Recent progress in protein 3D structure comparison

Quantitation of protein 3-D structure similarity is crucial in such fields as evolutionary studies, structural modeling and prediction of biological function. There are various approaches, many of which are tailored to specific problems. This review summarizes the recent developments in this field with particular interest in two main areas: i) improvements to and statistical interpretation of the root-man-square distance between equivalent atoms, rmsd; and ii) methods of protein structural classification based on geometrical features. Special attention is given to fast methods capable of analyzing large structural databases.     

Recombination reactions of oxygen atoms on an anodized aluminum plasma reactor wall, studied by a spinning wall method

We have studied the recombination of O atoms on an anodized Al surface in an oxygen plasma, using a new "spinning wall" technique. With this method, a cylindrical section of the wall of the plasma reactor is rotated and the surface is periodically exposed to an oxygen plasma and then to a differentially pumped mass spectrometer (MS). By varying the substrate rotation frequency (r), we vary the reaction time (t(r)), that is, the time between exposure of the surface to O atoms in the plasma and MS detection of desorbing O(2) (t(r) = 1/2r). As t(r) is increased from 0.7 to 40 ms, the O(2) desorption signal decreases by a factor of 2 for an O-atom flux of 1 x 10(16) cm(-2) s(-1) and by a factor of 6 when the O flux is 1 x 10(17) cm(-2) s(-1). The O(2) signal decay is highly nonexponential, slowing at longer times and reaching zero signal as r --> 0. A model of O-atom recombination is compared with these time-dependent results. The model assumes adsorption occurs at surface sites with a range of binding energies. O can detach from these sites, become mobile, and diffuse along the surface. This leads to desorption of O, reattachment at free adsorption sites, and recombination to form O(2) that promptly desorbs. With several adjustable parameters, the model reproduces the observed shapes of the O(2) desorption decay curves and the lack of detectable desorption of O and predicts a high O-atom recombination coefficient on anodized aluminum.     

The photoelectron spectrum of tetramethyldiazetine: The elucidation of ring size effects on azo group ionization potentials

The photoelectron spectrum of 3,3,4,4-tetramethyldiazetine (4-Me₄) has been measured. By comparison with the previously reported photoelectron spectra of 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline, 4-Me₄ has three resolved low energy ionization (8.87, 10.36, and 11.65 eV) with an anomalously low second ionization potential. MINDO/3-and ab initio STO-3G calculations on 3-, 4-, and 5-membered ring azo compounds (diazenes) have been carried out, and these allow definite conclusions about the order of n_?, n₊, and π ionization potentials to be made for the diazetine (n_? < N₊ < π) and for 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline(n_? < π n₊), in agreement with the predictions of Heilbronner. Ab initio STO-3G calculations on the nitrogen and alkyl fragments of the cyclic diazenes reveal the origin of ionization energy shifts with changes in ring size.     

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

A large succinic acid (HOOC(CH₂)₂COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation. Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002     

Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps

Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization.     

The Vapor-Liquid Polycondensation of Cyclohexylphosphoric Dichloride with Hydroquinone

The vapor-liquid polycondensation of cyclohexylphosphoric dichloride with hydroquinone was investigated. The influence of the temperature, reaction time, base concentration, and molar ratio of reagents on the yield, inherent viscosity, and molecular weight of the obtained polymer was studied. Second order, central, composite, rotatable experimental design was used in order to carry out this work and to mark limits of the experimental field for optimal yields and high inherent viscosities.     

Need and use of reference materials in a comprehensive countrywide monitoring of radionuclides

The reliability of measurement results is essential for forming a common database of a laboratory network, because a well-maintained and consistent database is the crucial point of countrywide monitoring. Reference materials are important tools in realizing some aspects of quality assurance; they are especially useful in harmonizing work within the network. Among usual types of reference materials in radio analytics solutions, matrix reference materials and some special reference objects are used. All classes of reference materials should be used depending on the purpose of the demonstration of quality, even in-house reference materials. Interlaboratory measurement comparison and performance evaluation programs play important quality assurance role in radio analytical laboratories. Fortunately, nowadays, the main task is to determine a very low radioactivity concentration in the environment; therefore, pre-concentration is necessary. Generally, the radionuclide bearing natural materials collected from sites where there had been sufficient time for natural processes to redistribute various chemically different species of radionuclides are more reliable reference materials than spiked materials—the main difference is the chemical bounding which is crucial from the point of view of the bioavailability. The need of reference material is summarized according to the intended use, like quality control, measurement validation, and instrument calibration.     

Structure of the Polymer Obtained from Bisphenol-A and Cl 2 P(O)CH 3

Using the step-by-step build-up approach, the possible conformations of compound PhOP(O)(Me)OPh(Me) 2 Ph were constructed and geometrically optimized. Among the obtained structures 32 conformations belonging to low, comparable energy levels were used to construct the most stable dimers and tetramers of the title polymer. The results allowed us to estimate the geometrical structure of the polymer.     

Explanation of Anomalous Gas-Chromatographic (Gc) Behaviour in a Homologous Series of 2-Chloroethyl Phosphonic Acid Dialkyl Esters

Abstract

The study of GC separation of 2-chloroethylphosphonic acid di-n-alkyl (1–5 C atoms) esters (synthesised by us) on silicone stationary phases (OV-1, OV-17, OV-225) revealed a deviation from the expected linear dependence of retention indexes (RI) versus the number of C atoms of the alkyl chain: the first member of the series presents stronger retention than one can expect. This anomalous behaviour was observed especially on polar stationary phase (OV-225, see Figure l), and was emphasised with the increase of the column temperature. In an attempt to rationalise the above mentioned facts, we tried to relate the RI values to a global polarity parameter: the dipole moment, μ. The μ values for ClC₂H₄P(O)(OR)₂ were calculated by a method described in [1] (tested by comparing the calculated μ values with experimental ones for alkyl phosphonic acid dialkylesters), using molecular mechanics (COSMIC package) in the search of the conformational space, AM1 method (MOPAC 6.0) for the μ values of the conformers, and Boltzmann distribution for the global value (see Table I). At low temperature, the μ values are not related to the Kovats indexes. Those calculated at 200°C (column temperature range) demonstrate that, indeed, only in the case of the methyl derivative, the temperature rising led to a higher μ (enhanced population of the more polar conformers: ac position for the C-Ethyl group - ac for the Cl, μ ≈ 27 D, or ±ap for one R, μ ≈ 3.8 ÷ 4.3 D). It can be concluded that dipole-dipole forces contribute to the separation process of the first members of the series.     

Biomedical Implications of Polyphosphates

Abstract

The polyphosphates have the capacity of forming chelates with most of that metal cations[l]. Polyphosphatic complexes with trace- and macroelements art used as fodder additives for animals. In our experiments we studied the effect 01pyrophosphate (PP), tripolyphosphate (TPP) and hexametaphosphate (HMP), at different concentrations (0.909 mM, 1.8 I8 mM and 2.727 mM), on the enzymatic activity of carbonic anhydrase (CA), and the effect of polyphosphate chelates or the enzymatic activity of alkaline phosphatase (AP), both zincenzymes. The meta; ion, which can be dissociated in the presence of a chelating agent, is essential foi their catalytic activity 121. The presence of metal atoms as essential constituents of some enzymes, and the metal requirements of others for maximum activity, provide an obvious link between enzymatic reaction and coordination chemistry.