A simple protocol for the comparative analysis of the structure and occurrence of biochemical pathways across superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html . The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in Cu(A) assembly in more than a thousand prokaryotes.     

Synthesis of new C-glycosyl aza-β3-amino acids building blocks

New C-glycosylated N^β-protected aza-β³-amino acid building blocks have been prepared from C-glycosyl aldehydes of gluco and galacto configuration by reductive amination and subsequent N-alkylation. These moieties were elaborated to β-dipeptides by elongation at the C- or the N-terminus establishing their ability to be incorporated in original glycosylated foldamers.     

The onset of coulomb explosions in polyatomic molecules

With the development of high intensity femtosecond lasers, the ionisation and dissociation dynamics of molecules has become an area of considerable interest. Using the technique of femtosecond laser mass spectrometry (FLMS), the molecules carbon disulphide, pyrimidine, toluene, cyclohexanone and benzaldehyde are studied with pulse widths of 50 fs in the near infrared (IR) wavelength region (790 nm). Results are presented and contrasted for laser beam intensities around 10(15) and 10(16) W cm(-2). For the lower intensities, the mass spectra yield dominant singly charged parent ions. Additionally, the appearance of doubly charged parent ions is evident for carbon disulphide, toluene and benzaldehyde with envelopes of doubly charged satellite species existing in these local regions. Carbon disulphide also reveals a small triply charged component. Such atomic-like features are thought to be a strong fingerprint of FLMS at these intensities. However, upon increasing the laser intensity to approximately 10(16) W cm(-2), parent ion dominance decreases and the appearance of multiply charged atomic species occurs, particularly carbon. This phenomenon has been attributed to Coulomb explosions in which the fast absorption of many photons may produce transient highly ionised parent species which can subsequently blow apart. Copyright 1999 John Wiley & Sons, Ltd.     

Uniform molecular analysis using femtosecond laser mass spectrometry

The potential of femtosecond laser time-of-flight mass spectrometry (FLMS) for uniform quantitative analysis of molecules has been investigated. Various samples of molecular gases and vapours have been studied, using ultra-fast ( approximately 50 fs) laser pulses with very high intensity (up to 1.6 x 10(16) Wcm(-2)) for non-resonant multiphoton ionisation/tunnel ionisation. Some of these molecules have high ionisation potentials, requiring up to ten photons for non-resonant ionisation. The relative sensitivity factors (RSF) have been determined as a function of the laser intensity and it has been demonstrated that for molecules with very different masses and ionisation potentials, uniform ionisation has been achieved at the highest laser intensities. Quantitative laser mass spectrometry of molecules is therefore a distinct possibility. Copyright 1999 John Wiley & Sons, Ltd.     

Second generation of fucose-based DC-SIGN ligands: affinity improvement and specificity versus Langerin

DC-SIGN and Langerin are two C-type lectins involved in the initial steps of HIV infections: the former acts as a viral attachment factor and facilitates viral invasion of the immune system, the latter has a protective effect. Potential antiviral compounds targeted against DC-SIGN were synthesized using a common fucosylamide anchor. Their DC-SIGN affinity was tested by SPR and found to be similar to that of the natural ligand Lewis-X (Le(X)). The compounds were also found to be selective for DC-SIGN and to interact only weakly with Langerin. These molecules are potentially useful therapeutic tools against sexually transmitted HIV infection.     

On the road to a termolecular complex with acetone: a heterometallic supramolecular network [[Rh(2)(O(2)CCF(3))(4)].micro(2)-OCMe(2).[Cu(4)(O(2)CCF(3))(4)]

A novel heterometallic supramolecular network [[Rh(2)(O(2)CCF(3))(4)].micro(2)-OCMe(2).[Cu(4)(O(2)CCF(3))(4)]](2)( infinity ) has been prepared by codeposition of the volatile mono(acetone) adduct [Rh(2)(O(2)CCF(3))(4).eta(1)-OCMe(2)](2) and copper(I) trifluoroacetate, [Cu(4)(O(2)CCF(3))(4)]. The product is of interest from the viewpoints of gas-phase supramolecular synthesis and a rare bridging coordination mode of acetone. It has been fully characterized by IR and NMR spectroscopy, elemental analysis, and X-ray diffraction. An X-ray structure revealed a layered 2D arrangement of the heterometallic [[Rh(2)(O(2)CCF(3))(4)].micro(2)-OCMe(2).[Cu(4)(O(2)CCF(3))(4)]] units built by axial intermolecular interactions of the open electrophilic Rh(II) and Cu(I) centers and O-atoms of neighboring carboxylate groups. The coordination of the acetone molecules within the [[Rh(2)(O(2)CCF(3))(4)].micro(2)-OCMe(2).[Cu(4)(O(2)CCF(3))(4)]] unit is asymmetric with the Rh-O and Cu-O distances being 2.2173(15) and 2.7197(17) A, respectively. This work shows the potential of gas-phase deposition that may provide additional possibilities in supramolecular synthesis by utilizing intermolecular interactions and coordination bonds in a new way compared with conventional solution chemistry.     

Aldehydes in the atmospheric environment: evaluation of human exposure in the north-west area of Milan

Human exposure to aldehydes has been evaluated in five urban locations and one rural-industrial location in the north-west area of Milan in winter 1999 and in summer 1998–99. Ambient air samples collected on dinitrophenylhydrazine (DNPH)-coated diffusive cartridges were analysed for aldehydes as their DNPH-derivatives. Aldehydes have been identified and their concentration measured via HPLC-UV and LC-APCI-MS negative ion mode methods. During the winter the range of total concentration of aldehydes was 16.7–30.7 μg/m³ at the urban locations and 11.7 μg/m³ at the rural-industrial location. Formaldehyde accounted for 50% of the total amount of carbonyl compounds in all locations; the percentage of acetaldehyde was more variable: 23–38% of the total carbonyls. The contribution of outdoor environment to the average human daily intake of formaldehyde in this area (urban and rural-industrial) is mostly 1–2% of the total human exposure.     

X-ray quality geometries of geodesic polyarenes from theoretical calculations: what levels of theory are reliable?

[structure: see text] Computational methods for calculating molecular geometries have not been well calibrated heretofore against X-ray data for bowl-shaped polycyclic aromatic hydrocarbons (PAHs). The analysis presented here capitalizes on a rare opportunity provided by corannulene to account explicitly for molecular distortions from crystal packing forces. Within the error limits of an extensive X-ray data set, B3LYP/6-31G* calculations were found to correctly reproduce all of the experimental bond distances and bond angles. The reliability and shortcomings of geometry calculations at other levels of theory are enumerated.