Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.     

Hydroxamic acid polymers

A polymer bearing hydroxamic acid groups and having a high affinity for iron(III) was prepared through the following procedure. Acryloylalanine (III), prepared by the reaction of acryloyl chloride with alanine, was treated with N-hydroxysuccinimide in the presence of dicyclohexylcarbodiimide to give the N-hydroxysuccinimide ester (IV). The ester IV was polymerized by using AIBN in dioxane to give polymer V. Treatment of polymer V with methylhydroxylamine in DMF gave the hydroxamic acid polymer II. The water-soluble polymer II was purified by dialysis or by gel-permeation chromatography (GPC) on Sephadex G-25. Analytical GPC on Sephadex G-200 and Sepharose 4B indicate that the average molecular weight of the polymer is in the range of 5 × 10⁵ to 1 × 10⁶. The presence of hydroxamic acid groups is confirmed by the intense red-brown color produced by the addition of iron(III) to a 50% aqueous DMF solution of the polymer under acidic conditions. In pure water the polymer-iron complex precipitates as a tan solid. Iron-binding studies of the polymer reveal that the iron(III) trihydroxamic acid complex FeA₃ forms at low concentrations of iron. At higher iron levels a lower order of stability is apparent, which can be accounted for by the conversion of FeA₃ to FeA₂⁺. In contrast, the FeA₃ complex of the trihydroxamic acid deferoxamine-B is stable at all iron levels. These results are consistent with the polymer structure, which for steric reasons would favor a stable complex, FeA₂⁺, between iron and two adjacent hydroxamic acid groups. An FeA₃ complex would be expected to have a lower stability as a result of either bond angle strain and atomic compression, or a lower probability in bringing a third hydroxamic acid into position to form the octahedral complex.     

Luminescent properties of PP and LDPE films and rods doped with the Eu(III)‐La(III) complex

The work is devoted to luminescent properties of trivalent lanthanide complexes dispersed in thermoplastic host matrices. Polyethylene films and polypropylene‐rods, both doped with these complexes, were manufactured using an extrusion technique. Two kinds of dopants were used: Eu(III)‐thenoyltrifluoroacetone‐1,10‐phenanthroline complex (1) and Eu(III)‐La(III)‐1,10‐phenanthroline complex (2). Absorption, excitation, emission spectra and lifetime of luminescence were studied. The impact of the polymer matrix on the emission spectra was investigated. Emission spectra of the films were studied at room and helium temperatures. Time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) surface mapping showed that in the Eu(III)‐La(III) complex europium forms islands (clusters) with a dimension of 1 µm, whereas lanthanum was dispersed more uniformly in the polymer matrix. Dependence of emission intensity on the excitation was determined. Copyright © 2006 John Wiley & Sons, Ltd.     

Triiron and Triruthenium Carbonyl Clusters Bearing Bridging Long Chain Diphosphine and Capping Chalcogenido Ligands

Treatment of Ru₃(CO)₁₂ with dpphSe₂ (dpph = 1,6-bis(diphenylphosphino)hexane) in refluxing toluene in the presence of Me₃NO afforded two new compounds, Ru₃(CO)₇(-CO)(₃-Se)(-dpph) (1) and Ru₃(CO)₇(₃-Se)₂(-dpph) (2). A similar reaction of Ru₃(CO)₁₂ with dpppeSe₂ (dpppe = 1,5-bis(diphenylphosphino)pentane) gave exclusively Ru₃(CO)₇(₃-Se)₂(-dpppe) (3). Treatment of Ru₃(CO)₁₂ with dpphS₂ and dpppeS₂ at 110°C in the presence of Me₃NO afforded Ru₃(CO)₇(₃-S)₂(-dpph) (4) and Ru₃(CO)₇(₃-S)₂(-dpppe) (5), respectively. Reactions of Fe₃(CO)₁₂ with dpphSe₂ and dpppeSe₂, under identical conditions, afforded Fe₃(CO)₇(₃-Se)₂(-dpph) (6) and Fe₃(CO)₇(₃-Se)₂(-dpppe) (7), respectively. Compounds 1–7 were characterized spectroscopically and the molecular structures of compounds 1–4 were determined by single crystal X-ray crystallography. The core of 1 contains an equilateral triangle of ruthenium atoms with one capping selenium, one bridging dpph, one doubly bridging carbonyl and seven terminal carbonyl ligands. Complexes 2–4 have a square-pyramidal structure with two metal and two chalcogenide atoms alternating in the basal plane and the third metal atom at the apex of the pyramid, and belong to the family of well-known nido clusters with seven skeletal electron pairs.     

An MO study of regioselective amine addition to ortho-quinones relevant to melanogenesis

Energy profiles for alternative intramolecular cyclisations of 4-(aminoalkyl)-ortho-quinones have been calculated using the AM1 method and ab initio energies of the transition states are determined. In all the cases cyclisation at position 5 occurs via a significantly lower energy transition state than cyclisation at position 3. This is consistent with experimental observations. Optimal trajectories for attack have been determined from a study of the reactions of methylamine with 4-methyl-ortho-quinone. For cyclisation of aminoalkyl derivatives deviation from the optimal direction is less for reaction at position 5 but constraint on angle of attack only partially accounts for the regioselectivity. Intrinsic differences in the electronic energies of the alternative transition states are the main contributor to regioselectivity. The relative energies of transition states can be modified by variation of the substituent at position 4. The calculations suggest that seven-membered ring formation may occur via a boat transition state and steric hindrance in the seven-membered transition states may account for the experimentally observed influence of N-substituents on the mode of reaction.     

ACTION SPECTRUM FOR SUBLIMINAL LIGHT CONTROL OF ADAPTATION IN Phycomyces PHOTOTROPISM

Abstract -Adaptation processes enable phototropism and other blue light responses of Phycomyces to operate over a 10-decade range of Ruencc rate. Phototropic latency, used routinely to monitor the kinetics of sensitivity recovery after a step down in fluence rate, can be shortened by application of dim light for 35 min during the early part of the latency period. This light is termed subliminal , because it does not elicit phototropism under these experimental conditions; rather, it exerts its influence on the underlying adaptation kinetics. Fluence rate-response data for this latency reduction, obtained at 17 wavelengths of subliminal light from 347 to 742 nm, showed a variety of shapes that could be fit by zero, one, or two sigmoidal components, plus a constant term. At most wavelengths, the fluence-rate threshold for latency reduction by subliminal light tended to be well below the absolute threshold for phototropism, indicating that this effect is highly sensitive. An action spectrum for the sensitivity of the subliminal light effect, derived from the fluence rate-response curves, shows major peaks around 400 and 500 nm and a broad band from 570 to 670 nm, followed by a steep absorption edge. The sensitivity in the near ultraviolet region is relatively very low. The magnitude of the latency reduction also depends strongly on wavelength with a maximum at about 450 nm. The Huence-rate response data and the action spectrum–which is markedly different from that for phototropism and other blue-light responses of Phycornyces – indicate the participation of multiple pigments, or pigment states, in the photocontrol of adaptation.     

S-oxygenation of thiocarbamides I: Oxidation of phenylthiourea by chlorite in acidic media

The oxidation of 1-phenyl-2-thiourea (PTU) by chlorite was studied in aqueous acidic media. The reaction is extremely complex with reaction dynamics strongly influenced by the pH of reaction medium. In excess chlorite concentrations the reaction stoichiometry involves the complete desulfurization of PTU to yield a urea residue and sulfate: 2ClO2- + PhN(H)CSNH2 + H2O --> SO4(2-) + PhN(H)CONH2 + 2Cl- + 2H+. In excess PTU, mixtures of sulfinic and sulfonic acids are formed. The reaction was followed spectrophotometrically by observing the formation of chlorine dioxide which is formed from the reaction of the reactive intermediate HOCl and chlorite: 2ClO2- + HOCl + H+ --> 2ClO2(aq) + Cl- + H2O. The complexity of the ClO2- - PTU reaction arises from the fact that the reaction of ClO2 with PTU is slow enough to allow the accumulation of ClO2 in the presence of PTU. Hence the formation of ClO2 was observed to be oligooscillatory with transient formation of ClO2 even in conditions of excess oxidant. The reaction showed complex acid dependence with acid catalysis in pH conditions higher than pKa of HClO2 and acid retardation in pH conditions of less than 2.0. The rate of oxidation of PTU was given by -d[PTU]/dt = k1[ClO2-][PTU] + k2[HClO2][PTU] with the rate law: -d[PTU]/dt = [Cl(III)](T)[PTU]0/K(a1) + [H+] [k1K(a1) + k2[H+]]; where [Cl(III)]T is the sum of chlorite and chlorous acid and K(a1) is the acid dissociation constant for chlorous acid. The following bimolecular rate constants were evaluated; k1 = 31.5+/-2.3 M(-1) s(-1) and k2 = 114+/-7 M(-1) s(-1). The direct reaction of ClO2 with PTU was autocatalytic in low acid concentrations with a stoichiometric ratio of 8:5; 8ClO2 + 5PhN(H)CSNH2 + 9H2O --> 5SO4(2-) + 5PhN(H)CONH2 + 8Cl- + 18H+. The proposed mechanism implicates HOCl as a major intermediate whose autocatalytic production determined the observed global dynamics of the reaction. A comprehensive 29-reaction scheme is evoked to describe the complex reaction dynamics.     

Synthesis and antimalarial effects of 5,6-dichloro-2-[(4-||4-(diethylamino)-i-methylbutyl] amino||-6-methyl-2-pyrirnidinyl)amino] benzimidazole and related benzimidazoles and lH-imidazo[4,5-b] pyridines

A group of fifty-five 2-[(4-11[(dialkylamino)alkyI]amino11-6-methyl-2-pyrimidinyl)amino]-benzimidazoles (VII) was synthesized in 3-88% yield by the condensation of the requisite 2-[(2-benzimidazolyl)amino]-4-chloro-6-methylpyrimidine (VI) with the appropriate polyamine in ethanol-hydrochloric acid or neat with excess amine containing potassium iodide. The 2-[(2-benzimidazolyl)amino]-6-methyl-4-pyrirnidinol precursors (V), obtained in 11-51% yield by cyclization of 2-(cyanoamino)-4-hydroxy-6-methylpyrimidine with a suitably substituted o-phenylenediamine, were chlorinated with phosphorus oxychloride to give the intermediate 2-[(2-benzimidazolyl)amino]-4-chloro-6-rnethylpyrimidines (VI) (27-99%). Oxidation of 5,6-dichloro-2-[(4-11[4-(diethylamino)-l-methylbutyl] amino 11-6-methyl-2-pyrimidinyl) amino ]benzimidazole ( 29 ) with m-chloroperbenzoic acid gave the distal N⁴'-oxide ( 31 ) (19%). Fusion of 2,3-uiaminopyridine with 2-(cyanoamino)-4-hydroxy-6-methylpyrimidine provided 2-[(4-hydroxy-6-tnethyl-2-pyrimidinyl)amino]-lH-imitlazo[4,5-b]pyrimidine (VIII) (30%), which upon chlori-nation with phosphorus oxychloride (63%) followed by amination with i N, N-diethylethylene-diamine afforded 2-(4-11[2-(diethylamino)ethyl] amino 11-6-methyl-2-pyrimidinyl)-lH-imidazo [4,5-b]pyridine (X) (8%). Thirty-eight of the novel 2-[(4-amino-6-methyl-2-pyrimidinyl)amino]-benzimidazoles possessed “curative” activity against Plasmodium berghei at single subcutaneous doses ranging from 20.640 mg./kg. Orally, thirty-one compounds exhibited suppressive activity against P. berghei comparable with or superior to the reference drugs 1-(p-chlorophenyl)-3-(4-11[2-(diethylarnino)ethyl]amino 11-6-methyl-2-pyrimidinyl)guanidine (I) and quinine hydrochloride, while twelve of them were 5 to 28 times as potent as I and quinine hydrochloride. Eight compounds also displayed strong suppressive activity against P. gallinaceum in chicks. 5,6-Dichloro-2-[(4-112-(diethylamino)ethyl]amino11-6-methyl-2-pyrimidinyl] benzimidazole (18) showed marked activity against a cycloguanil-resistant line of P. berghei, and the most promising member of the series, namely 5,6-dichloro-2-[(4-11[4-(diethylamino)-l-methylbutyl]amino11-6-methyl-2-pyrimidinyl)amino]benzimidazole ( 29 ) (Q = 28), was designated for preclinical toxico-logical studies and clinical trial. Structure-activity relationships are discussed.     

Rapid shear viscosity calculation by momentum impulse relaxation molecular dynamics

Recently, Arya et al. [J. Chem. Phys. 113, 2079 (2000)] introduced a new molecular dynamics method to rapidly compute the viscosity of fluids. The technique, termed momentum impulse relaxation (MIR), involves the imposition of a Gaussian velocity profile on an equilibrated system, after which the decay in the profile is monitored as a function of time. The shear viscosity is computed by matching the rate of decay of the velocity profile to the corresponding solution of the Navier-Stokes equation. The method was originally applied to simple systems (argon and n-butane) and found to give a comparable accuracy to conventional equilibrium and nonequilibrium methods with more than an order of magnitude reduction in computing time. In this work, we extend and generalize the method to examine larger molecules with higher viscosities than have been examined previously. A detailed analysis of the method is given, including the effect the velocity boundary conditions have on the viscosity, the sensitivity of the results to the velocity profile fitting procedure, the effect of preequilibration of the Gaussian profile, and the effect the system size and box shape have on the accuracy and speed of the method. It is shown that the MIR method can be extended to treat multiatom systems without loss of accuracy or computational efficiency.     

Triosmium clusters derived from the reactions of thioureas with dodecacarbonyltriosmium: Crystal structures of [Os3(CO)11{η 1-SC(NMe2)2}], [Os3(CO)9(μ-OH)(μ-OMeOCO){η 1-SC(NMe2)2}] and [(μ-H)Os3(CO)9{μ 3-NHC(S)NH2}]

The reaction of [Os₃(CO)₁₂] with tetramethylthiourea in the presence of a methanolic solution of Me₃NO·2H₂O at 60° yields the compounds [Os₃(CO)₁₁{η ¹-SC(NMe₂)₂}] (1) in 56% yield and [Os₃(CO)₉(μ-OH)(μ-MeOCO){η ¹-SC(NMe₂)₂}] (2) in 10% yield in which the tetramethylthiourea ligand is coordinatedvia the sulfur atom at an equatorial position. Compound2 is a 50 e^? cluster with two metal-metal bonds and the hydroxy and methoxycarbonyl ligands bridging the open metal-metal edge. In contrast, the analogous reaction of [Os₃(CO)₁₂] with thiourea gives the compounts [(μ-H)Os₃(CO)₁₀{μ-NHC(S)NH₂}] (3) in 8% yield and [(μ-H)Os₃(CO)₉{₃-NHC(S)NH₂}] (4) in 30% yield. In3, the thioureato ligand bridges two osmium atomsvia the sulfur atom, whereas in4 in addition to the sulfur bridge, one of the nitrogen atoms of thioureato moiety bonds to the remaining osmium atom. The decacarbonyl compounds 3 can also be obtained in 50% yield from the reaction of [Os₃(CO)₁₀(MeCN)₂] with thiourea at ambient temperature. Compound3 converts to4 (65%) photochemically. Compound1 reacts with PPh₃ and acetonitrile at ambient temperature to give the simple substitution products [Os₃(CO)₁₁(PPh₃)] and [Os₃(CO)₁₁(MeCN)], respectively, while with pyridine, the oxidative addition product [(μ-H)Os₃(CO)₁₀(μ-NC₅H₄] is formed at 80°C. All the new compounds are characterized by IR,¹-H-NMR and elemental analysis together with the X-ray crystal structures of1,2 and4. Compound1 crystallizes in the triclinic space group P $P\bar 1$ with unit cell parametersa = 8.626(3) Å,b = 11.639(3) Å,c = 12.568(3_ Å,α = 84.67(2)°,β = 75.36(2)°,γ = 79.49(3)°,V = 1199(1) ų, andZ = 2. Least-squares refinement of 4585 reflections gave a final agreement factor ofR = 0.0766 (R _w = 0.0823). Compound2 crystallizes in the monoclinic space group P2_1/n with unit cell parametersa = 9.149(5) Å,b = 17.483(5) Å,c = 15.094(4) Å,β = 91.75(2)°,V = 2413(2) ų, andZ = 4. Least-squares refinement of 3632 reflections gave a final agreement factor ofR = 0.0603 (R _w = 0.0802). Compound4 crystallizes in the monoclinic space group C2/c with unit cell parametersa = 13.915(7) Å,b = 14.718(6) Å,c = 17.109(6) Å,β = 100.44(3)°,V = 3446(5) ų, andZ = 8. Least-squares refinement of 2910 reflections gave a final agreement factor ofR = 0.0763 (R _w = 0.0863).