Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly]

Summary The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional ¹H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH_1–10, has been synthesized, cyclized, and studied by two-dimensional ¹H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH_1–10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH_1–10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L-and d-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.     

Nioboxidfluoride mit Blockstrukturen — Elektronenmikroskopische Durchstrahlungsaufnahmen und ihre Simulation

Niobiumoxidefluorides Nb₅₉O₁₄₇F, Nb₃₁O₇₇F, Nb₆₅O₁₆₁F₃ and Nb₃₄O₈₄F₂ were prepared by reaction of Nb₂O₅ and Nb₃O₇F at 1 270°C. These niobiumoxidefluorides have blockstructures which were examined by high resolution electron microscopy. The observed images of the crystal structures were compared with computer simulated images.

     

Studies in azide chemistry. Part 12. One-pot conversion of 4-azidotetrafluoropyridine to 1,3,4-trifluoro-7,9-dimethyl-11H-pyrido[4,3-c]benzo[1,2]diazepine

Thermolysis of 4-azidotetrafluoropyridine in the presence of an excess of mesidine at 170 °C yields tetrafluoro-4-(2,4,6-trimethylphenylazo)- pyridine, which undergoes intramolecular dehydrofluorination $\text{in situ}$ to provide 1,3,4-trifluoro-7,9-dimethyl-11$\text{H}$-pyrido[4,3-$\text{c}$]benzo[1,2]diazepine.     

On the construction of least favourable pairs of distributions

Summary Convex programming techniques were used by Witting and Krafft in [4] in order to reduce a testing problem for composite hypotheses to one for simple hypotheses. This is realized in terms of least favourable pairs of distributions, which represent the solution of the dual of a suitable program. Without further assumptions on the hypotheses, however, the results, derived that way (cf. Baumann [1], Österreicher [6] and Kusolitsch and Österreicher [5]), are of less practical impact. This is due to the fact that in this case the least favourable pairs depend on the level of the testing problem. Conditions avoiding this, were given by Huber and Strassen in [3]. These conditions make use of 2-alternating capacities in the sense of Choquet. The present paper offers a rather general principle of constructing the least favourable distribution in the case, when one of the two hypotheses is simple. This method works also for the local variation model and the Prohorov neighbourhood model in the case of monotone likelyhood ratio. For simple cases—subsuming the gross error model and the total variation model, for which the solution was given by Huber in [2]—a least favourable pair is obtained by using the mentioned technique of construction two times successively.     

Mathematical properties of the vacuum polarization function

This paper is an investigation of certain mathematical properties of the vacuum polarization function (s). We show that (s) is a Herglotz function, has no complex zeroes, and belongs to the class of functions called typically real. In addition, we obtain upper bounds on the higher derivatives of (s), at s=0, given that we know the value of the first derivative at that point.Research supported in part by NASA Grant NSG-8035     

Filtered backprojection for the reconstruction of a high-resolution (4,2)D CH3-NH NOESY spectrum on a 29 kDa protein

Projection-reconstruction (PR) NMR enables rapid collection of multidimensional NMR data. NOESY represents a particularly difficult challenge for currently existing reconstruction algorithms, as it requires the quantitative reconstruction of an unknown number of peaks, at full sensitivity. We have demonstrated the successful application of PR-NMR to NOESY by determining the 4D methyl/amide NOESY spectrum of a 29 kDa protein, human carbonic anhydrase II, from 2D projections, using filtered backprojection for reconstruction. Compared with a 3D control spectrum, all expected peaks were faithfully reconstructed, with correct volumes and with no artifacts. Filtered backprojection thus provides a way to obtain high-resolution 4D NOESY data in the time required for conventional 3D data collection.     

Molecular orbital theoretical prediction of the isomeric products formed from reactions of arene oxides and related metabolites of polycyclic aromatic hydrocarbons

MO theoretical calculations based on the perturbational method of Dewar provide good correlation between predicted and observed structures of products formed during: (1) isomerization of arene oxides to phenols; (2) hydration and nucleophilic addition to arene oxides; and (3) dehydration of arene dihydrodiols. The method is equally applicable to the arene oxides, dihydrodiols, etc. derived from carcinogenic and noncarcinogenic polycyclic hydrocarbons. Extension to the related enzymatic reactions occurring during metabolism of carcinogenic hydrocarbons and to the reactions of the biologically active arene diolepoxides and aryloxirenes suggests the potential utility of this approach in predicting (a) metabolite structure and (b) the structural requirements for carcinogenic and mutagenic activity.     

Determination of D- and L-amino acids in biological samples by two-dimensional column liquid chromatography

Summary A two-dimensional, column liquid chromatographic system is used for the determination of the D- and L-enantiomers of amino acids in biological samples. Separation of the amino acids is first on ion-exchange column by gradient elution with a sodium citratesodium chloride buffer. Enantioseparation is by subsequent injection of 3 l heart-cuts of the individual amino acids onto a second column with a chiral crown ether stationary phase. Finally, fluorescence detection is after post-column labelling of the amino acids using ano-phthalaldehyde-2-mercaptoethanol reagent solution. The high separation power and selectivity of the system allow processing of complex samples with hardly any additional treatment and the determination of small quantities of D-amino acids in the presence of excess L-form. Applicability of the system is illustrated by the determination of D- and L-aspartate, serine, glutamate and alanine in various complex biological samples, such as protein hydrolysates, urine and biotechnological and food samples. Data are given on detectability, repeatability and linearity.     

A “vertex electron pair” scheme (VEPS) for describing the skeletal electron distribution in borane-type clusters

A predominantly localized electron pair scheme is outlined for describing the electron distribution and bonding in closo borane anions B_nH_n²⁻ and related electron deficient deltahedral clusters, in which a skeletal electron pair is assigned to each vertex, one pair being regarded as delocalized just inside the roughly spherical surface on which the skeletal atoms lie. The scheme gives a clearer picture of the electron distribution than is conveyed by resonating 2- and 3-centre bonds in the polyhedron edges and faces, and allows the bond orders of the polyhedron edge links to be calculated readily. The consequence of formal removal of BH²⁺ units from closo species B_nH_n²⁻ to generate nido species B_n−1H_n−1⁴⁻ and arachno species B_n−2H_n−2⁶⁻ is explored, and seen to allow rationalization of two features of such deltahedral-fragment clusters: (i) why a high-connectivity vertex is left vacant and (ii) why the frontier orbitals of such species concentrate electronic charge around their open faces. Moreover, in the case of D_4‘h B₄H₄⁶⁻ (cf. C₄H₄²⁻) and D_5h B₅H₅⁶⁻ (cf. C₅H₅⁻), the approach leads directly to the familiar picture for aromatic ring systems in which the highest filled, doubly degenerate π-bonding molecular orbital concentrates electronic charge in rings above and below the polygon on which the skeletal nuclei lie. It also leads to the expectation that arachno clusters with non-adjacent vacant vertices will be more stable than those with adjacent vacant vertices.     

Investigation of potential-sensitive fluorescent dyes for application in nitrate sensitive polymer membranes

The applicability of various potential-sensitive dyes (PSD) for optical sensing of anions is reported. Specifically, nitrate-responsive polymer membranes have been developed which are composed of a plasticized polymer, an anion exchange catalyst, and a fluorescent dye. On exposure to nitrate, the fluorescence intensity of such membranes increases, while the wavelengths of the excitation and emission maxima remain virtually unchanged. The membranes typically are 2–4 μm thick and exhibit highest sensitivity to nitrate in the 2 to 200 mgl^–1 range. Signal changes on exposure to 100 mmol/l nitrate can be as high as +300%. The detection limit is 0.2 mgl^–1. The cationic PSD octadecyl acridine organe was tested in combination with a tin-organic and an indium-organic anion carrier rather than with tridodecylmethylammonium chloride, but both carriers were found to display no improved selectivity. Received: 2 December 1995 / Revised: 28 March 1996 / Accepted: 5 April 1996