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.     

Ab initio excited-state dynamics of the photoactive yellow protein chromophore

The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.     

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.     

Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model

Summary Using the X-ray crystal structure of the human topoisomerase I (top1) – DNA cleavable complex and the Sybyl software package, we have developed a general model for the ternary cleavable complex formed with four protoberberine alkaloids differing in the substitution on the terminal phenyl rings and covering a broad range of the top1-poisoning activities. This model has the drug intercalated with its planar chromophore between the −1 and +1 base pairs flanking the cleavage site, with the nonplanar portion pointing into the minor groove. The ternary complexes were geometry-optimized and relative interaction energies, computed by using the Tripos force field, were found to rank in correct order the biological potency of the compounds; in addition, the model is also consistent with the top1-poisoning inactivity of berberine, a major prototype of the protoberberine alkaloids. The model might serve as a rational basis for elaboration of the most active compound as a lead structure, in order to develop more potent top1 poisons as next generation anti-cancer drugs.     

ATRP grafting of styrene from benzyl chloride functionalized polysiloxanes: An AFM and TGA study of the Cu(0)/bpy catalyst

Various combinations of Cu(0), CuCl, 2,2′-bipyridine (bpy) and 1,10-phenanthroline (phen) were used as catalysts for the grafting polymerizations of styrene from polysiloxane macroinitiators functionalized with benzyl chloride. While Cu(0)/bpy alone promotes the grafting, narrower polydispersities were obtained in the presence of CuCl. Analysis of the Cu(0) surface before and after polymerization by a combination of AFM, TGA and FTIR investigations reveals the formation of bpy or phen films on Cu(0). In the presence of CuCl, the ligand film appears decorated with CuCl particles which increase in size with increasing the CuCl concentration. The initial layer occurs most likely as a result of complexation between the ligands and the Cu(0) surface and acts as a support for the rest of the film. These observations are consistent with the film formation on Cu(0) from related nitrogen donors and indicate that the reactivity of the Cu surface may depend not only on its prior treatment but also on the deposition of ligands from the reaction mixture.     

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     

catena‐Poly[[copper(II)‐μ‐2‐[bis­(2‐pyridylmeth­yl)amino]butyrato‐κ4N,N′,N′′,O:κO′] perchlorate]

The copper(II) ion in the syn–anti carboxyl­ate‐bridged one‐dimensional zigzag chain title complex, {[Cu(C₁₆H₁₈N₃O₂)]ClO₄}_n, exhibits a distorted trigonal–bipyramidal environment. Two N atoms and one carboxyl­ate O atom of the ligand form the basal plane, while the axial positions are filled by an N atom of the ligand and one O atom belonging to the carboxyl­ate group of an adjacent mol­ecule. The crystal packing is enhanced by C—H⋯O(perchlorate) hydrogen bonds.     

Long-range interaction in the D and D′ states of H2

The interaction energy between two hydrogen atoms in the D and D′ ¹Π_u states of the hydrogen molecule has been calculated for large internuclear distances (12 ? R ? 25 bohr). The variational method and a very flexible trial wave-function were used. The results indicate that for the states under consideration the Rayleigh-Schrödinger perturbation theory with the multipole expansion of the interaction hamiltonian gives reliable results only for R > 25 bohr i.e. in the region where the interaction energies are practically negligible.     

Simple Method for Simultaneous Determination of Selenium and Arsenic in Human Hair by Means of Atomic Fluorescence Spectrometry with Hydride Generation Technique

This study describes a simple, rapid and reliable method for simultaneous determination of selenium and arsenic in human hair by means of atomic fluorescence spectrometry combined with a hydride generation technique (HG-AFS). The procedure developed encompasses microwave digestion of a sample in the nitric acid environment only. The interferences caused by nitrous oxides are eliminated by removing a gas from above the digested solution with a stream of argon. The sample is then chemically treated in a flow-through hydride generation system and exposed to measurements in a double-channel atomic fluorescence spectrometer. The method permits determining both analytes in the linear range of 0.5–100µgL^–1 with a detection limit equal to 0.2µgL^–1, as well as with very good repeatability not exceeding 1% for Se and 2% for As. No mutual interferences from either of the analytes in the concentrations ranges matching the hair composition were found. The method was verified in terms of accuracy with the use of a reference material and then applied to the analysis of the natural samples of human hair.     

Reaction of Trimethylbenzene over Alumina-Pillared Montmorillonite

The reaction of trimethylbenzene (TMB) over alumina-pillared montmorillonite (Al-PM) had been investigated in a fixed-bed flow reactor at 300 °C and atmospheric pressure. Al-PM calcined in the range 300-500 °C exhibited decreased layer distance, surface area and acid amount. The strong acid sites of Al-PM calcined at 500 °C were greatly diminished according to measurements of ammonia temperature-programmed desorption. Under our conditions the reaction proceeded mainly via isomerization and disproportionation with little dealkylation. The conversion of reactant decreased in the order 1,2,3-TMB ≥ 1,2,4-TMB > 1,3,5-TMB and the selectivity of isomerization in the order 1,2,3-TMB > 1,3,5-TMB > 1,2,4-TMB, corresponding to the order of diminishing thermal instability. Both the catalytic activity and the selectivity ratio of disproportionation to isomerization decreased with increased calcined temperature and time-on-stream. o-Xylene content in the total xylene produced from 1,2,4-TMB or 1,2,3-TMB greatly exceeded the composition at thermodynamic equilibrium. These results arc consistent with the decrease of both the strong acid sites and the pore size of Al-PM which exhibits the restricted transition state selectivity.