Simulation of carbohydrate-protein interactions: Computer-aided design of a second generation GM1 mimic

The oligosaccharide of ganglioside GM1 [Gal1-3GalNAc1-4(NeuAc2-3)Gal1-4Glc1-1Cer] is the cellular target of two bacterial enterotoxins: the cholera toxin (CT) and the heat-labile toxin of E.coli (LT). We recently reported that the pseudosaccharide 2[Gal1-3GalNAc1-4(NeuAc2-3)DCCHD] is a high-affinity ligand for CT, and thus a functional mimic of GM1 (Bernardi, A., Checchia, A., Brocca, P., Sonnino, S. and Zuccotto, F., J. Am. Chem. Soc., 121 (1999) 2032–2036). In this paper we describe the design of a second-generation mimic, formally obtained from 2 by inverting the configuration of a single stereocenter, thus transforming a N-acetyl galactosamine into a N-acetyl glucosamine. The design process involved modeling of the free ligand and its LT complex, followed by qualitative and quantitative comparison with the corresponding structures of 2. The protocol employed relied on both conformational search and molecular dynamics methodologies to account for the flexibility of both the ligand and the protein receptor. The conformational search of the LT:inhibitor complex showed that, compared to 2, the new compound can insert one more hydroxy group within the protein binding site. Molecular dynamics simulations showed that, in turn, this may trigger a series of rearrangements and reorientations of side chains and crystallographic water molecules in the toxin, leading to new H-bond contacts which may result in enhanced affinity of the new inhibitor. FEP calculations were performed by mutating the structure of 2 in solution and in the protein complex, and the prediction was made that the second-generation mimic should be a stronger binder than its parent compound.     

Symmetry-adapted Localized Wannier Functions Suitable for Periodic Local Correlation Methods

A scheme for the a posteriori symmetrization of a set of localized Wannier functions is presented and illustrated with some examples. The method has been implemented in the periodic code CRYSTAL using the LCAO approach and it is shown that they can be useful in the computational implementation of periodic local correlation methods. The resulting functions feature very accurate symmetry correspondences without a significant loss of the original localization properties.     

Simultaneous C-H-N and S microdetermination by combustion and gas chromatography

Summary A method based on flash-combustion of the sample in a flow of temporarely oxygen-enriched helium, catalytic oxidation and reduction of the combustion gases within the same reactor, gas-chrom- matographic separation and thermal-conductivity detection of the end-products, has been developed in order to determine C-H-N-S simultaneously in organic and inorganic substances, with a 0.1–2 mg sample. To develop this method, optimization of analytical parameters was necessary because of the chemical and physical behaviour of oxides of sulphur in the analyser. Therefore flashcombustion in a tin container, use of a tungstic oxide oxidative layer close to a copper reductive layer, setting the copper temperature at 850° C and selective halogen adsorption are the main features. The temperature of 850° C for the copper gives a quantitative yield of SO₂ in spite of the reaction between sulphur oxides and cupric oxide, and also gives quantitative reduction of the nitrogen oxides. The individual components of the combustion mixture are separated by means of a Porapak QS column and detected in the sequence Na, CO₂, H₂O and SO₂, the signals being automatically integrated and printed. Detector response for SO₂ is linear from someg up to 10 mg.

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Zusammenfassung Zur gleichzeitigen Bestimmung von C, H, N und S in 0,1 bis 2 mg anorganischer oder organischer Substanz wurde ein Verfahren entwickelt, wobei die Substanz in zeitweilig sauerstoff-angereichertem Helium verbrannt, die Verbrennungsprodukte im selben Reaktionsrohr zunächst katalytisch oxydiert, dann reduziert werden. Anschließend werden die Endprodukte gas-chromatographisch getrennt und mittels Wärmeleitfähigkeitsmessung bestimmt. Zur Entwicklung dieses Verfahrens mußten die analytischen Parameter wegen des chemischen und physikalischen Verhaltens der Schwefeloxide optimiert werden. Daher werden Flammenverbrennung in einem Zinngefäß, Verwendung von Wolframoxid als oxydierende Schicht unmittelbar neben Kupfer als reduzierender Schicht, die auf 850° C gehalten wird, sowie selektive Adsorption der Halogene als wichtigste Schritte betrachtet. Die Temperatur von 850° C gewährleistet quantitative Ausbeute an SO₂ im Gegensatz zur Reaktion zwischen Schwefeloxiden und Kupferoxid und führt auch zur quantitativen Reduktion der Stickstoffoxide. Die einzelnen Teile des Verbrennungsgemisches werden mit einer Säule aus Porapak QS getrennt und in der Reihenfolge N₂, CO₂, H₂O und SO₂ nachgewiesen, wobei die Signale automatisch integriert und gedruckt werden. Der Detektorausschlag für SO₂ ist von einigen Mikrogramm bis 10 mg linear.

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Dedicated to Prof. H. Lieb for his 90th birthday.

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Presented at the International Symposium on Microchemical Techniques, May 23–27, 1977, Davos, Switzerland.     

High diastereoselectivity in lewis acid mediated aldol condensations using thioester silyl ketene acetals.

BF₃ OEt₂ mediated aldol condensations of thioester silyl ketene acetals are stereoconvergent, and exhibit high internal (anti) and relative (Cram) diastereoselectivity.     

Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations

Microsecond time scale molecular dynamics simulations of the 13-residue peptide RN24 were carried out to investigate the mechanism of helix nucleation and propagation. An extended and an ideal alpha-helical conformation were used as starting structures. NOE-derived interatomic distances were compared with distances calculated from the simulations, showing good agreement between experimental and simulation results. Based on almost 200 helix nucleation events observed, beta-turn and 3(10)-helix play an important role in helix nucleation; in most cases, helix nucleation is preceded by the formation of a short-lived beta-turn (60% probability) or 3(10)-helix (20% probability), and the conversion from beta-turn to alpha-turn involves bifurcated hydrogen bonds. Helix propagation in RN24 appears to occur preferentially from the N-terminus to the C-terminus, and helix unfolding preferentially in the opposite direction.     

Lower semicontinuous perturbations of maximal monotone differential inclusions

We prove existence of solutions to 1 $$\dot x \in - Ax + F\left( {t,x} \right),x\left( a \right) = x^0 ,$$ whereA is a maximal monotone operator inR ⁿ andF is a multifunction measurable in (t, x) and l.s.c. inx, satisfying a sublinear growth condition.     

Remote control of enzyme selectivity: the case of stevioside and steviolbioside

The remote control of lipase PS site- and regioselectivity by substrate modification has been observed in the acetylation of stevioside (1) and steviolbioside (2): deglucosylation at position C-19 changed the acylation site of the sophorose moiety linked at C-13. In fact, while esterification of 1 gave mainly the corresponding 6″-O-acetylated derivative, acylation of 2 gave exclusively the 6′-O-monoester. A possible rationale has been suggested, based on the conformational behavior of the substrates in different simulated solvents.     

The determination of oxygen in brass and zinc by a vacuum carbon-reduction techniques

A vacuum carbon-reduction technique for the determination of oxygen in brass and zinc has been studied. As a preliminary, zinc is removed from the samples, sealed in predegassed graphite capsules, in a silica furnace maintained at ca. 850°C under vacuum in a vacuum fusion instrument. The residual contents of the capsules are then analysed in sequence at 1450°C in the main furnace of the apparatus, to which they are transferred without breaking the vacuum. The procedure developed affords a detection limit of 0.5–1 ppm of oxygen for samples weighing ca. 1.5 g.     

Contribution of mass spectrometric techniques to the structure elucidation of antibiotic GE2270A,a novel inhibitor of bacterial protein synthesis

GE2270A is a novel antibiotic active against Gram-positive bacteria and anaerobes. Its structure originates from a peptidic backbone, the amino acids of which have been modified to produce a macrocycle and a side-chain. It contains a heterocyclic chrornophonc system, a number of thiazoleamino acids and three unmodified natural amino acids. The structure [relative molecular mass (RMM) 1289] was determined using various spectroscopic techniques, of which fast atom bombardment mess spectrometry, gas chromatography/mass spectrometry, desorption chemical ionization mass spectrometry and fast atom bombardment tandem mass spectrometry played an important role. The mass spectrometric approach was applied to the intact molecule and to the various hydrolysis products, including the chromophoric part (RMM 634).     

Structural and spectroscopic investigations of blue, vanadium-doped ZrSiO4 pigments prepared by a sol-gel route

A sol-gel reaction starting from silicon and zirconium alkoxides, in water-ethanol mixtures, was employed to obtain vanadium-doped zirconium silicate powders (zircon). The reactions were performed by modulating both (a) the amount of the vanadium salt in the starting mixture and also (b) the amount of mineralizer (NaF). The products of the sol-gel reaction were calcined at 600, 800, 1000, and 1200 degrees C. The samples were characterized by X-ray powder diffraction (XRPD), electron paramagnetic resonance spectroscopy (EPR), scanning electron microscopy (SEM), X-ray absorption near-edge spectroscopy (XANES), and diffuse UV-vis-near-IR reflectance spectroscopy. Results from the structural, morphological, and optical characterization are examined and cross-compared to produce a consistent picture of the key factors leading to the formation, growth, and optical properties of the reaction products.