Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

UV index experimental values during the years 2000 and 2001 from the Spanish broadband UV-B radiometric network

An analysis is made of experimental ultraviolet erythemal solar radiation data measured during the years 2000 and 2001 by the Spanish UV-B radiation evaluation and prediction network. This network consists of 16 Robertson-Berger type pyranometers for evaluating solar erythemal radiation and five Brewer spectroradiometers for evaluating the stratospheric ozone. On the basis of these data the Ultraviolet Index (UVI) was evaluated for the measuring stations that are located either in coastal regions or in the more densely populated regions inland on the Iberian Peninsula. It has been checked that in most cases the maximum irradiance values corresponded to solar noon, although there were exceptions that could be explained by cloudiness. The maximum experimental values of the UVI were around 9 during the summer, though frequently passing this value at the inland measurement stations. The annual accumulated dose of irradiation on a horizontal plane has also been studied, as well as the evolution through the year in units of energy, standard erythemal doses and minimum erythemal doses, according to different phototypes.     

13C-NMR relaxation studies of alkali metal cryptate complexes

The ¹³C spin-lattice relaxation times (T₁'s) of cryptands [2.1.1], [2.2.1] and [2.2.2] as well as those of the corresponding cryptate complexes with Li⁺, Na⁺, and K⁺ in CDCl₃ and CH₃OH:D₂O (90:10) were measured and the results are interpreted in terms of molecular compression and desolvation effects.     

Determination of hopane biomarkers in Arabian crude oils by gas chromatography-tandem mass spectrometry

Gas chromatography-mass spectrometry with the mass spectrometer operated in the tandem mode at a constant accelerating voltage was used to analyse for triterpanes in Arabian crude oils. Specific molecular parent-daughter ion pairs were selected for quantitative measurements owing to their metastable transitions in the first field-free region. More accurate relative distribution ratios of hydrocarbon biomarkers were determined by this sequential gating technique than by the conventional diagnostic daughter ion mass fragmentogram in common GC-MS. The data and spectra obtained from MS-MS operation may serve as unique “fingerprints” for these regional crudes     

Interfacial adsorption of microorganisms and its effect on oxygen absorption by fermentation broths

Steady-state mass transfer experiments were done to determine whether certain strains of bacteria in homogeneous suspension will accumulate at the gas:liquid interface and thereby significantly increase the oxygen transfer rate to the suspension. In particular, with suspensions ofB. licheniformis, the measured transfer rates are as much as three times the rate expected for a uniform suspension. In contrast, suspensions ofM. luteus show no increase in oxygen flux above expected values. The fact thatB. licheniformis is motile, whereasM. luteus is not suggests that cell motility may play an important role in the accumulation process.

     

Approximate transferability in alkanenitriles

The atomic and bond properties of a series of alkanenitriles were calculated in order to analyze the transferability of the CN, methyl, and methylene groups. The calculations were carried out using the atoms in molecules (AIM) theory on RHF/6‐31++G**// RHF/6‐31G** wave functions obtained for compounds CN–R (R ranging from H to C₁₁H₂₃). Linear correlations between L(Ω) and N(Ω) were used to establish N(CH₂) and N(CH₃) nearly transferable values. Average values and maximum differences to the mean value of several properties were used for classifying the CN group. It shows a transferable behavior along the CN–R series for R>Et. The methyl group presents specific properties when R<Pr. The methylene groups can be classified considering both their position with respect to the end of the chain and the position with respect to the CN group. The atomic energy displays a dependence on the molecular size. Although this behavior does not allow to consider this property as transferable, both the ab initio total electronic molecular energies and the experimental heats of formation can be fitted, by linear regression analysis, as a function of the number of methylene groups. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Integrated production of ethanol fuel and protein from Coastal Bermudagrass

The herbaceous crops that may provide fermentable carbohydrates for production of fuels and chemicals also contain 10–20% protein. Protein coproduction with biomass-derived fuels and chemicals has important advantages: (1) food and fuel production can be integrated, and (2) protein is a high-value product that may significantly improve overall process economics. We report the results of an integrated approach to producing protein and fermentable sugars from one herbaceous species, Coastal Bermudagrass (CBG). The ammonia fiber explosion (AFEX) process makes possible over 90% conversion of cellulose and hemicellulose to simple sugars (about 650 mg reducing sugars/g dry CBG) at 5 IU cellulase/g vs < 20% conversion for untreated CBG. The AFEX treatment also improves protein extraction from CBG; over 80% protein recovery is possible from AFEX-treated CBG vs about 30% recovery from untreated CBG.     

Quassinoids from Picrasma crenata

From woods of Picrasma crenata, a new stereoisomer dihydronorneoquassin was obtained together with others well knowns dihydronorneoquassin, parain, alpha-neoquassin, beta-neoquassin and quassin. The structures were determined by spectroscopic data and chemical evidence.     

A Protein‐Resistant Matrix for Electrochemical Based Recognition Assays

In this work, two well known polymers, carboxymethyl dextran and poly(ethyleneglycol), are used for easily producing a platform for electrochemical affinity assays, avoiding nonspecific adsorption of proteins. In this way, modified electrode surfaces able to bind a recognition agent are constructed through simple and reliable reactions.     

How bridging ligands and neighbouring groups tune the gold-gold bond strength

Gold-gold interactions in small polynuclear complexes are analysed using extended Hückel calculations. They are influenced by the nature of the ligand donor atoms, by the bridging ligands, but most by the formal oxidation state of the metal. Au---Au bonds are much stronger in complexes of Au(II) and Au(III), but a weak interaction between two d¹⁰ centres exists for Au(I) complexes, owing to mixing of the s and p orbitals with the d orbitals. Phosphines induce stronger metal-metal bonds when coordinated trans to the Au---Au bond in [Au(II)[(CH₂)₂PPh₂]L]₂ (Ph = phenyl), but have the opposite effect when bonded orthogonally to the metal-metal axis in Au(I) binuclear species. When two gold atoms are bridged by a single carbon atom, belonging either to mesityl (Mes = 2,4,6-Me₃C₆H₂) or CR₂, the former produces stronger Au(I)---Au(I) interactions, reflected in shorter distances. Formal oxidation states are proposed for the gold atoms in two mixed-valence clusters, [Au4(C₆F₅)₂((PPh₃)_{2CH})2(PPh3)2](ClO4)2 and [{(2,4,6-C6F3H2)Au(CH2PPh2CH2)2Au{in2}-Au(CH₂PPh₂CH₂)₂Au](ClO₄)₂. The results suggest a higher oxidation state for the outer gold atoms, in both the T-shaped tetranuclear cluster and the Au₆ linear chain.