Some approaches to the multiple-minima problem in the calculation of polypeptide and protein structures

Various methods are used to surmount the multiple-minima problem that is encountered in the multidimensional conformational energy surface of a polypeptide. A summary is given here of two of these methods: (i) The build-up procedure that is modified to include statistical data on the positional frequencies of occurrence of amino acid residues along the chain, and (ii) the diffusion equation method that smoothes out the potential surface, leaving only the potential well containing the global minimum.     

Towards an automated, standardized protocol for determination of equilibrium potential of ion-selective electrodes

An automated real-time method for determination of ISE steady state value and response time is developed, following most recent IUPAC recommendations. Specifically, detection of the ‘steady state’ is related to (1) the time derivative of the emf as it reaches a limiting value (ΔE/Δt_limit, e.g., 0.1–1.0 mV min⁻¹) and (2) the duration of time for which the absolute value of the time derivative remains less than this limiting value (stability window, denoted win_st). A suite of representative ISEs, including glass, solid state, and polymer-based electrodes, is examined to determine sensitivity of results to parameterization choice. Measurements taken over a wide range of concentration values and in un-processed samples (i.e., without use of ionic strength adjustment) provide insight into behavior of ISEs in applications where analyte concentrations span a wide range and/or sample pre-processing may not be an option, e.g., use of sensors for in situ environmental sampling. Results show that declared steady state emf is strongly sensitive to variations in ΔE/Δt_limit but relatively unaffected by changes in the stability window when win_st ≥30 s. Linearity of calibration curves produced, quantified by root mean squared error (RMSE) against a linear fit, improves as ΔE/Δt_limit decreases, however the percentage of measurements which reach a declared steady state within the prescribed sample window (∼6.5 min) falls with corresponding decreases in the ΔE/Δt_limit parameter. Response time, defined as the time required to reach declared steady emf, is also a strong function of parameterization. Dependence of response times on sample composition and/or ISE membrane composition and type are also discussed; results for ISEs in samples comprised exclusively of interfering ions are included. In general, limiting emf derivatives of {0.25–0.4 mV min⁻¹} and stability windows of {30–40 s} achieve both good analytical accuracy and compliance with potentially short sampling window requirements. Methodology based on use of these parameters can improve sampling speed and accuracy as well as promote inter-comparison of data and ISE characterizations among research teams.     

Comparative inhibition by substrate analogues 3-methoxy- and 3-hydroxydesaminokynurenine and an improved 3 step purification of recombinant human kynureninase.

Background  

Kynureninase is a key enzyme on the kynurenine pathway of tryptophan metabolism. One of the end products of the pathway is the neurotoxin quinolinic acid which appears to be responsible for neuronal cell death in a number of important neurological diseases. This makes kynureninase a possible therapeutic target for diseases such as Huntington's, Alzheimer's and AIDS related dementia, and the development of potent inhibitors an important research aim.     

Reduced basis set for the gold atom in cluster complexes

To extend the metal cluster size used in interfacing between bulk metals and molecules in ab initio studies of molecular electronics and chemisorption, a reduced size atomic orbital basis set for the gold atom has been generated. Based on the SKBJ relativistic effective core potential set, the three component 5d Gaussian orbital basis set is completely contracted. Comparisons between the full and reduced basis set in Au atom clusters and cluster complexes for geometry, bond distances, dipole moments, atomic charges, spin, bond dissociation energies, lowest energy harmonic frequencies, electron affinities, ionization energies, and density of states distributions show the contracted set to be a viable replacement for the full basis set. This result is obtained using both the B3LYP and BPW91 exchange-correlation potentials in density functional theory.     

Photolithographic synthesis of peptoids

We describe a novel photolithographic approach to the synthesis of peptoids (oligo-N-substituted glycines). This strategy enables the construction of a spatially addressable peptoid microarray, thus providing a potentially powerful tool for the discovery of protein ligands.     

N-Acetylneuraminic Acid: Neoglycoproteins and Pseudopolysaccharides

Abstract

A simplified procedure for the synthesis of acetochloroneuraminic acid is described starting from the methyl ester. N-acetyl neuraminic acid α-allyl glycoside was prepared in high yield using silver salicylate as catalyst. Reductive ozonolysis of the allyl group, followed by direct reductive ami nation to protein carriers, gave immunogenic neoglycoproteins. Copolymerization of the α-allyl glycoside with acrylamide produced a water-soluble pseudopolysaccharide useful for the EL ISA technique.     

Determination of flavanol and procyanidin (by degree of polymerization 1-10) content of chocolate, cocoa liquors, powder(s), and cocoa flavanol extracts by normal phase high-performance liquid chromatography: collaborative study

An international collaborative study was conducted on an HPLC method with fluorescent detection (FLD) for the determination of flavanols and procyanidins in materials containing chocolate and cocoa. The sum of the oligomeric fractions with degree of polymerization 1-10 was the determined content value. Sample materials included dark and milk chocolates, cocoa powder, cocoa liquors, and cocoa extracts. The content ranged from approximately 2 to 500 mg/g (defatted basis). Thirteen laboratories representing commercial, industrial, and academic institutions in six countries participated in the study. Fourteen samples were sent as blind duplicates to the collaborators. Results from 12 laboratories yielded repeatability relative standard deviation (RSDr) values that were below 10% for all materials analyzed, ranging from 4.17 to 9.61%. The reproducibility relative standard deviation (RSD(R)) values ranged from 5.03 to 12.9% for samples containing 8.07 to 484.7 mg/g. In one sample containing a low content of flavanols and procyanidins (approximately 2 mg/g), the RSD(R) was 17.68%. Based on these results, the method is recommended for Official First Action for the determination of flavanols and procyanidins in chocolate, cocoa liquors, powder(s), and cocoa extracts.     

The electronic spectrum of the C(s)-C11H3 radical

The electronic gas-phase absorption spectrum of the bent carbon-chain radical, HC(4)CHC(6)H with C(s) symmetry, is recorded in the 595 nm region by cavity ring-down spectroscopy through an expanding hydrogen plasma. An unambiguous spectroscopic identification becomes possible from a systematic deuterium labeling experiment. A comparison of the results with recently reported spectra of the nonlinear HC(4)CHC(4)H and HC(4)C(C(2)H)C(4)H radicals with C(2v) symmetry provides a more comprehensive understanding of the molecular behavior of π-conjugated bent carbon-chain systems upon electronic excitation. We find that the electronic excitation in the bent carbon-chain HC(4)CHC(2n)H (n = 1-4) series exhibits a similar trend as in the linear HC(2n+1)H (n = 3-6) series, shifting optical absorptions towards longer wavelengths for increasing overall bent chain lengths. The π-conjugation in bent HC(4)CHC(2n)H (n = 1-4) chains is found to be generally smaller than in the linear HC(2n+1)H (n = 3-6) case for equivalent numbers of C-atoms. The addition of an electron-donating group to the bent chain causes a slight decrease of the effective conjugation.     

The smallest stable fullerene, M@C28 (m = Ti, Zr, U): stabilization and growth from carbon vapor

The smallest fullerene to form in condensing carbon vapor has received considerable interest since the discovery of Buckminsterfullerene, C(60). Smaller fullerenes remain a largely unexplored class of all-carbon molecules that are predicted to exhibit fascinating properties due to the large degree of curvature and resulting highly pyramidalized carbon atoms in their structures. However, that curvature also renders the smallest fullerenes highly reactive, making them difficult to detect experimentally. Gas-phase attempts to investigate the smallest fullerene by stabilization through cage encapsulation of a metal have been hindered by the complexity of mass spectra that result from vaporization experiments which include non-fullerene clusters, empty cages, and metallofullerenes. We use high-resolution FT-ICR mass spectrometry to overcome that problem and investigate formation of the smallest fullerene by use of a pulsed laser vaporization cluster source. Here, we report that the C(28) fullerene stabilized by encapsulation with an appropriate metal forms directly from carbon vapor as the smallest fullerene under our conditions. Its stabilization is investigated, and we show that M@C(28) is formed by a bottom-up growth mechanism and is a precursor to larger metallofullerenes. In fact, it appears that the encapsulating metal species may catalyze or nucleate endohedral fullerene formation.