Protein structure along the order-disorder continuum

Thermal fluctuations cause proteins to adopt an ensemble of conformations wherein the relative stability of the different ensemble members is determined by the topography of the underlying energy landscape. "Folded" proteins have relatively homogeneous ensembles, while "unfolded" proteins have heterogeneous ensembles. Hence, the labels "folded" and "unfolded" represent attempts to provide a qualitative characterization of the extent of structural heterogeneity within the underlying ensemble. In this work, we introduce an information-theoretic order parameter to quantify this conformational heterogeneity. We demonstrate that this order parameter can be estimated in a straightforward manner from an ensemble and is applicable to both unfolded and folded proteins. In addition, a simple formula for approximating the order parameter directly from crystallographic B factors is presented. By applying these metrics to a large sample of proteins, we show that proteins span the full range of the order-disorder axis.     

Bestimmung des Gesamtglucosinolatgehaltes in vegetativen Pflanzenteilen durch quantitative Analyse enzymatisch freisetzbaren Sulfates

Summary With regard to agronomical and ecological aspects there is an increasing interest in total glucosinolate determination in vegetative plant materials. In contrast to time and work consuming chromatographic and insufficient colorimetric methods commonly used, a new simple as well as rapid method is presented, which bases on the enzymatical release of sulfate from the glucosinolate molecule. In order to avoid losses of glucosinolates during sampling and preparation for the analysis of vegetative samples total and undamaged plants are dried at 85 °C. The extraction of free sulfate is done by an 120 extract in 1 mol/l ascorbic acid, whereas the enzymatically released sulfate is determined by an 120 extract in an aqueous solution containing 750 units/ml H1-sulfatase. In the next step sulfate is precipitated from a defined Ba-solution and quantified indirectly by an emission-spectrometric determination of the remaining Ba-concentration. The glucosinolate content of the sample results from differences in the sulfate concentrations of both extracts. On an average 98.4% of pure sinigrin added to a model system was recovered in the experiments. A comparison of results determined by the enzymatic method with HPLC yields a close (r = 0.98) correlation between both methods.     

Information theory of miniaturization advantages of column liquid chromatography for quantitative analysis

Summary The influences of decreasing column diameter and length on two analytical goals, the precision and solvent efficiency, in reversed-phase liquid-chromatography are studied. Low solvent consumption is one of analytical advantages of miniaturized columns and is shown to be quantitatively evaluated by the precision and solvent efficiency which are defined to be the total Shannon mutual information obtained from an assay and the information obtained in a unit solvent volume, respectively. Analysis of paraben food additives on a microbore column is taken as an example. In trace analysis, the relative standard deviation (RSD) of measurements theoretically derived from the precision is shown to approach to the observed ones.     

Trace analysis of selected benzidine and diaminodiphenylmethane derivates in urine by means of liquid chromatography using precolumn sample preconcentration,UV and electrochemical detection

Summary For the title compounds 4,4-DADPM, MOCA, 3,3-DCB, 4-ADP and 4-ADPA listing on the EPA priority pollutant list, an analytical practicable, reliable, reproducible and sensitive procedure is required. Therefore a new method has been developed for the routine determination of these toxic aromatic amines in urine at the ppb level. The quantitative determination of amines is a suitable procedure of occupationally exposed persons. Urine sample preparation is done using simple liquid-liquid extraction followed by a precolumn enrichment (PRP₁-material; Hamilton). Breakthrough measurements were done using an enrichment column packed with PRP₁ material. The capacities of the studied amines ranged from 21.9mg/g to 96.6mg/g, while influent concentrations differed from 28.3mg/l to 332.0mg/l. The advantages of electrochemical detection regarding to selectivity and sensitivity are clearly indicated in this paper. Separation has been achieved applying reversed-phase-high-performance-liquid chromatography (LiChrosorb RP 18/5m) followed by electrochemical or UV-detection. The detection limits employing an electrochemical detector at a potential of 1 V range from 2.2ng to 12.1ng. UV detection at 254 nm and 280 nm is about 10–100 times less sensitive. Recoveries from spiked water samples at the 5ppb levels were 75% to 96% respectively. The standard deviation of the developed procedure varies from 5.3% to 14%. Day-to-day repeatability is good.     

Information on DNA conformation derived from transverse pore gradient gel electrophoresis in conjunction with an advanced data analysis applied to capillary electrophoresis in polymer media.

Abnormally slow migration of DNA is conventionally viewed as being due to an abnormal conformation relative to "linear" standards. The evidence for this rests on a few instances where nonlinear DNA structures have been established by independent methods and yield low mobilities relative to standards. Transverse pore gradient gel electrophoresis of authentically bent kinetoplast DNA and of an upstream activator sequence (UAS) of an E. coli operon promoter shows in addition that curves of migration distance vs. gel concentration ("Ferguson curves") of such abnormally conformed DNA differ from those of "linear" standards. Since Ferguson curves are interpretable with regard to molecular size in concordance with a mathematical model (Ogston model), transverse pore gradient gel electrophoresis provides a simple means of correlating abnormally slow migration of DNA with molecular size. In addition, transverse pore gradient gel electrophoresis is able to distinguish between DNA banding which exhibits a steeper dependence on gel concentration than "linear" standards from one which shows the same dependence. The former appears characteristic of circularly bent DNA and gives rise to a substantial retardation, the latter of bending across a knot or kink in the DNA chain associated with a relatively minor retardation relative to standards. Circularly bent restriction fragments formed from kinetoplast DNA retain the characteristic intersecting Ferguson curves on the transverse pore gradient gel. Another authentically "abnormal" DNA structure recognizable on transverse pore gradient gels is supercoiled DNA derived from the reaction of topoisomerase with a plasmid. Different lengths of supercoiled sequences give rise to parallel Ferguson curves clearly intersecting with those of linear standards.(ABSTRACT TRUNCATED AT 250 WORDS)     

Synthesis of pyridonoanthrapyrimidines

The reaction of 6- and 8-chloroacetylaminopyrimidinoanthrones with pyridine in the case of the 8-isomer leads to the formation of a pyridone ring, while in the case of the 6-isomer it stops at the formation of the -pyridinium salt. The latter, like -pyridinium salts obtained from the 8-isomer and 1-chloroacetylaminoanthraquinone, is cyclized under the action of aniline. In this case aminopyridonoanthrapyrimidines and 1-aminoanthrapyridone are obtained. The cyclic salt, in turn, is converted to an amine, and by reductive elimination of a pyridinium group, to an unsubstituted pyridonoanthrapyrimidine. The acetylation of amines leads to the formation of an oxazole ring. Pyridonoanthrapyrimidines can also be produced from -amino-derivatives of anthrapyridone by cyclization of dimethylformamidinium salts.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 989–993, July, 1984.     

Automated data interpretation based on the concept of "negative signature mass" for mass-mapping disulfide structures of cystinyl proteins

An efficient method for data processing and interpretation is needed to support and extend disulfide mass-mapping methodology based on partial reduction and cyanylation-induced cleavage to proteins containing more than four cystines. Here, the concept of "negative signature mass" is introduced as the novel feature of an algorithm designed to identify the disulfide structure of a cystinyl protein given an input of mass spectral data and an amino acid sequence. The "negative signature mass" process is different from the conventional approach in that it does not directly rule-in disulfide linkages, but rather eliminates linkages from a list of all possible theoretical linkages, with the goal of ruling out enough linkages so that only one disulfide structure can be constructed. The operating principles and the effectiveness of the algorithm are described in the context of analyzing ribonuclease A, a 124-residue protein containing eight cysteines in the form of four cystines (disulfides).     

Electron transfer in supercritical carbon dioxide: ultraexothermic charge recombination at the end of the "inverted region"

Charge-recombination rates in contact radical-ion pairs, formed between aromatic hydrocarbons and nitriles in supercritical CO(2) and heptane, decrease with the exothermicity of the reactions until they reach -70 kcal mol(-1), but from there on an increase is observed. The first decrease in rate is typical of the "inverted region" of electron-transfer reactions. The change to an increase in the rate for ultra-exothermic electron transfer indicates a new free-energy relationship. We show that the resulting "double-inverted region" is not due to a change in mechanism. It is an intrinsic property of electron-transfer reactions, and it is due to the increase of the reorganisation energy with the reaction exothermicity.     

Potential of microbore HPLC within a multiresidue method for the trace analysis of plant-protective substances in water

The performance of microbore HPLC as a "measurement channel" within a true multiclass/multiresidue method for monitoring plant protectants in raw and potable water is demonstrated. The method has a modular design and consists of a non-selective sampling and preparation line generating 250 microL of an "extract" from a 100-mL water sample; this extract can be introduced to up to four measurement channels, as required by the analytical task. The microbore HPLC channel can be used to quantify 34 plant protectants in the 0.1 microg L(-1) concentration range by use of diode-array detection at seven different wavelengths. A solvent change is necessary to link sample preparation to microbore HPLC; this uses 50 microL of the "extract" and is accomplished directly in an autosampler vial. Performance characteristics were evaluated for tap water spiked at 0.2 microg L(-1). Average recoveries were between 65 and 100% and method detection limits were 0.07 microg L(-1) or better. The ability to provide comparable and accurate results was proven by participation in an interlaboratory comparison trial. The procedure for preparing microbore columns from 750 microm i.d. PEEK tubing is described in detail to enable the reader to prepare his own columns. The reproducibility of this preparation procedure was proven by an analysis-of-variance test.     

A new sensitive alternative of static headspace gas analysis with sample-addition calibration

Summary A method is described which makes it possible to with-draw in a defined way headspace gas samples amounting to as much as several tens of milliliters from an equilibrated gas-liquid system. The apparatus consists of an equilibration vessel provided with a septum through which a Tenax GC-packed trap can be connected with the headspace compartment via an injection needle. At the bottom of the vessel, a syringe is situated by means of which a liquid sample is introduced into the vessel. A portion of liquid sample is introduced into the equilibration vessel, equilibrium is established, a certain volume of the headspace gas is pushed out through the trap by introducing another portion of liquid sample, and the analytes entrapped are determined by GC. Then the entire procedure is repeated, and the initial contents of the analytes in the liquid sample are calculated from the two GC analyses. The possibilities and reliability of the method are discussed.Presented at the 14th International Symposium on Chromatography London, September, 1982     

Topological ring currents in the "empty" ring of benzo-annelated perylenes

Cyclic conjugation in benzo-annelated perylenes is examined by means of the topological π-electron ring currents calculated for each of their constituent rings, in a study that is an exact analogy of a recent investigation by Gutman et al. based on energy-effect values for the corresponding rings in each of these structures. "Classical" approaches, such as Kekule? structures, Clar "sextet" formulas, and circuits of conjugation, predict that the central ring in perylene is "empty" and thus contributes negligibly to cyclic conjugation. However, conclusions from the present calculations of topological ring currents agree remarkably with those arising from the earlier study involving energy-effect values in that, contrary to what would be predicted from the classical approaches, rings annelated in an angular fashion relative to the central ring of these perylene structures materially increase the extent of that ring's involvement in cyclic conjugation. It is suggested that such close quantitative agreement between the predictions of these two superficially very different indices (energy effect and topological ring current) might be due to the fact that, ultimately, both depend, albeit in ostensibly quite different ways, only on an adjacency matrix that contains information about the carbon-carbon connectivity of the conjugated system in question.     

Darwinian Docking

The Darwinian model of evolution is an optimization strategy that can be adapted to docking. It differs from the common use of genetic algorithms, primarily in its acceptance of diverse solutions over finding "global" optima. A related problem is selecting compounds using multiple criteria. I discuss these ideas and present the outlines of a protocol for selecting "hits" and "leads" in drug discovery.     

A formal total synthesis of (+/-)-neplanocin A

Stereoselective formal synthesis of (+/-)-neplanocin A from a cyclopentane derivative employing an elegant strategy involving reiterative usage of an already existing acetonide protecting group is reported. The acetonide protecting group that is carried forward intact right from the starting adduct to an advanced intermediate is shuffled around twice as in a "relay race" through the synthetic sequence, thus avoiding unnecessary employment of additional protecting groups.     

Effective multipoles and Yukawa electrostatics in dressed molecule theory

In this paper we derive the multipolar expansion of the screened Coulomb potential in electrolyte solutions with molecular solvent. The solute and solvent molecules can have arbitrary sizes, shapes, and internal charge distributions. We use the exact statistical mechanical definition of renormalized charge distributions coming from "dressed molecule theory" to determine the effective multipoles of a molecule immersed in an electrolyte. The effects of many-body correlations are fully included in our formally exact theory. We restrict ourselves to sufficiently dilute solutions so the screened Coulomb potential decays for large distances like a Yukawa function, exp(-kappa r)/r, where r is the distance and 1/kappa is the decay length (it is normally different from the Debye length). The resulting "Yukawa electrostatics" differ in many respects from ordinary, unscreened electrostatics. The "Yukawa charge" of a molecule (the lowest order moment in the multipolar expansion) is in general not equal to its Coulombic charge and it is not the integral of the renormalized charge distribution of the molecule. Moreover, as shown in this paper, the multipolar expansion of the Yukawa potential does not correspond, contrary to the case of the Coulomb potential, to its asymptotic expansion for large r. As a consequence, the charge term in the multipolar expansion is not the leading term in the asymptotic expansion. Instead, for large r values, multipoles of all orders contribute to the leading asymptotic term. Thus, the electrostatic potential from, for example, an electroneutral solvent molecule in an electrolyte solution has generally the same range as that from an ion. The proper asymptotic expansion for electrostatic interactions in electrolytes is derived. It is briefly shown how the multipole expansion formalism can also be applied in the Poisson-Boltzmann approximation for primitive model electrolytes.     

Long-term atmospheric deposition wet-dry fluxes. Critical loads exceedences in an urban area

The present work provides an overview of the most relevant results concerning a five years monitoring programme of wet and dry deposition (1995-1999) in the city of Bologna. The aim of this research is to get an overall picture of atmospheric pollutants deposition inventory in an urban territory and to allow an assessment of the vulnerability of the area by comparing actual fluxes of acidity and nutrient nitrogen with the respective "critical loads" associated to the territory, in the framework of the UNECE LRTAP (Long Range Transboundary Air Pollution Convention). This comparison, for the Bologna monitoring station, shows "exceedance classes" from 4 to 6 for acidity and from 1 to 5 for nutrient nitrogen, reflecting an urban-industrial context, though a trend in reducing occurs from 1995 to 1999. A water layer surface sampler (DAS-MTX sampler) was employed for "surrogate" dry deposition collection. The contribute of dry fraction to the total deposition fluxes appears to prevail on wet fraction for many pollutants (up to more than 90% for total calcium and alkalinity). A comparison with long term monitoring results from some stations in Italian territory, shows that the differences among chemical species deposition fluxes may be ascribed both to the long distance aerial transport of pollutants and to site characteristics.     

Energy dependence of the epithermal neutron spectrum shape parameter α with respect to application of comparator-type NAA

The epithermal neutron spectrum shape parameter in nuclear reactors is explained from a theoretical point of view in terms of the neutron slowing down density function. The latter is approximated by Fermi's age theory. Values for are calculated for a simple approximation of a nuclear reactor: a disk shaped fission neutron source in an infinite graphite moderator. The model produces -values with the correct sign and magnitude, compared to experimental values from the literature, determined in a real reactor. It is shown that varies strongly with distance to the neutron source and less strongly with neutron energy. The inappropriateness of average -values, obtained from the slope of quasi-straight lines produced by log-log plots of E^– versus E, for the correction of non-ideal epithermal neutron activation is discussed. Conclusions are formulated concerning the impact of an energy dependent on comparator type NAA.     

Integer linear programming as a tool for constructing trees from quartet data

The task of the quartet puzzling problem is to find a best-fitting binary X-tree for a finite n-set from confidence values for the 3n4 binary trees with exactly four leaves from X, its fitness being measured by the sum of the confidence values of all "induced" four-leaves subtrees. We describe a method for finding an exact solution of this problem by integer linear programming. Similar procedures can also be used for finding, e.g. best-fitting "circular" networks. A crucial problem in this context is, of course, how to obtain the input confidence values for the quartet trees. We propose to use inner products of rate-matrix diagonals calculated for pairs of taxa and present the trees resulting from applying our approach to two data sets of up to 36 mitochondrial sequences of mammals including an outgroup.     

The Energy of Interaction between Water Monolayer and Carbon Surface and the Determination of H-Bond Energy from the Isotherms of Water Desorption by Organic Molecules into an Aqueous Solution

It is proven that, when passing from a liquid into an adsorption phase on a carbon surface, the maximal number of H-bonds between water molecules decreases from four to three because of the screening of one unpaired electron of the oxygen atom of an adsorbed water molecule by aromatic rings of the carbon surface. An energy gain equal to the energy of one H-bond arises upon water desorption by organic molecules adsorbed from an aqueous solution. The ratio between the number of H-bonds of a group of water molecules, which is displaced into a solution by one organic molecule, in the solution and in the adsorption phase is independent of the number of molecules in this group and is, on the average, equal to 2.038 for all possible structures of H-bonds in both phases. The allowance for this ratio in the isotherm of water desorption into a solution and the introduction of a coefficient, which depends on the relative water content ( ) in the adsorption phase, in the form of into the equation of the desorption isotherm make it possible to determine the balance of the change in the Gibbs energy at the desorption equilibrium and the standard Gibbs energy = –1.76 kJ/mol of water desorption into a solution from a carbon surface. This value determined by an independent method is = –1.79 kJ/mol; i.e., both values are close to each other. The RTlnf energy of the additional H-bond, which is formed between water molecules upon passing from the adsorption phase into the solution, is found by the extrapolation of the isotherms of water desorption by molecules of several benzene derivatives. This energy ranges from 9.13 to 9.24 kJ/mol, thus corresponding to the energy of one H-bond, as measured by IR spectroscopy and NMR.     

Structural Characterization of Chemical Species in Solution by a Theoretical Analysis of XANES Spectra

A theoretical analysis method using a discrete variational X (DV-X) molecular orbital (MO) calculation, based on electron transition from an inner orbital to an unoccupied orbital, is introduced to analyze X-ray absorption near-edge structure (XANES) spectra in a lower energy region below the X-ray absorption edge. The computational procedure is described in detail and the evaluation of an obtained result is also explained. Applications of this method are presented for Cu(II) ions in liquid ammonia, macrocyclic Cu(II) complex in aqueous solution, and Al(III) ions in aqueous solution.