H chemical shift of the C3-H is also shifted upfield by 1.31 ppm while the chemical shift of the C4 HD-CoA carbon is unchanged upon binding. These changes in chemical shift are unexpected given the results of previous Raman studies which revealed that the C3=C2-C1=O HD enone fragment is polarized upon binding to MCAD such that the electron density at the C3 and C1 carbons is reduced, not increased (Pellet et al. Biochemistry 2000, 39, 13982-13992). To investigate the apparent discrepancy between the NMR and Raman data for HD-CoA bound to MCAD, (13)C NMR spectra have been obtained for HD-CoA bound to enoyl-CoA hydratase, an enzyme system that has also previously been studied using Raman spectroscopy. Significantly, binding to enoyl-CoA hydratase causes the chemical shifts of the C1 and C3 HD carbons to move downfield by 4.8 and 5.6 ppm, respectively, while the C2 resonance moves upfield by 2.2 ppm, in close agreement with the alterations in electron density at these carbons predicted from Raman spectroscopy (Bell, A. F.; Wu, J.; Feng, Y.; Tonge, P. J. Biochemistry 2001, 40, 1725-33). The large increase in shielding experienced by the C1 and C3 HD carbons in the HD-CoA/MCAD complex is proposed to arise from the ring current field from the isoalloxazine portion of the flavin cofactor. The flavin ring current, which is only present when the enzyme is placed in an external magnetic field, also explains the differences in (13)C NMR chemical shifts for acetoacetyl-CoA when bound as an enolate to MCAD and enoyl-CoA hydratase and is used to rationalize the observation that the line widths of the C1 and C3 resonances are narrower when the ligands are bound to MCAD than when they are free in the protein solution.     

Pulsed EPR/ENDOR characterization of perturbations of the Cu(A) center ground state by axial methionine ligand mutations.

The effect of axial ligand mutation on the Cu(A) site in the recombinant water soluble fragment of subunit II of Thermus thermophilus cytochrome c oxidase ba(3) has been investigated. The weak methionine ligand was replaced by glutamate and glutamine which are stronger ligands. Two constructs, M160T0 and M160T9, that differ in the length of the peptide were prepared. M160T0 is the original soluble fragment construct of cytochrome ba(3) that encodes 135 amino acids of subunit II, omitting the transmembrane helix that anchors the domain in the membrane. In M160T9 nine C-terminal amino acids are missing, including one histidine. The latter has been used to reduce the amount of a secondary T2 copper which is most probably coordinated to a surface histidine in M160T0. The changes in the spin density in the Cu(A) site, as manifested by the hyperfine couplings of the weakly and strongly coupled nitrogens, and of the cysteine beta-protons, were followed using a combination of advanced EPR techniques. X-band ( approximately 9 GHz) electron-spin-echo envelope modulation (ESEEM) and two-dimensional (2D) hyperfine sublevel correlation (HYSCORE) spectroscopy were employed to measure the weakly coupled (14)N nuclei, and X- and W-band (95 GHz) pulsed electron-nuclear double resonance (ENDOR) spectroscopy for probing the strongly coupled (14)N nuclei and the beta-protons. The high field measurements were extremely useful as they allowed us to resolve the T2 and Cu(A) signals in the g( perpendicular) region and gave (1)H ENDOR spectra free of overlapping (14)N signals. The effects of the M160Q and M160E mutations were: (i) increase in A( parallel)((63,65)Cu), (ii) larger hyperfine coupling of the weakly coupled backbone nitrogen of C153, (iii) reduction in the isotropic hyperfine interaction, a(iso), of some of the beta-protons making them more similar, (iv) the a(iso) value of one of the remote nitrogens of the histidine residues is decreased, thus distinguishing the two histidines, and finally, (v) the symmetry of the g-tensor remained axial. These effects were associated with an increase in the Cu-Cu distance and subtle changes in the geometry of the Cu(2)S(2) core which are consistent with the electronic structural model of Gamelin et al. (Gamelin, D. R.; Randall, D. W.; Hay, M. T.; Houser, R. P.; Mulder, T. C.; Canters, G. W.; de Vries, S.; Tolman, W. B.; Lu, Y.; Solomon, E. I. J. Am. Chem. Soc. 1998, 120, 5246-5263).     

Determination of the distance between the two neutral flavin radicals in augmenter of liver regeneration by pulsed ELDOR

Pulsed electron-electron double resonance (ELDOR) has been used to obtain structural information from a FAD-dependent sulfhydryl oxidase, Augmenter of Liver Regeneration (ALR). ALR is a homodimer with each subunit containing a noncovalently bound FAD cofactor. Both FADs may be converted into the blue neutral radical form by aerobic treatment with DTT. From three-pulse and four-pulse ELDOR experiments, a distance of 26.1 +/- 0.8 A could be determined between the FAD cofactors in human ALR. Taking into account the electron spin density distribution in a neutral flavin radical obtained from density functional theory calculations, a distance of 26.9 A could be estimated for the separation of the spin centers in the X-ray structure of rat ALR. The good agreement confirms that rat ALR may be used as a model for mechanistic discussions of human ALR. The experiments also demonstrate that neutral flavin radicals have the appropriate properties to be used as intrinsic spin labels for distance determinations in proteins.     

The reaction OH + C2H4: an example of rotational channel switching

The low-temperature data for the reaction between OH and C(2)H(4) is treated canonically as either a two-well or one-well problem using the "Multiwell" suite of codes, in which a "well" refers to a minimum in the potential energy surface. The former is analogous to the two transition state model of Greenwald et al. [Greenwald, E. E.; North, S. W.; Georgievskii, Y.; Klippenstein, S. J. J. Phys. Chem. A2005, 109, 6031], while the latter reflects the dominance of the so-called "inner transition state". External rotations are treated adiabatically, causing changes in the magnitude of effective barriers as a function of temperature. Extant data are well-described with either model using only the average energy transferred in a downward direction, upon collision, ΔE(d)(T), as a fitting parameter. The best value for the parameters describing the rate coefficient as a function of temperature (200 < T/K < 400) (Data at lower temperature is too sparse to yield a recommendation.) and pressure in the form used in the NASA/JPL format [Sander, S. P.; Abbatt, J.; Barker, J. R.; Burkholder, J. B.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Moortgat, G. K et al., Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 17, Jet Propulsion Laboratory, 2011] are k(0) = 1.0 × 10(-28)(T/300)(-3.5) cm(6) molecule(-2) s(-1) and k(∞) to 8.0 × 10(-12)(T/300)(-2.3) cm(3) molecule(-1) s(-1).     

Formation and stabilization model of the 42-mer Abeta radical: implications for the long-lasting oxidative stress in Alzheimer's disease

Amyloid fibrils mainly consist of 40-mer and 42-mer peptides (Abeta40, Abeta42). Abeta42 is believed to play a crucial role in the pathogenesis of Alzheimer's disease because its aggregative ability and neurotoxicity are considerably greater than those of Abeta40. The neurotoxicity of Abeta peptides involving the generation of free radicals is closely related to the S-oxidized radical cation of Met-35. However, the cation's origin and mechanism of stabilization remain unclear. Recently, structural models of fibrillar Abeta42 and Abeta40 based on systematic proline replacement have been proposed by our group [Morimoto, A.; et al. J. Biol. Chem. 2004, 279, 52781] and Wetzel's group [Williams, A. D.; et al. J. Mol. Biol. 2004, 335, 833], respectively. A major difference between these models is that our model of Abeta42 has a C-terminal beta-sheet region. Our biophysical study on Abeta42 using electron spin resonance (ESR) suggests that the S-oxidized radical cation of Met-35 could be generated by the reduction of the tyrosyl radical at Tyr-10 through a turn structure at positions 22 and 23, and stabilized by a C-terminal carboxylate anion through an intramolecular beta-sheet at positions 35-37 and 40-42 to form a C-terminal core that would lead to aggregation. A time-course analysis of the generation of radicals using ESR suggests that stabilization of the radicals by aggregation might be a main reason for the long-lasting oxidative stress of Abeta42. In contrast, the S-oxidized radical cation of Abeta40 is too short-lived to induce potent neurotoxicity because no such stabilization of radicals occurs in Abeta40.     

From homogeneous dispersion to micelles-a molecular dynamics simulation on the compromise of the hydrophilic and hydrophobic effects of sodium dodecyl sulfate in aqueous solution

The structural and functional diversity of surfactant systems has attracted simulation works in atomistic, coarse grain, and mesoscopic models (Bandyopadhyay, S.; et al. Langmuir 2000, 16, 942; Senapati, S.; et al. J. Phys. Chem. B 2003, 107, 12906; Maiti, P. K.; et al. Langmuir 2002, 18, 1908; Srinivas, G.; et al. J. Phys. Chem. B 2004, 108, 8153; Groot, R. D.; et al. J. Chem. Phys. 1999, 110, 9739; Rekvig, L.; et al. Langmuir 2003, 19, 8195). However, atomistic models have suffered from their tremendous computational cost and are, so far, not able to simulate the structural behaviors in sufficient spatio-temporal scales (Shelley, J. C.; Shelley, M. Y. Curr. Opin. Colloid Interface Sci. 2000, 5, 101). The other two approaches are not microscopic enough to describe the configurations of the surfactants that determine their behaviors (Shelley and Shelley). In this study, we propose to simplify atomistic models based on the observation that the compromise of the hydrophilic and hydrophobic effects (Li, J.; Kwauk, M. Chem. Eng. Sci. 2003, 58, 521-535) and molecular structures of surfactants are the dominant factors shaping their structures in the systems. With this simplification, we are able to simulate with moderate computing cost the whole process of micelle formation from an initially uniform dispersion of sodium dodecyl sulfate (SDS) in aqueous solution. The resulting micelle structures are different from those predicted by atomistic simulations that started with a predefined micelle configuration at the same surfactant concentrations. However, if we use their initial micelle configuration, micelle structures the same as theirs are obtained. Analyses show that our results are more realistic and that the results of the atomistic simulations suffer from artificial initial conditions. Therefore, our model may serve as a reasonable simplification of atomistic models in terms of the general structure of micelles.