Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales

Time series models, which are constructed from the projections of the molecular-dynamics (MD) runs on principal components (modes), are used to mimic the dynamics of two proteins: tendamistat and immunity protein of colicin E7 (ImmE7). Four independent MD runs of tendamistat and three independent runs of ImmE7 protein in vacuum are used to investigate the energy landscapes of these proteins. It is found that mean-square displacements of residues along the modes in different time scales can be mimicked by time series models, which are utilized in dividing protein dynamics into different regimes with respect to the dominating motion type. The first two regimes constitute the dominance of intraminimum motions during the first 5 ps and the random walk motion in a hierarchically higher-level energy minimum, which comprise the initial time period of the trajectories up to 20-40 ps for tendamistat and 80-120 ps for ImmE7. These are also the time ranges within which the linear nonstationary time series are completely satisfactory in explaining protein dynamics. Encountering energy barriers enclosing higher-level energy minima constrains the random walk motion of the proteins, and pseudorelaxation processes at different levels of minima are detected in tendamistat, depending on the sampling window size. Correlation (relaxation) times of 30-40 ps and 150-200 ps are detected for two energy envelopes of successive levels for tendamistat, which gives an overall idea about the hierarchical structure of the energy landscape. However, it should be stressed that correlation times of the modes are highly variable with respect to conformational subspaces and sampling window sizes, indicating the absence of an actual relaxation. The random-walk step sizes and the time length of the second regime are used to illuminate an important difference between the dynamics of the two proteins, which cannot be clarified by the investigation of relaxation times alone: ImmE7 has lower-energy barriers enclosing the higher-level energy minimum, preventing the protein to relax and letting it move in a random-walk fashion for a longer period of time.     

Atom transfer radical polymerization of 1-phenoxycarbonyl ethyl methacrylate monomer

Atom transfer radical polymerization conditions with copper(I) bromide/2,2^′-bipyridine (Cu/2,2^′-bpy) as the catalyst system were employed for the homopolymerization and random copolymerization of 1-phenoxycarbonyl ethyl methacrylate (PCMA) with methyl methacrylate (MMA). Temperature studies indicated that the polymerizations occurred smoothly in bulk at 110 °C. Poly(PCMA)(polydispersity index=1.27) homopolymer was characterized and then used as macroinitiator for increasing its molecular weight. The homopolymerization of PCMA was also carried out under free radical conditions using 2,2^′-azobisisobutyronitrile as an initiator.The monomer and polymers were characterized by FT-IR and ¹H and ¹³C-NMR techniques. The glass transition temperatures, the solubility parameters and average-molecular weights of the polymers were determined. Thermal stabilities of the polymers were given as compared with each other by using TGA curves. Thermal degradation products of poly(PCMA)s obtained by ATRP and free radical polymerization were compared with each other by using ¹H-NMR technique.     

Determination of vanadium in biological matrices by flame atomic absorption spectrometry with activated carbon enrichment

For the determination of vanadium in biological materials by flame AAS an enrichment is described which comprises chelation with oxine and adsorption on activated carbon: The relative standard deviation for 10 g V/L was found to be 6% (n=15).Dedicated to Professor Dr. Dieter Klockow on the occasion of his 60th birthday     

Labelling of castor oil for myocardial study

The labelling of castor oil, hydrolyzed castor oil and oleic acid by iodine monochloride and chloramine-T has been investigated. The effect of iodinating agent and concentration of castor oil on labelling yield has been studied. A comparative pharmacological study with analogous aliphatic fatty acids was caried out. Castor oil labelled with iodine monochloride concentrates in heart and liver in good proportion, better than other natural fatty acids and nearly equal to analogous fatty acids. Infrared study revealed that the OH group in ricinoleic acid may protect the¹²⁵I added across the double bond with minor changes in biochemical properties and better extraction by the muscle of the heart.     

Plant tissue-based amperometric electrode for eliminating ascorbic acid interferences

An application of tissue-based electrodes aimed at eliminating interferences from co-existing electroactive constituents is described. The concept is illustrated using a zucchini-containing carbon paste electrode. The presence of the enzyme ascorbic acid oxidase (AAO) in the zucchini tissue effectively eliminates contributions from ascorbic acid, thus allowing selective measurement of dopamine or norepinephrine. In comparison with analogous enzyme-based AAO electrodes, the tissue “eliminator” electrode offers high biocatalytic stability and activity and extremely low cost. The effects of various experimental variables are studied using pulse voltammetry, chronoamperometry and flow-injection amperometry. The electrode has a useful lifetime of 4 weeks. Simultaneous elimination of uric acid interferences is obtained via the co-immobilization of uricase. Oxygen background currents are eliminated in the presence of ascorbic acid.     

Reaction of Pyrimidinonethione Derivatives: Synthesis of N‐Methyl‐2‐Hydrizinopyrimidine‐4‐One,Thiazolo[3,4‐b] N‐Methylpyrimidinone; 2‐(1‐Pyrazolonyl) N‐Methylpyrimidine‐4‐one and 2‐Hydrazino‐N‐Methyl Pyrimidine‐4‐One Derivatives

6‐Aryl‐5‐cyano‐4‐pyrimidinone‐2‐thion derivatives 1a‐c reacted with methyl iodide (1:2) to give the corresponding 2‐S,N‐dimethyl pyrimidine‐4‐one derivatives 2a‐c . Compounds 2a‐c were in turn, reacted with hydrazine hydrate to give the sulfur free reaction products 3a‐c . These reaction products were taken as the starting materials for the synthesis of several new heterocyclic derivatives. Reaction of 3a‐c with acetic anhydride and formic acid gave pyrimido triazines 4a‐c and 7a‐c , respectively. Their reactions with active methylene containing reagents gave the corresponding 2‐(1‐pyrazonyl)‐N‐methyl pyrimidine derivatives 9a‐c and 10a‐c , respectively. Their reactions with aromatic aldehydes afforded the corresponding 2‐hydrazono pyrimidine derivatives 11a‐c . The structure of these reactions products were established based on both elemental analysis and spectral data studies.     

Enthalpic relaxation of convective desiccated trehalose-water glasses

Minimizing molecular mobility for desiccation preservation of biologics close to ambient temperature using trehalose glasses require quantitative characterization of their enthalpic relaxation at various end water contents. Differential scanning calorimetry (DSC) was used to characterize three different water contents: 0%, 1.5% and 10% over a wide range of aging temperatures. Results showed the characteristic time (τ) varies both with the water content and the aging temperature. τ increased with lowered aging temperature but showed a non-monotonous relationship as a function of water content. Fragility of trehalose glasses was analyzed using thermophysical parameters obtained from relaxation studies. The study showed trehalose to be a fragile glass former at all water contents, with 0% water samples showing a relatively stronger glass. A compromise between molecular mobility and glass fragility led to an optimal water content close to 1.5% and an aging temperature close to room temperature. This would ensure a τ value of 9000 h, which corresponds to a storage period of a year.     

Determination of in vitro antioxidant and radical scavenging activities of propofol

Propofol (2,6-diisopropylphenol) is a hypnotic intravenous agent with in vivo antioxidant properties. This study was undertaken to examine the in vitro antioxidant activity of propofol using different antioxidant tests including by 1,1-diphenyl-2-picryl-hydrazil (DPPH.) radical scavenging, metal chelating, hydrogen peroxide scavenging, superoxide anion radical scavenging, reducing power and total antioxidant activities. At the concentrations of 25, 50, and 75 microg/ml, propofol exhibited 97.7, 98.6 and 100% inhibition on peroxidation of linoleic acid emulsion, respectively. On the other hand, at the 75 microg/ml concentration of standard antioxidants such as butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT) and alpha-tocopherol exhibited 88.7, 94.5, and 70.4% inhibition on peroxidation of linoleic acid emulsion, respectively. In addition, at same concentrations, propofol was shown that it had effective reducing power, DPPH. free radical scavenging, superoxide anion radical scavenging, hydrogen peroxide scavenging and metal chelating activities. These various antioxidant activities were compared to standard antioxidants such as BHA, BHT and alpha-tocopherol. These results indicate that propofol prevents lipid peroxidation and radicalic chain reactions. At the same time, propofol revealed more effective antioxidant capacity than BHA, BHT and alpha-tocopherol.     

Synthesis and Reactions of Some New Heterocyclic Compounds Containing Cycloalka[e]thieno[2,3‐b]pyridine Moiety

Hydrolysis of ethyl 3-amino-4-aryl-cycloalka[e]thieno[2,3-b]pyridine-2-carboxylates ( 3a-d) gave the corresponding o-aminocarboxylic acids 4a-d . Heating the latter compounds ( 4a-d) with acetic anhydride furnished the oxazinone derivatives 5a-d which, in turn, underwent recyclization reaction to give the corresponding pyrimidinones 6a-d upon treatment with ammonium acetate in acetic acid. Reaction of 3-amino-4-aryl-cycloalka[e]thieno[2,3-b]pyridine-2-carboxamides ( 3f,h ) with triethyl orthoformate gave pyrimidinone derivatives 7a,b . Reaction of 3-amino-4-phenyl-cycloalka[e]thieno[2,3-b]pyridine-2-carboxamides 3e,h with aromatic aldehydes furnished tetrahydropyridothienopyrimidinones 8a-d . Chlorination of 7a,b and 6a-d by using phosphorous oxychloride produced 4-chlorocycloalka[5′,6′]pyrido[3′,2′:4,5]thieno[3,2-d]pyrimidine derivatives 9a-f which were used as key intermediates in the synthesis of several new cycloalkapyrido-thienopyrimidines 10a-f ˜ 14a-f . Moreover, some cycloalkapyridothienotriazinones 15a,b-17a,b were synthesized.     

A novel (E,E)-dioxime and its mono-, di- and trinuclear complexes bearing tetradentate octyl sulfanyl phenylamino substituents. Synthesis,characterization and electrochemical properties of its transition metal complexes

A new vic-dioxime, 13,14-bis-(hydroxyimino)-9,12,15,18-diazadithiaoctacosane, has been synthesized from 2-octylsulfanylaminobenzene and (E,E)-dichloroglyoxime. Mononuclear transition metal complexes of Ni^II, Cu^II, Co^II and Fe^II have been prepared and were found to have a metal–ligand ratio of 1:2. The synthesis of di- and trinuclear complexes was achieved with U^IVO₂ and Cu^II depending on the stoichiometry of the reactants. The complexes were characterized by elemental analysis, ¹H-n.m.r., u.v.–vis, i.r., f.a.b.-m.s. and by cyclic voltammetry.